From 1e47693b295eea4c2a5f7b6b0351305c10133a31 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Wed, 19 Jun 2024 15:03:44 +0200
Subject: [PATCH 001/414] Linting: Remove 'defaults' from conda environment.yml
 file.

See nf-core/modules#5829
---
 nf_core/module-template/environment.yml                         | 1 -
 .../pipeline-template/modules/nf-core/fastqc/environment.yml    | 1 -
 .../pipeline-template/modules/nf-core/multiqc/environment.yml   | 1 -
 nf_core/pipeline-template/nextflow.config                       | 2 +-
 .../subworkflows/nf-core/utils_nextflow_pipeline/main.nf        | 2 +-
 tests/test_utils.py                                             | 2 +-
 6 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/nf_core/module-template/environment.yml b/nf_core/module-template/environment.yml
index dcf510affb..f234f85422 100644
--- a/nf_core/module-template/environment.yml
+++ b/nf_core/module-template/environment.yml
@@ -4,6 +4,5 @@ name: "{{ component_name_underscore }}"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}"
diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml
index 1787b38a9a..0d5be45f26 100644
--- a/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml
+++ b/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml
@@ -2,6 +2,5 @@ name: fastqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::fastqc=0.12.1
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
index ca39fb67e2..329ddb4870 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
@@ -2,6 +2,5 @@ name: multiqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::multiqc=1.21
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 2e6a56b001..6202aa8319 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -98,7 +98,7 @@ profiles {
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
-        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        conda.channels          = ['conda-forge', 'bioconda']
         apptainer.enabled       = false
     }
     mamba {
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index ac31f28f66..e770d91b97 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -102,7 +102,7 @@ def checkCondaChannels() {
 
     // Check that all channels are present
     // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    def required_channels_in_order = ['conda-forge', 'bioconda']
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 85f4e3c548..48288be817 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -105,7 +105,7 @@ def test_load_pipeline_config(self):
     # def test_load_conda_env(self):
     #     """Load the pipeline Conda environment.yml file"""
     #     self.pipeline_obj._load_conda_environment()
-    #     assert self.pipeline_obj.conda_config["channels"] == ["conda-forge", "bioconda", "defaults"]
+    #     assert self.pipeline_obj.conda_config["channels"] == ["conda-forge", "bioconda"]
 
     def test_list_files_git(self):
         """Test listing pipeline files using `git ls`"""

From d6191cce7843918cf256da0f9b0fe0940e813288 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 19 Jun 2024 13:05:27 +0000
Subject: [PATCH 002/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9da8c1ab24..3e2be8fd91 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@
 
 - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976))
 - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014))
+- Remove defaults from conda environment.yml file. ([#3029](https://github.com/nf-core/tools/pull/3029))
 
 ### Download
 

From ee2241a4e763239c3d45f343f7d5e930c8f1561f Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 25 Jun 2024 14:52:57 +0200
Subject: [PATCH 003/414] Replace check_max with resourceLimits

---
 CHANGELOG.md                               |  1 +
 nf_core/pipeline-template/conf/base.config | 40 +++++++++++++---------
 nf_core/pipeline-template/nextflow.config  | 33 ------------------
 3 files changed, 24 insertions(+), 50 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 008c755848..c65b999a5a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -42,6 +42,7 @@
 
 - Don't cache pip in `linting.yml` ([#2961](https://github.com/nf-core/tools/pull/2961))
 - Lint pipelines with the nf-core template version and post comment if it is outdated ([#2978](https://github.com/nf-core/tools/pull/2978))
+- Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([]())
 
 ### General
 
diff --git a/nf_core/pipeline-template/conf/base.config b/nf_core/pipeline-template/conf/base.config
index 9c62bf0634..72a912fe47 100644
--- a/nf_core/pipeline-template/conf/base.config
+++ b/nf_core/pipeline-template/conf/base.config
@@ -11,9 +11,15 @@
 process {
 
     // TODO nf-core: Check the defaults for all processes
-    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
-    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+    cpus   = { 1      * task.attempt }
+    memory = { 6.GB   * task.attempt }
+    time   = { 4.h    * task.attempt }
+
+    resourceLimits = [
+                        cpus: params.max_cpus,
+                        memory: params.max_memory,
+                        time: params.max_time
+                    ]
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
@@ -27,30 +33,30 @@ process {
     // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 1                   }
+        memory = { 6.GB * task.attempt }
+        time   = { 4.h  * task.attempt }
     }
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { 2     * task.attempt }
+        memory = { 12.GB * task.attempt }
+        time   = { 4.h   * task.attempt }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { 6     * task.attempt }
+        memory = { 36.GB * task.attempt }
+        time   = { 8.h   * task.attempt }
     }
     withLabel:process_high {
-        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { 12    * task.attempt }
+        memory = { 72.GB * task.attempt }
+        time   = { 16.h  * task.attempt }
     }
     withLabel:process_long {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { 20.h  * task.attempt }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory = { 200.GB * task.attempt }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 2e6a56b001..0316c2e0c5 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -265,36 +265,3 @@ manifest {
 
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
-
-// Function to ensure that resource requirements don't go beyond
-// a maximum limit
-def check_max(obj, type) {
-    if (type == 'memory') {
-        try {
-            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
-                return params.max_memory as nextflow.util.MemoryUnit
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'time') {
-        try {
-            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                return params.max_time as nextflow.util.Duration
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'cpus') {
-        try {
-            return Math.min( obj, params.max_cpus as int )
-        } catch (all) {
-            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
-            return obj
-        }
-    }
-}

From ce49baddf0a39478d1d5483d5cfeac56c32e1e77 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 25 Jun 2024 14:55:43 +0200
Subject: [PATCH 004/414] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c65b999a5a..60808610d0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -42,7 +42,7 @@
 
 - Don't cache pip in `linting.yml` ([#2961](https://github.com/nf-core/tools/pull/2961))
 - Lint pipelines with the nf-core template version and post comment if it is outdated ([#2978](https://github.com/nf-core/tools/pull/2978))
-- Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([]())
+- Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([#3037](https://github.com/nf-core/tools/pull/3037))
 
 ### General
 

From c8abbef61080458001fe8eb590a26a05c627cea1 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 25 Jun 2024 15:13:28 +0200
Subject: [PATCH 005/414] Code alignment, and try to get test to run on GHA
 Actions runner

---
 .github/workflows/create-test-wf.yml       | 2 +-
 nf_core/pipeline-template/conf/base.config | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index a95a477459..cb2aad2675 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -75,7 +75,7 @@ jobs:
           pwd
           # echo content of current directory
           ls -la
-          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
+          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results --max_cpus 4
 
       - name: Upload log file artifact
         if: ${{ always() }}
diff --git a/nf_core/pipeline-template/conf/base.config b/nf_core/pipeline-template/conf/base.config
index 72a912fe47..fb3a8456bd 100644
--- a/nf_core/pipeline-template/conf/base.config
+++ b/nf_core/pipeline-template/conf/base.config
@@ -16,9 +16,9 @@ process {
     time   = { 4.h    * task.attempt }
 
     resourceLimits = [
-                        cpus: params.max_cpus,
+                        cpus:   params.max_cpus,
                         memory: params.max_memory,
-                        time: params.max_time
+                        time:   params.max_time
                     ]
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }

From 4f7139953d11cfacd4844ae1d96c6fdd440a6323 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 28 Jun 2024 16:39:51 +0200
Subject: [PATCH 006/414] Template: Run awsfulltest on PRs to `master` with two
 PR approvals

---
 .../.github/workflows/awsfulltest.yml         | 23 +++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index 56ecb60302..f0d0724424 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -1,18 +1,33 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on published releases.
+# This workflow is triggered on PRs opened against the master branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  pull_request:
+    branches:
+      - master
   workflow_dispatch:
+  pull_request_review:
+    types: [submitted]
+
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == '{{ name }}'
+    if: github.repository == '{{ name }}' && github.event.review.state == 'approved'
     runs-on: ubuntu-latest
     steps:
+      - uses: octokit/request-action@v2.x
+        id: check_approvals
+        with:
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - id: test_variables
+        run: |
+          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
+          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
+          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required

From 407075741219497441444beba9bad62604844732 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Fri, 28 Jun 2024 14:42:04 +0000
Subject: [PATCH 007/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6d3f4f088c..d417b9d57a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Template
 
 - Change paths to test data ([#2985](https://github.com/nf-core/tools/pull/2985))
+- Run awsfulltest on PRs to `master` with two PR approvals ([#3042](https://github.com/nf-core/tools/pull/3042))
 
 ### Linting
 

From 044fc1d6750f4cf9d3ccf87bcb6ed9f3e61760b8 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 1 Jul 2024 14:30:55 +0200
Subject: [PATCH 008/414] Remove default basic resource limits in template
 (should be set by users)

---
 nf_core/pipeline-template/conf/base.config | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/nf_core/pipeline-template/conf/base.config b/nf_core/pipeline-template/conf/base.config
index fb3a8456bd..fa292339e3 100644
--- a/nf_core/pipeline-template/conf/base.config
+++ b/nf_core/pipeline-template/conf/base.config
@@ -15,12 +15,6 @@ process {
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }
 
-    resourceLimits = [
-                        cpus:   params.max_cpus,
-                        memory: params.max_memory,
-                        time:   params.max_time
-                    ]
-
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'

From 528a207ca8e2e5169140876b5d7cdbf5c5845d5f Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 1 Jul 2024 14:31:31 +0200
Subject: [PATCH 009/414] Add a basic set of resource limits in test configs,
 matching GithubActions runner limits

---
 nf_core/pipeline-template/conf/test.config | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/nf_core/pipeline-template/conf/test.config b/nf_core/pipeline-template/conf/test.config
index 827e21b7b7..2b9715efb6 100644
--- a/nf_core/pipeline-template/conf/test.config
+++ b/nf_core/pipeline-template/conf/test.config
@@ -10,6 +10,14 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '16.GB',
+        time: '1.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'

From 936802fbfc553dde07a2acb9df134c995f5ab2d3 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 1 Jul 2024 14:37:13 +0200
Subject: [PATCH 010/414] Bump minimum NXF version to allow resourceLimits

---
 nf_core/pipeline-template/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 0316c2e0c5..d575c6186f 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -258,7 +258,7 @@ manifest {
     homePage        = 'https://github.com/{{ name }}'
     description     = """{{ description }}"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=24.04.2'
     version         = '{{ version }}'
     doi             = ''
 }

From 06a1dbe41203c284b92d34912d14f12d77aebb72 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 1 Jul 2024 14:43:23 +0200
Subject: [PATCH 011/414] Add linting check for now deprecated params

---
 nf_core/pipelines/lint/nextflow_config.py | 89 ++++++++++++++++++-----
 1 file changed, 69 insertions(+), 20 deletions(-)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index f62100a70a..f1c4c536c5 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -87,6 +87,9 @@ def nextflow_config(self):
     * ``params.nf_required_version``: The old method for specifying the minimum Nextflow version. Replaced by ``manifest.nextflowVersion``
     * ``params.container``: The old method for specifying the dockerhub container address. Replaced by ``process.container``
     * ``igenomesIgnore``: Changed to ``igenomes_ignore``
+    * ``params.max_cpus``: Old method of specifying the maximum number of CPUs a process can request. Replaced by native Nextflow `resourceLimits`directive.
+    * ``params.max_memory``: Old method of specifying the maximum number of memory can request. Replaced by native Nextflow `resourceLimits`directive.
+    * ``params.max_time``: Old method of specifying the maximum number of CPUs can request. Replaced by native Nextflow `resourceLimits`directive.
 
         .. tip:: The ``snake_case`` convention should now be used when defining pipeline parameters
 
@@ -170,6 +173,9 @@ def nextflow_config(self):
         "params.igenomesIgnore",
         "params.name",
         "params.enable_conda",
+        "params.max_cpus",
+        "params.max_memory",
+        "params.max_time",
     ]
 
     # Remove field that should be ignored according to the linting config
@@ -200,9 +206,13 @@ def nextflow_config(self):
             ignored.append(f"Config variable ignored: {self._wrap_quotes(cf)}")
             break
         if cf not in self.nf_config.keys():
-            passed.append(f"Config variable (correctly) not found: {self._wrap_quotes(cf)}")
+            passed.append(
+                f"Config variable (correctly) not found: {self._wrap_quotes(cf)}"
+            )
         else:
-            failed.append(f"Config variable (incorrectly) found: {self._wrap_quotes(cf)}")
+            failed.append(
+                f"Config variable (incorrectly) found: {self._wrap_quotes(cf)}"
+            )
 
     # Check and warn if the process configuration is done with deprecated syntax
     process_with_deprecated_syntax = list(
@@ -222,9 +232,13 @@ def nextflow_config(self):
         if k in ignore_configs:
             continue
         if self.nf_config.get(k) == "true":
-            passed.append(f"Config ``{k}`` had correct value: ``{self.nf_config.get(k)}``")
+            passed.append(
+                f"Config ``{k}`` had correct value: ``{self.nf_config.get(k)}``"
+            )
         else:
-            failed.append(f"Config ``{k}`` did not have correct value: ``{self.nf_config.get(k)}``")
+            failed.append(
+                f"Config ``{k}`` did not have correct value: ``{self.nf_config.get(k)}``"
+            )
 
     if "manifest.name" not in ignore_configs:
         # Check that the pipeline name starts with nf-core
@@ -233,7 +247,9 @@ def nextflow_config(self):
             if not manifest_name.startswith("nf-core/"):
                 raise AssertionError()
         except (AssertionError, IndexError):
-            failed.append(f"Config ``manifest.name`` did not begin with ``nf-core/``:\n    {manifest_name}")
+            failed.append(
+                f"Config ``manifest.name`` did not begin with ``nf-core/``:\n    {manifest_name}"
+            )
         else:
             passed.append("Config ``manifest.name`` began with ``nf-core/``")
 
@@ -249,7 +265,9 @@ def nextflow_config(self):
             )
 
         else:
-            passed.append("Config variable ``manifest.homePage`` began with https://github.com/nf-core/")
+            passed.append(
+                "Config variable ``manifest.homePage`` began with https://github.com/nf-core/"
+            )
 
     # Check that the DAG filename ends in ``.svg``
     if "dag.file" in self.nf_config:
@@ -257,12 +275,21 @@ def nextflow_config(self):
         if self.nf_config["dag.file"].strip("'\"").endswith(default_dag_format):
             passed.append(f"Config ``dag.file`` ended with ``{default_dag_format}``")
         else:
-            failed.append(f"Config ``dag.file`` did not end with ``{default_dag_format}``")
+            failed.append(
+                f"Config ``dag.file`` did not end with ``{default_dag_format}``"
+            )
 
     # Check that the minimum nextflowVersion is set properly
     if "manifest.nextflowVersion" in self.nf_config:
-        if self.nf_config.get("manifest.nextflowVersion", "").strip("\"'").lstrip("!").startswith(">="):
-            passed.append("Config variable ``manifest.nextflowVersion`` started with >= or !>=")
+        if (
+            self.nf_config.get("manifest.nextflowVersion", "")
+            .strip("\"'")
+            .lstrip("!")
+            .startswith(">=")
+        ):
+            passed.append(
+                "Config variable ``manifest.nextflowVersion`` started with >= or !>="
+            )
         else:
             failed.append(
                 "Config ``manifest.nextflowVersion`` did not start with ``>=`` or ``!>=`` : "
@@ -272,7 +299,9 @@ def nextflow_config(self):
     # Check that the pipeline version contains ``dev``
     if not self.release_mode and "manifest.version" in self.nf_config:
         if self.nf_config["manifest.version"].strip(" '\"").endswith("dev"):
-            passed.append(f"Config ``manifest.version`` ends in ``dev``: ``{self.nf_config['manifest.version']}``")
+            passed.append(
+                f"Config ``manifest.version`` ends in ``dev``: ``{self.nf_config['manifest.version']}``"
+            )
         else:
             warned.append(
                 f"Config ``manifest.version`` should end in ``dev``: ``{self.nf_config['manifest.version']}``"
@@ -291,18 +320,32 @@ def nextflow_config(self):
 
     if "custom_config" not in ignore_configs:
         # Check if custom profile params are set correctly
-        if self.nf_config.get("params.custom_config_version", "").strip("'") == "master":
+        if (
+            self.nf_config.get("params.custom_config_version", "").strip("'")
+            == "master"
+        ):
             passed.append("Config `params.custom_config_version` is set to `master`")
         else:
-            failed.append("Config `params.custom_config_version` is not set to `master`")
+            failed.append(
+                "Config `params.custom_config_version` is not set to `master`"
+            )
 
-        custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/{}".format(
-            self.nf_config.get("params.custom_config_version", "").strip("'")
+        custom_config_base = (
+            "https://raw.githubusercontent.com/nf-core/configs/{}".format(
+                self.nf_config.get("params.custom_config_version", "").strip("'")
+            )
         )
-        if self.nf_config.get("params.custom_config_base", "").strip("'") == custom_config_base:
-            passed.append(f"Config `params.custom_config_base` is set to `{custom_config_base}`")
+        if (
+            self.nf_config.get("params.custom_config_base", "").strip("'")
+            == custom_config_base
+        ):
+            passed.append(
+                f"Config `params.custom_config_base` is set to `{custom_config_base}`"
+            )
         else:
-            failed.append(f"Config `params.custom_config_base` is not set to `{custom_config_base}`")
+            failed.append(
+                f"Config `params.custom_config_base` is not set to `{custom_config_base}`"
+            )
 
         # Check that lines for loading custom profiles exist
         lines = [
@@ -344,7 +387,9 @@ def nextflow_config(self):
 
         match = re.search(r"\bprofiles\s*{", cleaned_content)
         if not match:
-            failed.append("nextflow.config does not contain `profiles` scope, but `test` profile is required")
+            failed.append(
+                "nextflow.config does not contain `profiles` scope, but `test` profile is required"
+            )
         else:
             # Extract profiles scope content and check for test profile
             start = match.end()
@@ -360,7 +405,9 @@ def nextflow_config(self):
             if re.search(r"\btest\s*{", profiles_content):
                 passed.append("nextflow.config contains configuration profile `test`")
             else:
-                failed.append("nextflow.config does not contain configuration profile `test`")
+                failed.append(
+                    "nextflow.config does not contain configuration profile `test`"
+                )
 
     # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json
     ignore_defaults = []
@@ -404,7 +451,9 @@ def nextflow_config(self):
                 schema_default = str(schema.schema_defaults[param_name])
                 config_default = str(self.nf_config[param])
             if config_default is not None and config_default == schema_default:
-                passed.append(f"Config default value correct: {param}= {schema_default}")
+                passed.append(
+                    f"Config default value correct: {param}= {schema_default}"
+                )
             else:
                 failed.append(
                     f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`."

From 47abfc2a2dbf9f8ae42a70bc5b833e1836fdb121 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 1 Jul 2024 14:44:55 +0200
Subject: [PATCH 012/414] Add linting check for check_ params and continue
 removing from everywhere (not finished)

---
 nf_core/pipeline-template/conf/test.config    |  5 ---
 nf_core/pipeline-template/nextflow.config     |  6 ----
 .../pipeline-template/nextflow_schema.json    | 35 -------------------
 3 files changed, 46 deletions(-)

diff --git a/nf_core/pipeline-template/conf/test.config b/nf_core/pipeline-template/conf/test.config
index 2b9715efb6..0f1d974101 100644
--- a/nf_core/pipeline-template/conf/test.config
+++ b/nf_core/pipeline-template/conf/test.config
@@ -22,11 +22,6 @@ params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index d575c6186f..7d9040104c 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -50,12 +50,6 @@ params {
     config_profile_url         = null
     {%- endif %}
 
-    // Max resource options
-    // Defaults only, expecting to be overwritten
-    max_memory                 = '128.GB'
-    max_cpus                   = 16
-    max_time                   = '240.h'
-
     // Schema validation default options
     validationFailUnrecognisedParams = false
     validationLenientMode            = false
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 18bad71b76..07a90f6259 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -124,41 +124,6 @@
                 }
             }
         },
-        "max_job_request_options": {
-            "title": "Max job request options",
-            "type": "object",
-            "fa_icon": "fab fa-acquisitions-incorporated",
-            "description": "Set the top limit for requested resources for any single job.",
-            "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
-            "properties": {
-                "max_cpus": {
-                    "type": "integer",
-                    "description": "Maximum number of CPUs that can be requested for any single job.",
-                    "default": 16,
-                    "fa_icon": "fas fa-microchip",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
-                },
-                "max_memory": {
-                    "type": "string",
-                    "description": "Maximum amount of memory that can be requested for any single job.",
-                    "default": "128.GB",
-                    "fa_icon": "fas fa-memory",
-                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
-                },
-                "max_time": {
-                    "type": "string",
-                    "description": "Maximum amount of time that can be requested for any single job.",
-                    "default": "240.h",
-                    "fa_icon": "far fa-clock",
-                    "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
-                }
-            }
-        },
         "generic_options": {
             "title": "Generic options",
             "type": "object",

From d863c4d8fcbe3ef41ae8f0d16f1c314e0c45a6d9 Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@kuleuven.be>
Date: Wed, 3 Jul 2024 08:29:04 +0000
Subject: [PATCH 013/414] add default limit_output argument for write_diff_file
 & print_diff

---
 nf_core/modules/modules_differ.py | 24 +++++++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py
index dc2b163dd4..fb1fc31dc1 100644
--- a/nf_core/modules/modules_differ.py
+++ b/nf_core/modules/modules_differ.py
@@ -133,6 +133,7 @@ def write_diff_file(
         for_git=True,
         dsp_from_dir=None,
         dsp_to_dir=None,
+        limit_output=False,
     ):
         """
         Writes the diffs of a module to the diff file.
@@ -174,8 +175,14 @@ def write_diff_file(
             else:
                 fh.write(f"Changes in module '{Path(repo_path, module)}'\n")
 
-            for _, (diff_status, diff) in diffs.items():
-                if diff_status != ModulesDiffer.DiffEnum.UNCHANGED:
+            for file, (diff_status, diff) in diffs.items():
+                if diff_status == ModulesDiffer.DiffEnum.UNCHANGED:
+                    # The files are identical
+                    fh.write(f"'{Path(dsp_from_dir, file)}' is unchanged\n")
+                elif limit_output and file != "main.nf":
+                    # Skip printing the diff for files other than main.nf
+                    fh.write(f"Changes in '{Path(module, file)}' not shown\n")
+                else:
                     # The file has changed write the diff lines to the file
                     for line in diff:
                         fh.write(line)
@@ -219,7 +226,15 @@ def append_modules_json_diff(diff_path, old_modules_json, new_modules_json, modu
 
     @staticmethod
     def print_diff(
-        module, repo_path, from_dir, to_dir, current_version=None, new_version=None, dsp_from_dir=None, dsp_to_dir=None
+        module,
+        repo_path,
+        from_dir,
+        to_dir,
+        current_version=None,
+        new_version=None,
+        dsp_from_dir=None,
+        dsp_to_dir=None,
+        limit_output=False,
     ):
         """
         Prints the diffs between two module versions to the terminal
@@ -261,6 +276,9 @@ def print_diff(
             elif diff_status == ModulesDiffer.DiffEnum.REMOVED:
                 # The file was removed between the commits
                 log.info(f"'{Path(dsp_from_dir, file)}' was removed")
+            elif limit_output and file != "main.nf":
+                # Skip printing the diff for files other than main.nf
+                log.info(f"Changes in '{Path(module, file)}' not shown")
             else:
                 # The file has changed
                 log.info(f"Changes in '{Path(module, file)}':")

From 5b9d3f54eb206b835035ccdc349130026c42eb9d Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 3 Jul 2024 08:33:07 +0000
Subject: [PATCH 014/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6d3f4f088c..fc4a233491 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -38,6 +38,7 @@
 - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036))
 - Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007))
 - Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041))
+- add default limit_output argument for write_diff_file & print_diff ([#3047](https://github.com/nf-core/tools/pull/3047))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From 1997ee41a974e26dd6e9de7e30e91ff0240fe49f Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@kuleuven.be>
Date: Wed, 3 Jul 2024 09:38:23 +0000
Subject: [PATCH 015/414] adding limit_output to click

---
 nf_core/__main__.py          | 10 ++++++++++
 nf_core/components/update.py | 17 +++++++++++++----
 nf_core/modules/update.py    |  2 ++
 3 files changed, 25 insertions(+), 4 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index ea0018e2af..86bcde86e3 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1214,6 +1214,14 @@ def modules_install(ctx, tool, dir, prompt, force, sha):
     default=False,
     help="Prompt for the version of the module",
 )
+@click.option(
+    "-l",
+    "--limit-output",
+    "limit_output",
+    is_flag=True,
+    default=False,
+    help="Limit ouput to only the difference in main.nf",
+)
 @click.option("-s", "--sha", type=str, metavar="<commit sha>", help="Install module at commit SHA")
 @click.option(
     "-a",
@@ -1256,6 +1264,7 @@ def modules_update(
     preview,
     save_diff,
     update_deps,
+    limit_output,
 ):
     """
     Update DSL2 modules within a pipeline.
@@ -1277,6 +1286,7 @@ def modules_update(
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
+            limit_output,
         )
         exit_status = module_install.update(tool)
         if not exit_status and install_all:
diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index a54c47232e..3c3cdca6c9 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -38,6 +38,7 @@ def __init__(
         remote_url=None,
         branch=None,
         no_pull=False,
+        limit_output=False,
     ):
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
         self.force = force
@@ -76,7 +77,7 @@ def _parameter_checks(self):
         if not self.has_valid_directory():
             raise UserWarning("The command was not run in a valid pipeline directory.")
 
-    def update(self, component=None, silent=False, updated=None, check_diff_exist=True) -> bool:
+    def update(self, component=None, silent=False, updated=None, check_diff_exist=True, limit_output=False) -> bool:
         """Updates a specified module/subworkflow or all modules/subworkflows in a pipeline.
 
         If updating a subworkflow: updates all modules used in that subworkflow.
@@ -231,6 +232,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                             version,
                             dsp_from_dir=component_dir,
                             dsp_to_dir=component_dir,
+                            limit_output=limit_output,
                         )
                         updated.append(component)
                     except UserWarning as e:
@@ -271,6 +273,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                         version,
                         dsp_from_dir=component_dir,
                         dsp_to_dir=component_dir,
+                        limit_output=limit_output,
                     )
 
                     # Ask the user if they want to install the component
@@ -875,7 +878,9 @@ def get_components_to_update(self, component):
 
         return modules_to_update, subworkflows_to_update
 
-    def update_linked_components(self, modules_to_update, subworkflows_to_update, updated=None, check_diff_exist=True):
+    def update_linked_components(
+        self, modules_to_update, subworkflows_to_update, updated=None, check_diff_exist=True, limit_output=False
+    ):
         """
         Update modules and subworkflows linked to the component being updated.
         """
@@ -883,7 +888,9 @@ def update_linked_components(self, modules_to_update, subworkflows_to_update, up
             if s_update in updated:
                 continue
             original_component_type, original_update_all = self._change_component_type("subworkflows")
-            self.update(s_update, silent=True, updated=updated, check_diff_exist=check_diff_exist)
+            self.update(
+                s_update, silent=True, updated=updated, check_diff_exist=check_diff_exist, limit_output=limit_output
+            )
             self._reset_component_type(original_component_type, original_update_all)
 
         for m_update in modules_to_update:
@@ -891,7 +898,9 @@ def update_linked_components(self, modules_to_update, subworkflows_to_update, up
                 continue
             original_component_type, original_update_all = self._change_component_type("modules")
             try:
-                self.update(m_update, silent=True, updated=updated, check_diff_exist=check_diff_exist)
+                self.update(
+                    m_update, silent=True, updated=updated, check_diff_exist=check_diff_exist, limit_output=limit_output
+                )
             except LookupError as e:
                 # If the module to be updated is not available, check if there has been a name change
                 if "not found in list of available" in str(e):
diff --git a/nf_core/modules/update.py b/nf_core/modules/update.py
index 9d53bf2017..f6cf5235a4 100644
--- a/nf_core/modules/update.py
+++ b/nf_core/modules/update.py
@@ -15,6 +15,7 @@ def __init__(
         remote_url=None,
         branch=None,
         no_pull=False,
+        limit_output=False,
     ):
         super().__init__(
             pipeline_dir,
@@ -29,4 +30,5 @@ def __init__(
             remote_url,
             branch,
             no_pull,
+            limit_output,
         )

From 27475f73ccb5dd4529f4e1b6a5f80841ee802b00 Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@kuleuven.be>
Date: Wed, 3 Jul 2024 11:16:29 +0000
Subject: [PATCH 016/414] add to subworkflow as well

---
 nf_core/__main__.py            | 10 ++++++++++
 nf_core/components/update.py   |  2 +-
 nf_core/subworkflows/update.py |  2 ++
 3 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 86bcde86e3..815c98c1eb 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -2157,6 +2157,14 @@ def subworkflows_remove(ctx, dir, subworkflow):
     metavar="<commit sha>",
     help="Install subworkflow at commit SHA",
 )
+@click.option(
+    "-l",
+    "--limit-output",
+    "limit_output",
+    is_flag=True,
+    default=False,
+    help="Limit ouput to only the difference in main.nf",
+)
 @click.option(
     "-a",
     "--all",
@@ -2198,6 +2206,7 @@ def subworkflows_update(
     preview,
     save_diff,
     update_deps,
+    limit_output,
 ):
     """
     Update DSL2 subworkflow within a pipeline.
@@ -2219,6 +2228,7 @@ def subworkflows_update(
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
+            limit_output,
         )
         exit_status = subworkflow_install.update(subworkflow)
         if not exit_status and install_all:
diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index 3c3cdca6c9..8beab7a925 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -40,7 +40,7 @@ def __init__(
         no_pull=False,
         limit_output=False,
     ):
-        super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
+        super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull, limit_output)
         self.force = force
         self.prompt = prompt
         self.sha = sha
diff --git a/nf_core/subworkflows/update.py b/nf_core/subworkflows/update.py
index 3cd4ad59fd..9b6bf16928 100644
--- a/nf_core/subworkflows/update.py
+++ b/nf_core/subworkflows/update.py
@@ -15,6 +15,7 @@ def __init__(
         remote_url=None,
         branch=None,
         no_pull=False,
+        limit_output=False,
     ):
         super().__init__(
             pipeline_dir,
@@ -29,4 +30,5 @@ def __init__(
             remote_url,
             branch,
             no_pull,
+            limit_output,
         )

From 2cb6946d100c0b61e238668b0b2b889decd64a28 Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@kuleuven.be>
Date: Wed, 3 Jul 2024 11:18:49 +0000
Subject: [PATCH 017/414] better changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9355b3ca12..b01e13ce83 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -39,7 +39,7 @@
 - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036))
 - Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007))
 - Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041))
-- add default limit_output argument for write_diff_file & print_diff ([#3047](https://github.com/nf-core/tools/pull/3047))
+- Add `--limit-output` argument for modules/subworkflow update ([#3047](https://github.com/nf-core/tools/pull/3047))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From f35b1f0f840b8324e0cf6c795538cd372cc5c99c Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@kuleuven.be>
Date: Wed, 3 Jul 2024 11:40:16 +0000
Subject: [PATCH 018/414] debug prints

---
 nf_core/components/update.py | 27 ++++++++++++++++++++-------
 1 file changed, 20 insertions(+), 7 deletions(-)

diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index 8beab7a925..72c053cfd8 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -40,18 +40,20 @@ def __init__(
         no_pull=False,
         limit_output=False,
     ):
-        super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull, limit_output)
+        super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
         self.force = force
         self.prompt = prompt
         self.sha = sha
         self.update_all = update_all
         self.show_diff = show_diff
         self.save_diff_fn = save_diff_fn
+        self.limit_output = limit_output
         self.update_deps = update_deps
         self.component = None
         self.update_config = None
         self.modules_json = ModulesJson(self.dir)
         self.branch = branch
+        log.info(f"init component limit_output ={self.limit_output}")
 
     def _parameter_checks(self):
         """Checks the compatibilty of the supplied parameters.
@@ -77,7 +79,7 @@ def _parameter_checks(self):
         if not self.has_valid_directory():
             raise UserWarning("The command was not run in a valid pipeline directory.")
 
-    def update(self, component=None, silent=False, updated=None, check_diff_exist=True, limit_output=False) -> bool:
+    def update(self, component=None, silent=False, updated=None, check_diff_exist=True) -> bool:
         """Updates a specified module/subworkflow or all modules/subworkflows in a pipeline.
 
         If updating a subworkflow: updates all modules used in that subworkflow.
@@ -232,7 +234,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                             version,
                             dsp_from_dir=component_dir,
                             dsp_to_dir=component_dir,
-                            limit_output=limit_output,
+                            limit_output=self.limit_output,
                         )
                         updated.append(component)
                     except UserWarning as e:
@@ -264,6 +266,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                         self.manage_changes_in_linked_components(component, modules_to_update, subworkflows_to_update)
 
                 elif self.show_diff:
+                    log.info(f"limit_output ModulesDiffer: {self.limit_output}")
                     ModulesDiffer.print_diff(
                         component,
                         modules_repo.repo_path,
@@ -273,7 +276,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                         version,
                         dsp_from_dir=component_dir,
                         dsp_to_dir=component_dir,
-                        limit_output=limit_output,
+                        limit_output=self.limit_output,
                     )
 
                     # Ask the user if they want to install the component
@@ -879,7 +882,11 @@ def get_components_to_update(self, component):
         return modules_to_update, subworkflows_to_update
 
     def update_linked_components(
-        self, modules_to_update, subworkflows_to_update, updated=None, check_diff_exist=True, limit_output=False
+        self,
+        modules_to_update,
+        subworkflows_to_update,
+        updated=None,
+        check_diff_exist=True,
     ):
         """
         Update modules and subworkflows linked to the component being updated.
@@ -889,7 +896,10 @@ def update_linked_components(
                 continue
             original_component_type, original_update_all = self._change_component_type("subworkflows")
             self.update(
-                s_update, silent=True, updated=updated, check_diff_exist=check_diff_exist, limit_output=limit_output
+                s_update,
+                silent=True,
+                updated=updated,
+                check_diff_exist=check_diff_exist,
             )
             self._reset_component_type(original_component_type, original_update_all)
 
@@ -899,7 +909,10 @@ def update_linked_components(
             original_component_type, original_update_all = self._change_component_type("modules")
             try:
                 self.update(
-                    m_update, silent=True, updated=updated, check_diff_exist=check_diff_exist, limit_output=limit_output
+                    m_update,
+                    silent=True,
+                    updated=updated,
+                    check_diff_exist=check_diff_exist,
                 )
             except LookupError as e:
                 # If the module to be updated is not available, check if there has been a name change

From f7e830381e6e22e2c08083c1c3bb29df79c0841c Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@kuleuven.be>
Date: Wed, 3 Jul 2024 11:47:52 +0000
Subject: [PATCH 019/414] fix file suffix checking

---
 nf_core/components/update.py      | 2 --
 nf_core/modules/modules_differ.py | 4 ++--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index 72c053cfd8..37e3f62126 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -53,7 +53,6 @@ def __init__(
         self.update_config = None
         self.modules_json = ModulesJson(self.dir)
         self.branch = branch
-        log.info(f"init component limit_output ={self.limit_output}")
 
     def _parameter_checks(self):
         """Checks the compatibilty of the supplied parameters.
@@ -266,7 +265,6 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                         self.manage_changes_in_linked_components(component, modules_to_update, subworkflows_to_update)
 
                 elif self.show_diff:
-                    log.info(f"limit_output ModulesDiffer: {self.limit_output}")
                     ModulesDiffer.print_diff(
                         component,
                         modules_repo.repo_path,
diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py
index fb1fc31dc1..5273857705 100644
--- a/nf_core/modules/modules_differ.py
+++ b/nf_core/modules/modules_differ.py
@@ -179,7 +179,7 @@ def write_diff_file(
                 if diff_status == ModulesDiffer.DiffEnum.UNCHANGED:
                     # The files are identical
                     fh.write(f"'{Path(dsp_from_dir, file)}' is unchanged\n")
-                elif limit_output and file != "main.nf":
+                elif limit_output and not (file.endswith(".nf")):
                     # Skip printing the diff for files other than main.nf
                     fh.write(f"Changes in '{Path(module, file)}' not shown\n")
                 else:
@@ -276,7 +276,7 @@ def print_diff(
             elif diff_status == ModulesDiffer.DiffEnum.REMOVED:
                 # The file was removed between the commits
                 log.info(f"'{Path(dsp_from_dir, file)}' was removed")
-            elif limit_output and file != "main.nf":
+            elif limit_output and not (file.endswith(".nf")):
                 # Skip printing the diff for files other than main.nf
                 log.info(f"Changes in '{Path(module, file)}' not shown")
             else:

From bc8d096e71cebeb22d7e9ac7a10455901e715e5f Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@kuleuven.be>
Date: Wed, 3 Jul 2024 11:49:21 +0000
Subject: [PATCH 020/414] remove unnecessary()

---
 nf_core/modules/modules_differ.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py
index 5273857705..7de68b9cc5 100644
--- a/nf_core/modules/modules_differ.py
+++ b/nf_core/modules/modules_differ.py
@@ -179,7 +179,7 @@ def write_diff_file(
                 if diff_status == ModulesDiffer.DiffEnum.UNCHANGED:
                     # The files are identical
                     fh.write(f"'{Path(dsp_from_dir, file)}' is unchanged\n")
-                elif limit_output and not (file.endswith(".nf")):
+                elif limit_output and not file.endswith(".nf"):
                     # Skip printing the diff for files other than main.nf
                     fh.write(f"Changes in '{Path(module, file)}' not shown\n")
                 else:
@@ -276,7 +276,7 @@ def print_diff(
             elif diff_status == ModulesDiffer.DiffEnum.REMOVED:
                 # The file was removed between the commits
                 log.info(f"'{Path(dsp_from_dir, file)}' was removed")
-            elif limit_output and not (file.endswith(".nf")):
+            elif limit_output and not file.endswith(".nf"):
                 # Skip printing the diff for files other than main.nf
                 log.info(f"Changes in '{Path(module, file)}' not shown")
             else:

From e5e34aacbe20b77df6c9f178cbe220a8161b45a5 Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@kuleuven.be>
Date: Wed, 3 Jul 2024 11:55:25 +0000
Subject: [PATCH 021/414] use suffix instead

---
 nf_core/modules/modules_differ.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py
index 7de68b9cc5..f97c7dce5b 100644
--- a/nf_core/modules/modules_differ.py
+++ b/nf_core/modules/modules_differ.py
@@ -179,7 +179,7 @@ def write_diff_file(
                 if diff_status == ModulesDiffer.DiffEnum.UNCHANGED:
                     # The files are identical
                     fh.write(f"'{Path(dsp_from_dir, file)}' is unchanged\n")
-                elif limit_output and not file.endswith(".nf"):
+                elif limit_output and not file.suffix == ".nf":
                     # Skip printing the diff for files other than main.nf
                     fh.write(f"Changes in '{Path(module, file)}' not shown\n")
                 else:
@@ -276,7 +276,7 @@ def print_diff(
             elif diff_status == ModulesDiffer.DiffEnum.REMOVED:
                 # The file was removed between the commits
                 log.info(f"'{Path(dsp_from_dir, file)}' was removed")
-            elif limit_output and not file.endswith(".nf"):
+            elif limit_output and not file.suffix == ".nf":
                 # Skip printing the diff for files other than main.nf
                 log.info(f"Changes in '{Path(module, file)}' not shown")
             else:

From a61da2d98f1c24905d09a87e7e4efb83c6fbb35c Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@kuleuven.be>
Date: Wed, 3 Jul 2024 12:02:26 +0000
Subject: [PATCH 022/414] add method argument docs

---
 nf_core/modules/modules_differ.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py
index f97c7dce5b..34966b2ffd 100644
--- a/nf_core/modules/modules_differ.py
+++ b/nf_core/modules/modules_differ.py
@@ -155,6 +155,7 @@ def write_diff_file(
                             adds a/ and b/ prefixes to the file paths
             dsp_from_dir (str | Path): The 'from' directory displayed in the diff
             dsp_to_dir (str | Path): The 'to' directory displayed in the diff
+            limit_output (bool): If true, don't write the diff for files other than main.nf
         """
         if dsp_from_dir is None:
             dsp_from_dir = from_dir
@@ -181,7 +182,7 @@ def write_diff_file(
                     fh.write(f"'{Path(dsp_from_dir, file)}' is unchanged\n")
                 elif limit_output and not file.suffix == ".nf":
                     # Skip printing the diff for files other than main.nf
-                    fh.write(f"Changes in '{Path(module, file)}' not shown\n")
+                    fh.write(f"Changes in '{Path(module, file)}' but not shown\n")
                 else:
                     # The file has changed write the diff lines to the file
                     for line in diff:
@@ -249,6 +250,7 @@ def print_diff(
             new_version (str): The version of the module the diff is computed against
             dsp_from_dir (str | Path): The 'from' directory displayed in the diff
             dsp_to_dir (str | Path): The 'to' directory displayed in the diff
+            limit_output (bool): If true, don't print the diff for files other than main.nf
         """
         if dsp_from_dir is None:
             dsp_from_dir = from_dir
@@ -278,7 +280,7 @@ def print_diff(
                 log.info(f"'{Path(dsp_from_dir, file)}' was removed")
             elif limit_output and not file.suffix == ".nf":
                 # Skip printing the diff for files other than main.nf
-                log.info(f"Changes in '{Path(module, file)}' not shown")
+                log.info(f"Changes in '{Path(module, file)}' but not shown")
             else:
                 # The file has changed
                 log.info(f"Changes in '{Path(module, file)}':")

From 667c53f95b54b3ceb54671d22f72bc312be0ae9b Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@kuleuven.be>
Date: Wed, 3 Jul 2024 14:24:02 +0000
Subject: [PATCH 023/414] add tests

---
 tests/modules/update.py      | 113 +++++++++++++++++++++++++++++++++
 tests/subworkflows/update.py | 120 +++++++++++++++++++++++++++++++++++
 tests/test_modules.py        |   2 +
 tests/test_subworkflows.py   |   2 +
 4 files changed, 237 insertions(+)

diff --git a/tests/modules/update.py b/tests/modules/update.py
index 81eb85716e..0fddcc8ba8 100644
--- a/tests/modules/update.py
+++ b/tests/modules/update.py
@@ -1,5 +1,8 @@
 import filecmp
+import io
+import logging
 import os
+import re
 import shutil
 import tempfile
 from pathlib import Path
@@ -67,6 +70,71 @@ def test_install_at_hash_and_update(self):
     assert correct_git_sha == current_git_sha
 
 
+def test_install_at_hash_and_update_limit_output(self):
+    """Installs an old version of a module in the pipeline and updates it with limited output reporting"""
+    assert self.mods_install_old.install("trimgalore")
+
+    # Capture the logger output
+    log_capture = io.StringIO()
+    ch = logging.StreamHandler(log_capture)
+    logger = logging.getLogger()
+    logger.addHandler(ch)
+
+    update_obj = ModuleUpdate(
+        self.pipeline_dir,
+        show_diff=False,
+        update_deps=True,
+        remote_url=GITLAB_URL,
+        branch=OLD_TRIMGALORE_BRANCH,
+        limit_output=True,
+    )
+
+    # Copy the module files and check that they are affected by the update
+    tmpdir = tempfile.mkdtemp()
+    trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore")
+    trimgalore_path = os.path.join(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
+    shutil.copytree(trimgalore_path, trimgalore_tmpdir)
+
+    assert update_obj.update("trimgalore") is True
+    assert cmp_module(trimgalore_tmpdir, trimgalore_path) is False
+
+    # Check that the modules.json is correctly updated
+    mod_json_obj = ModulesJson(self.pipeline_dir)
+    mod_json = mod_json_obj.get_modules_json()
+    # Get the up-to-date git_sha for the module from the ModuleRepo object
+    correct_git_sha = update_obj.modules_repo.get_latest_component_version("trimgalore", "modules")
+    current_git_sha = mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"]
+    assert correct_git_sha == current_git_sha
+
+    # Get the captured log output
+    log_output = log_capture.getvalue()
+    log_lines = log_output.split("\n")
+
+    # Check for various scenarios
+    for line in log_lines:
+        if re.match(r"'.+' is unchanged", line):
+            # Unchanged files should be reported for both .nf and non-.nf files
+            assert True
+        elif re.match(r"'.+' was created", line):
+            # Created files should be reported for both .nf and non-.nf files
+            assert True
+        elif re.match(r"'.+' was removed", line):
+            # Removed files should be reported for both .nf and non-.nf files
+            assert True
+        elif re.match(r"Changes in '.+' but not shown", line):
+            # Changes not shown should only be for non-.nf files
+            file_path = re.search(r"'(.+)'", line).group(1)
+            assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}"
+        elif re.match(r"Changes in '.+':$", line):
+            # Changes shown should only be for .nf files
+            file_path = re.search(r"'(.+)'", line).group(1)
+            assert Path(file_path).suffix == ".nf", f"Changes in non-.nf file were shown: {line}"
+
+    # Clean up
+    logger.removeHandler(ch)
+    log_capture.close()
+
+
 def test_install_at_hash_and_update_and_save_diff_to_file(self):
     """Installs an old version of a module in the pipeline and updates it"""
     self.mods_install_old.install("trimgalore")
@@ -91,6 +159,51 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self):
     # TODO: Apply the patch to the module
 
 
+def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self):
+    """Installs an old version of a module in the pipeline and updates it"""
+    self.mods_install_old.install("trimgalore")
+    patch_path = os.path.join(self.pipeline_dir, "trimgalore.patch")
+    update_obj = ModuleUpdate(
+        self.pipeline_dir,
+        save_diff_fn=patch_path,
+        sha=OLD_TRIMGALORE_SHA,
+        remote_url=GITLAB_URL,
+        branch=OLD_TRIMGALORE_BRANCH,
+        limit_output=True,
+    )
+
+    # Copy the module files and check that they are affected by the update
+    tmpdir = tempfile.mkdtemp()
+    trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore")
+    trimgalore_path = os.path.join(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
+    shutil.copytree(trimgalore_path, trimgalore_tmpdir)
+
+    assert update_obj.update("trimgalore") is True
+    assert cmp_module(trimgalore_tmpdir, trimgalore_path) is True
+
+    # Check that the patch file was created
+    assert os.path.exists(patch_path), f"Patch file was not created at {patch_path}"
+
+    # Read the contents of the patch file
+    with open(patch_path) as f:
+        patch_content = f.read()
+
+    # Check the content of the patch file
+    patch_lines = patch_content.split("\n")
+    for line in patch_lines:
+        if re.match(r"'.+' is unchanged", line):
+            # Unchanged files should be reported for both .nf and non-.nf files
+            assert True
+        elif re.match(r"Changes in '.+' but not shown", line):
+            # Changes not shown should only be for non-.nf files
+            file_path = re.search(r"'(.+)'", line).group(1)
+            assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}"
+        elif re.match("diff --git", line):
+            # Diff should only be shown for .nf files
+            file_path = re.search(r"b/(.+)$", line).group(1)
+            assert Path(file_path).suffix == ".nf", f"Diff shown for non-.nf file: {line}"
+
+
 def test_update_all(self):
     """Updates all modules present in the pipeline"""
     update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=False)
diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py
index 9ddc9bec0c..7d1a3808dc 100644
--- a/tests/subworkflows/update.py
+++ b/tests/subworkflows/update.py
@@ -1,4 +1,7 @@
 import filecmp
+import io
+import logging
+import re
 import shutil
 import tempfile
 from pathlib import Path
@@ -57,6 +60,73 @@ def test_install_at_hash_and_update(self):
     )
 
 
+def test_install_at_hash_and_update_limit_output(self):
+    """Installs an old version of a subworkflow in the pipeline and updates it with limit_output=True"""
+    assert self.subworkflow_install_old.install("fastq_align_bowtie2")
+
+    # Capture the logger output
+    log_capture = io.StringIO()
+    ch = logging.StreamHandler(log_capture)
+    logger = logging.getLogger()
+    logger.addHandler(ch)
+
+    update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False, update_deps=True, limit_output=True)
+    old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+
+    # Copy the subworkflow files and check that they are affected by the update
+    tmpdir = tempfile.mkdtemp()
+    sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
+    shutil.copytree(sw_path, tmpdir)
+
+    assert update_obj.update("fastq_align_bowtie2") is True
+    assert cmp_component(tmpdir, sw_path) is False
+
+    # Check that the modules.json is correctly updated
+    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+    assert (
+        old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
+            "git_sha"
+        ]
+        != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
+            "git_sha"
+        ]
+    )
+
+    # Get the captured log output
+    log_output = log_capture.getvalue()
+    log_lines = log_output.split("\n")
+
+    # Check for various scenarios
+    nf_changes_shown = False
+    for line in log_lines:
+        if re.match(r"'.+' is unchanged", line):
+            # Unchanged files should be reported for both .nf and non-.nf files
+            assert True
+        elif re.match(r"'.+' was created", line):
+            # Created files should be reported for both .nf and non-.nf files
+            assert True
+        elif re.match(r"'.+' was removed", line):
+            # Removed files should be reported for both .nf and non-.nf files
+            assert True
+        elif re.match(r"Changes in '.+' but not shown", line):
+            # Changes not shown should only be for non-.nf files
+            file_path = re.search(r"'(.+)'", line).group(1)
+            assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}"
+        elif re.match(r"Changes in '.+':$", line):
+            # Changes shown should only be for .nf files
+            file_path = re.search(r"'(.+)'", line).group(1)
+            assert Path(file_path).suffix == ".nf", f"Changes in non-.nf file were shown: {line}"
+            nf_changes_shown = True
+
+    # Ensure that changes in at least one .nf file were shown
+    assert nf_changes_shown, "No changes in .nf files were shown"
+
+    # Clean up
+    logger.removeHandler(ch)
+    log_capture.close()
+    shutil.rmtree(tmpdir)
+
+
 def test_install_at_hash_and_update_and_save_diff_to_file(self):
     """Installs an old version of a sw in the pipeline and updates it. Save differences to a file."""
     assert self.subworkflow_install_old.install("fastq_align_bowtie2")
@@ -79,6 +149,56 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self):
         )
 
 
+def test_install_at_hash_and_update_and_save_diff_limit_output(self):
+    """Installs an old version of a sw in the pipeline and updates it. Save differences to a file."""
+    assert self.subworkflow_install_old.install("fastq_align_bowtie2")
+    patch_path = Path(self.pipeline_dir, "fastq_align_bowtie2.patch")
+    update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True, limit_output=True)
+
+    # Copy the sw files and check that they are affected by the update
+    tmpdir = tempfile.mkdtemp()
+    shutil.rmtree(tmpdir)
+    sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
+    shutil.copytree(sw_path, tmpdir)
+
+    assert update_obj.update("fastq_align_bowtie2") is True
+    assert cmp_component(tmpdir, sw_path) is True
+
+    # Check that the patch file was created
+    assert patch_path.exists(), f"Patch file was not created at {patch_path}"
+
+    nf_changes_shown = False
+    non_nf_changes_not_shown = False
+
+    with open(patch_path) as fh:
+        content = fh.read()
+
+        # Check the first line
+        assert re.match(
+            r"Changes in module 'nf-core/fastq_align_bowtie2' between \([a-f0-9]+\) and \([a-f0-9]+\)",
+            content.split("\n")[0],
+        ), "Unexpected first line in patch file"
+
+        # Check for .nf file changes shown
+        nf_changes_shown = bool(re.search(r"Changes in '.*\.nf':\n", content))
+
+        # Check for non-.nf file changes not shown
+        non_nf_changes_not_shown = bool(re.search(r"Changes in '.*[^.nf]' but not shown", content))
+
+        # Check that diff content is only for .nf files
+        diff_lines = re.findall(r"diff --git.*", content)
+        for line in diff_lines:
+            assert re.search(r"\.nf$", line), f"Diff shown for non-.nf file: {line}"
+
+    # Ensure that changes in .nf files were shown and non-.nf files were not shown
+    assert nf_changes_shown, "No changes in .nf files were shown in the patch file"
+    assert non_nf_changes_not_shown, "Changes in non-.nf files were not properly limited in the patch file"
+
+    # Clean up
+    patch_path.unlink()
+    shutil.rmtree(tmpdir)
+
+
 def test_update_all(self):
     """Updates all subworkflows present in the pipeline"""
     # Install subworkflows fastq_align_bowtie2, bam_sort_stats_samtools, bam_stats_samtools
diff --git a/tests/test_modules.py b/tests/test_modules.py
index 107b245663..7dd3132d33 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -269,6 +269,8 @@ def test_modulesrepo_class(self):
         test_install_and_update,
         test_install_at_hash_and_update,
         test_install_at_hash_and_update_and_save_diff_to_file,
+        test_install_at_hash_and_update_and_save_diff_to_file_limit_output,
+        test_install_at_hash_and_update_limit_output,
         test_update_all,
         test_update_different_branch_mix_modules_branch_test,
         test_update_different_branch_mixed_modules_main,
diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py
index 786ba53836..b7ebe952db 100644
--- a/tests/test_subworkflows.py
+++ b/tests/test_subworkflows.py
@@ -175,7 +175,9 @@ def tearDown(self):
     from .subworkflows.update import (  # type: ignore[misc]
         test_install_and_update,
         test_install_at_hash_and_update,
+        test_install_at_hash_and_update_and_save_diff_limit_output,
         test_install_at_hash_and_update_and_save_diff_to_file,
+        test_install_at_hash_and_update_limit_output,
         test_update_all,
         test_update_all_linked_components_from_subworkflow,
         test_update_all_subworkflows_from_module,

From e2c04cc1c5c4ba7bddcc7c17ec7fd67765a56e63 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jul 2024 13:48:29 +0200
Subject: [PATCH 024/414] update output_dir for api docs to new website
 structure

---
 docs/api/generate-api-docs.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/api/generate-api-docs.sh b/docs/api/generate-api-docs.sh
index f2b905c0c3..cc65e1bb14 100644
--- a/docs/api/generate-api-docs.sh
+++ b/docs/api/generate-api-docs.sh
@@ -28,7 +28,7 @@ done
 
 # Set the output directory if not set
 if [[ -z "$output_dir" ]]; then
-    output_dir="../src/content/api_reference"
+    output_dir="../sites/docs/src/content/api_reference"
 fi
 
 # if no release is specified, use all releases

From ade71b7852947459ab242999306204e85bd10300 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Fri, 5 Jul 2024 11:49:37 +0000
Subject: [PATCH 025/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 16db104fc6..559a427e90 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -42,6 +42,7 @@
 - Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038))
 - Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041))
 - Update gitpod/workspace-base Docker digest to 0f38224 ([#3048](https://github.com/nf-core/tools/pull/3048))
+- update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From edcda568d640a3d96fe7b653e8c9d6317a68be45 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 5 Jul 2024 14:19:26 +0000
Subject: [PATCH 026/414] Update pre-commit hook astral-sh/ruff-pre-commit to
 v0.5.1

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6cefa7fc0f..c1dc7978f6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0
+    rev: v0.5.1
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

From 0ee58ee7f609e44c5150aafda0f2a51435114457 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Fri, 5 Jul 2024 14:20:14 +0000
Subject: [PATCH 027/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 559a427e90..6da61b3fe3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -43,6 +43,7 @@
 - Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041))
 - Update gitpod/workspace-base Docker digest to 0f38224 ([#3048](https://github.com/nf-core/tools/pull/3048))
 - update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From b61d781507b68efab8b8e277806cb3b2290fa8f5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 9 Jul 2024 09:08:22 +0200
Subject: [PATCH 028/414] update awsfulltest linting tests to new structure

---
 nf_core/pipelines/lint/actions_awsfulltest.py |  4 +++-
 tests/lint/actions_awsfulltest.py             | 16 ++++++++--------
 2 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/nf_core/pipelines/lint/actions_awsfulltest.py b/nf_core/pipelines/lint/actions_awsfulltest.py
index d5a061c935..4cf3bece28 100644
--- a/nf_core/pipelines/lint/actions_awsfulltest.py
+++ b/nf_core/pipelines/lint/actions_awsfulltest.py
@@ -41,7 +41,9 @@ def actions_awsfulltest(self):
 
         # Check that the action is only turned on for published releases
         try:
-            if wf[True]["release"]["types"] != ["published"]:
+            if wf[True]["pull_request"]["branches"] != ["master"]:
+                raise AssertionError()
+            if wf[True]["pull_request_review"]["types"] != ["submitted"]:
                 raise AssertionError()
             if "workflow_dispatch" not in wf[True]:
                 raise AssertionError()
diff --git a/tests/lint/actions_awsfulltest.py b/tests/lint/actions_awsfulltest.py
index caf7bbf366..d1479bb1e1 100644
--- a/tests/lint/actions_awsfulltest.py
+++ b/tests/lint/actions_awsfulltest.py
@@ -1,4 +1,4 @@
-import os
+from pathlib import Path
 
 import yaml
 
@@ -6,7 +6,7 @@
 
 
 def test_actions_awsfulltest_warn(self):
-    """Lint test: actions_awsfulltest - WARN"""
+    """Lint test: actions_awsfulltest - PASS"""
     self.lint_obj._load()
     results = self.lint_obj.actions_awsfulltest()
     assert "`.github/workflows/awsfulltest.yml` is triggered correctly" in results["passed"]
@@ -15,14 +15,14 @@ def test_actions_awsfulltest_warn(self):
 
 
 def test_actions_awsfulltest_pass(self):
-    """Lint test: actions_awsfulltest - PASS"""
+    """Lint test: actions_awsfulltest - WARN"""
 
     # Edit .github/workflows/awsfulltest.yml to use -profile test_full
     new_pipeline = self._make_pipeline_copy()
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
+    with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
         awsfulltest_yml = fh.read()
     awsfulltest_yml = awsfulltest_yml.replace("-profile test ", "-profile test_full ")
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
+    with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
         fh.write(awsfulltest_yml)
 
     # Make lint object
@@ -44,10 +44,10 @@ def test_actions_awsfulltest_fail(self):
 
     # Edit .github/workflows/awsfulltest.yml to use -profile test_full
     new_pipeline = self._make_pipeline_copy()
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
+    with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
         awsfulltest_yml = yaml.safe_load(fh)
-    del awsfulltest_yml[True]["release"]
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
+    del awsfulltest_yml[True]["pull_request_review"]
+    with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
         yaml.dump(awsfulltest_yml, fh)
 
     # Make lint object

From 48981f2dbfd8719a5adb6b5a7c529032ed6fdd7f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 9 Jul 2024 09:32:10 +0200
Subject: [PATCH 029/414] escape github variables in jinja template

---
 nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index f0d0724424..dc0450be43 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -20,12 +20,12 @@ jobs:
       - uses: octokit/request-action@v2.x
         id: check_approvals
         with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews
+          route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - id: test_variables
         run: |
-          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
+          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'{% endraw %}
           CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
           test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
       - name: Launch workflow via Seqera Platform

From fd71df4409cb3556f448f9ed04064a53c49375fc Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 9 Jul 2024 08:19:17 +0000
Subject: [PATCH 030/414] [automated] Fix code linting

---
 nf_core/__main__.py              | 4 +++-
 nf_core/commands_subworkflows.py | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 2be4697ffb..331f536834 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1601,7 +1601,9 @@ def command_subworkflows_update(
     """
     Update DSL2 subworkflow within a pipeline.
     """
-    subworkflows_update(ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save_diff, update_deps, limit_output)
+    subworkflows_update(
+        ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save_diff, update_deps, limit_output
+    )
 
 
 ## DEPRECATED commands since v3.0.0
diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py
index f220caf93c..a3abce3f85 100644
--- a/nf_core/commands_subworkflows.py
+++ b/nf_core/commands_subworkflows.py
@@ -251,7 +251,7 @@ def subworkflows_update(
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
-            limit_output
+            limit_output,
         )
         exit_status = subworkflow_install.update(subworkflow)
         if not exit_status and install_all:

From 0eaa72002e9c11679fcbbd43ea5c39b1679e2424 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 9 Jul 2024 10:54:23 +0200
Subject: [PATCH 031/414] update API docs with new pipeline command structure

---
 docs/api/_src/api/index.md                    | 15 ++--
 docs/api/_src/api/licences.md                 |  9 ---
 docs/api/_src/api/modules.md                  |  9 ---
 .../_src/api/{ => pipelines}/bump_version.md  |  2 +-
 docs/api/_src/api/{ => pipelines}/create.md   |  2 +-
 docs/api/_src/api/{ => pipelines}/download.md |  2 +-
 docs/api/_src/api/pipelines/index.md          |  8 ++
 docs/api/_src/api/{ => pipelines}/launch.md   |  2 +-
 docs/api/_src/api/{ => pipelines}/lint.md     |  4 +-
 docs/api/_src/api/{ => pipelines}/list.md     |  2 +-
 .../_src/api/{ => pipelines}/params-file.md   |  2 +-
 docs/api/_src/api/{ => pipelines}/schema.md   |  2 +-
 docs/api/_src/api/{ => pipelines}/sync.md     |  2 +-
 docs/api/_src/api/{ => pipelines}/utils.md    |  2 +-
 docs/api/_src/api/subworkflows.md             |  9 ---
 docs/api/_src/index.md                        | 22 ++----
 docs/api/_src/module_lint_tests/index.md      | 17 ++--
 .../actions_awsfulltest.md                    |  2 +-
 .../pipeline_lint_tests/actions_awstest.md    |  2 +-
 .../_src/pipeline_lint_tests/actions_ci.md    |  2 +-
 .../actions_schema_validation.md              |  2 +-
 .../_src/pipeline_lint_tests/base_config.md   |  2 +-
 .../_src/pipeline_lint_tests/files_exist.md   |  2 +-
 .../pipeline_lint_tests/files_unchanged.md    |  2 +-
 docs/api/_src/pipeline_lint_tests/index.md    | 31 ++++++--
 .../_src/pipeline_lint_tests/merge_markers.md |  2 +-
 .../pipeline_lint_tests/modules_config.md     |  2 +-
 .../_src/pipeline_lint_tests/modules_json.md  |  4 +-
 .../pipeline_lint_tests/modules_structure.md  |  2 +-
 .../pipeline_lint_tests/multiqc_config.md     |  2 +-
 .../pipeline_lint_tests/nextflow_config.md    |  2 +-
 .../_src/pipeline_lint_tests/nfcore_yml.md    |  2 +-
 .../pipeline_name_conventions.md              |  2 +-
 .../pipeline_lint_tests/pipeline_todos.md     |  2 +-
 docs/api/_src/pipeline_lint_tests/readme.md   |  2 +-
 .../pipeline_lint_tests/schema_description.md |  2 +-
 .../_src/pipeline_lint_tests/schema_lint.md   |  2 +-
 .../_src/pipeline_lint_tests/schema_params.md |  2 +-
 .../_src/pipeline_lint_tests/system_exit.md   |  2 +-
 .../pipeline_lint_tests/template_strings.md   |  2 +-
 .../version_consistency.md                    |  2 +-
 docs/api/_src/subworkflow_lint_tests/index.md | 14 ++--
 docs/api/make_lint_md.py                      | 77 ++++++++++---------
 43 files changed, 139 insertions(+), 142 deletions(-)
 delete mode 100644 docs/api/_src/api/licences.md
 delete mode 100644 docs/api/_src/api/modules.md
 rename docs/api/_src/api/{ => pipelines}/bump_version.md (72%)
 rename docs/api/_src/api/{ => pipelines}/create.md (73%)
 rename docs/api/_src/api/{ => pipelines}/download.md (73%)
 create mode 100644 docs/api/_src/api/pipelines/index.md
 rename docs/api/_src/api/{ => pipelines}/launch.md (73%)
 rename docs/api/_src/api/{ => pipelines}/lint.md (64%)
 rename docs/api/_src/api/{ => pipelines}/list.md (74%)
 rename docs/api/_src/api/{ => pipelines}/params-file.md (72%)
 rename docs/api/_src/api/{ => pipelines}/schema.md (73%)
 rename docs/api/_src/api/{ => pipelines}/sync.md (74%)
 rename docs/api/_src/api/{ => pipelines}/utils.md (74%)
 delete mode 100644 docs/api/_src/api/subworkflows.md

diff --git a/docs/api/_src/api/index.md b/docs/api/_src/api/index.md
index a1863f7e39..035a896888 100644
--- a/docs/api/_src/api/index.md
+++ b/docs/api/_src/api/index.md
@@ -1,8 +1,11 @@
-# API Reference
+# nf-core/tools documentation
 
-```{toctree}
-:glob: true
-:maxdepth: 1
+This API documentation is for the [`nf-core/tools`](https://github.com/nf-core/tools) package.
 
-*
-```
+## Contents
+
+- [Pipeline commands](./pipeline_lint_tests/) (run by `nf-core pipelines lint`)
+- [Module commands](./module_lint_tests/) (run by `nf-core modules lint`)
+- [Subworkflow commands](./subworkflow_lint_tests/) (run by `nf-core subworkflows lint`)
+- [nf-core/tools Python package API reference](./api/)
+  - [nf-core/tools pipeline commands API referece](./api/pipelines/)
diff --git a/docs/api/_src/api/licences.md b/docs/api/_src/api/licences.md
deleted file mode 100644
index 95b5f9768b..0000000000
--- a/docs/api/_src/api/licences.md
+++ /dev/null
@@ -1,9 +0,0 @@
-# nf_core.licences
-
-```{eval-rst}
-.. automodule:: nf_core.licences
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :private-members:
-```
diff --git a/docs/api/_src/api/modules.md b/docs/api/_src/api/modules.md
deleted file mode 100644
index e3f1e39bed..0000000000
--- a/docs/api/_src/api/modules.md
+++ /dev/null
@@ -1,9 +0,0 @@
-# nf_core.modules
-
-```{eval-rst}
-.. automodule:: nf_core.modules
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :private-members:
-```
diff --git a/docs/api/_src/api/bump_version.md b/docs/api/_src/api/pipelines/bump_version.md
similarity index 72%
rename from docs/api/_src/api/bump_version.md
rename to docs/api/_src/api/pipelines/bump_version.md
index 54c3774408..cd7dc280f6 100644
--- a/docs/api/_src/api/bump_version.md
+++ b/docs/api/_src/api/pipelines/bump_version.md
@@ -1,7 +1,7 @@
 # nf_core.bump_version
 
 ```{eval-rst}
-.. automodule:: nf_core.bump_version
+.. automodule:: nf_core.pipelines.bump_version
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/create.md b/docs/api/_src/api/pipelines/create.md
similarity index 73%
rename from docs/api/_src/api/create.md
rename to docs/api/_src/api/pipelines/create.md
index 5d5f6a62d1..576335e951 100644
--- a/docs/api/_src/api/create.md
+++ b/docs/api/_src/api/pipelines/create.md
@@ -1,7 +1,7 @@
 # nf_core.create
 
 ```{eval-rst}
-.. automodule:: nf_core.create
+.. automodule:: nf_core.pipelines.create
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/download.md b/docs/api/_src/api/pipelines/download.md
similarity index 73%
rename from docs/api/_src/api/download.md
rename to docs/api/_src/api/pipelines/download.md
index 18ab51376e..540fb92c49 100644
--- a/docs/api/_src/api/download.md
+++ b/docs/api/_src/api/pipelines/download.md
@@ -1,7 +1,7 @@
 # nf_core.download
 
 ```{eval-rst}
-.. automodule:: nf_core.download
+.. automodule:: nf_core.pipelines.download
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/pipelines/index.md b/docs/api/_src/api/pipelines/index.md
new file mode 100644
index 0000000000..a1863f7e39
--- /dev/null
+++ b/docs/api/_src/api/pipelines/index.md
@@ -0,0 +1,8 @@
+# API Reference
+
+```{toctree}
+:glob: true
+:maxdepth: 1
+
+*
+```
diff --git a/docs/api/_src/api/launch.md b/docs/api/_src/api/pipelines/launch.md
similarity index 73%
rename from docs/api/_src/api/launch.md
rename to docs/api/_src/api/pipelines/launch.md
index eef777ca87..0f7fc03f64 100644
--- a/docs/api/_src/api/launch.md
+++ b/docs/api/_src/api/pipelines/launch.md
@@ -1,7 +1,7 @@
 # nf_core.launch
 
 ```{eval-rst}
-.. automodule:: nf_core.launch
+.. automodule:: nf_core.pipelines.launch
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/lint.md b/docs/api/_src/api/pipelines/lint.md
similarity index 64%
rename from docs/api/_src/api/lint.md
rename to docs/api/_src/api/pipelines/lint.md
index 1380f7ec7b..aa62c404b8 100644
--- a/docs/api/_src/api/lint.md
+++ b/docs/api/_src/api/pipelines/lint.md
@@ -1,11 +1,11 @@
 # nf_core.lint
 
 :::{seealso}
-See the [Lint Tests](../pipeline_lint_tests/index.md) docs for information about specific linting functions.
+See the [Lint Tests](/docs/nf-core-tools/api_reference/dev/pipeline_lint_tests) docs for information about specific linting functions.
 :::
 
 ```{eval-rst}
-.. automodule:: nf_core.lint
+.. automodule:: nf_core.pipelines.lint
     :members: run_linting
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/list.md b/docs/api/_src/api/pipelines/list.md
similarity index 74%
rename from docs/api/_src/api/list.md
rename to docs/api/_src/api/pipelines/list.md
index 35c819bc56..7df7564544 100644
--- a/docs/api/_src/api/list.md
+++ b/docs/api/_src/api/pipelines/list.md
@@ -1,7 +1,7 @@
 # nf_core.list
 
 ```{eval-rst}
-.. automodule:: nf_core.list
+.. automodule:: nf_core.pipelines.list
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/params-file.md b/docs/api/_src/api/pipelines/params-file.md
similarity index 72%
rename from docs/api/_src/api/params-file.md
rename to docs/api/_src/api/pipelines/params-file.md
index c5bbfc0f1f..06f27cc592 100644
--- a/docs/api/_src/api/params-file.md
+++ b/docs/api/_src/api/pipelines/params-file.md
@@ -1,7 +1,7 @@
 # nf_core.params_file
 
 ```{eval-rst}
-.. automodule:: nf_core.params_file
+.. automodule:: nf_core.pipelines.params_file
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/schema.md b/docs/api/_src/api/pipelines/schema.md
similarity index 73%
rename from docs/api/_src/api/schema.md
rename to docs/api/_src/api/pipelines/schema.md
index a702d28058..c885d9ed23 100644
--- a/docs/api/_src/api/schema.md
+++ b/docs/api/_src/api/pipelines/schema.md
@@ -1,7 +1,7 @@
 # nf_core.schema
 
 ```{eval-rst}
-.. automodule:: nf_core.schema
+.. automodule:: nf_core.pipelines.schema
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/sync.md b/docs/api/_src/api/pipelines/sync.md
similarity index 74%
rename from docs/api/_src/api/sync.md
rename to docs/api/_src/api/pipelines/sync.md
index 8cc02209da..da1f468fe5 100644
--- a/docs/api/_src/api/sync.md
+++ b/docs/api/_src/api/pipelines/sync.md
@@ -1,7 +1,7 @@
 # nf_core.sync
 
 ```{eval-rst}
-.. automodule:: nf_core.sync
+.. automodule:: nf_core.pipelines.sync
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/utils.md b/docs/api/_src/api/pipelines/utils.md
similarity index 74%
rename from docs/api/_src/api/utils.md
rename to docs/api/_src/api/pipelines/utils.md
index 1353f97ef5..86b8c3f36f 100644
--- a/docs/api/_src/api/utils.md
+++ b/docs/api/_src/api/pipelines/utils.md
@@ -1,7 +1,7 @@
 # nf_core.utils
 
 ```{eval-rst}
-.. automodule:: nf_core.utils
+.. automodule:: nf_core.pipelines.utils
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/subworkflows.md b/docs/api/_src/api/subworkflows.md
deleted file mode 100644
index 438ccd0185..0000000000
--- a/docs/api/_src/api/subworkflows.md
+++ /dev/null
@@ -1,9 +0,0 @@
-# nf_core.subworkflows
-
-```{eval-rst}
-.. automodule:: nf_core.subworkflows
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :private-members:
-```
diff --git a/docs/api/_src/index.md b/docs/api/_src/index.md
index 037ca95475..d81a0e90d4 100644
--- a/docs/api/_src/index.md
+++ b/docs/api/_src/index.md
@@ -1,22 +1,10 @@
 # nf-core/tools documentation
 
-```{toctree}
-:caption: 'Contents:'
-:glob: true
-:hidden: true
-:maxdepth: 2
-
-pipeline_lint_tests/index.rst
-module_lint_tests/index.rst
-subworkflow_lint_tests/index.rst
-api/index.rst
-```
-
-This documentation is for the `nf-core/tools` package.
+This API documentation is for the [`nf-core/tools`](https://github.com/nf-core/tools) package.
 
 ## Contents
 
-- [Pipeline code lint tests](pipeline_lint_tests/index.md) (run by `nf-core pipelines lint`)
-- [Module code lint tests](module_lint_tests/index.md) (run by `nf-core modules lint`)
-- [Subworkflow code lint tests](subworkflow_lint_tests/index.md) (run by `nf-core subworkflows lint`)
-- [nf-core/tools Python package API reference](api/index.md)
+- [Pipeline code lint tests](./pipeline_lint_tests/) (run by `nf-core pipelines lint`)
+- [Module code lint tests](./module_lint_tests/) (run by `nf-core modules lint`)
+- [Subworkflow code lint tests](./subworkflow_lint_tests/) (run by `nf-core subworkflows lint`)
+- [nf-core/tools Python package API reference](./api/)
diff --git a/docs/api/_src/module_lint_tests/index.md b/docs/api/_src/module_lint_tests/index.md
index dee84d06d8..7039ba2598 100644
--- a/docs/api/_src/module_lint_tests/index.md
+++ b/docs/api/_src/module_lint_tests/index.md
@@ -1,8 +1,11 @@
-# Module lint tests
+# Module Lint Tests
 
-```{toctree}
-:glob: true
-:maxdepth: 1
-
-*
-```
+    - [environment_yml](./environment_yml/)
+    - [main_nf](./main_nf/)
+    - [meta_yml](./meta_yml/)
+    - [module_changes](./module_changes/)
+    - [module_deprecations](./module_deprecations/)
+    - [module_patch](./module_patch/)
+    - [module_tests](./module_tests/)
+    - [module_todos](./module_todos/)
+    - [module_version](./module_version/)
diff --git a/docs/api/_src/pipeline_lint_tests/actions_awsfulltest.md b/docs/api/_src/pipeline_lint_tests/actions_awsfulltest.md
index c0f0aef5a4..4bb47569ac 100644
--- a/docs/api/_src/pipeline_lint_tests/actions_awsfulltest.md
+++ b/docs/api/_src/pipeline_lint_tests/actions_awsfulltest.md
@@ -1,5 +1,5 @@
 # actions_awsfulltest
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.actions_awsfulltest
+.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_awsfulltest
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/actions_awstest.md b/docs/api/_src/pipeline_lint_tests/actions_awstest.md
index 42441c8ac5..b250571a04 100644
--- a/docs/api/_src/pipeline_lint_tests/actions_awstest.md
+++ b/docs/api/_src/pipeline_lint_tests/actions_awstest.md
@@ -1,5 +1,5 @@
 # actions_awstest
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.actions_awstest
+.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_awstest
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/actions_ci.md b/docs/api/_src/pipeline_lint_tests/actions_ci.md
index 78ea3aea0d..68cbc089ad 100644
--- a/docs/api/_src/pipeline_lint_tests/actions_ci.md
+++ b/docs/api/_src/pipeline_lint_tests/actions_ci.md
@@ -1,5 +1,5 @@
 # actions_ci
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.actions_ci
+.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_ci
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/actions_schema_validation.md b/docs/api/_src/pipeline_lint_tests/actions_schema_validation.md
index f0c98eb213..860acb2d2e 100644
--- a/docs/api/_src/pipeline_lint_tests/actions_schema_validation.md
+++ b/docs/api/_src/pipeline_lint_tests/actions_schema_validation.md
@@ -1,5 +1,5 @@
 # actions_schema_validation
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.actions_schema_validation
+.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_schema_validation
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/base_config.md b/docs/api/_src/pipeline_lint_tests/base_config.md
index 4a56ef9789..803627ced0 100644
--- a/docs/api/_src/pipeline_lint_tests/base_config.md
+++ b/docs/api/_src/pipeline_lint_tests/base_config.md
@@ -1,5 +1,5 @@
 # base_config
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.base_config
+.. automethod:: nf_core.pipelines.lint.PipelineLint.base_config
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/files_exist.md b/docs/api/_src/pipeline_lint_tests/files_exist.md
index 309ea62f0b..69890d1690 100644
--- a/docs/api/_src/pipeline_lint_tests/files_exist.md
+++ b/docs/api/_src/pipeline_lint_tests/files_exist.md
@@ -1,5 +1,5 @@
 # files_exist
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.files_exist
+.. automethod:: nf_core.pipelines.lint.PipelineLint.files_exist
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/files_unchanged.md b/docs/api/_src/pipeline_lint_tests/files_unchanged.md
index 2f3b04fe1b..3f626e5b8d 100644
--- a/docs/api/_src/pipeline_lint_tests/files_unchanged.md
+++ b/docs/api/_src/pipeline_lint_tests/files_unchanged.md
@@ -1,5 +1,5 @@
 # files_unchanged
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.files_unchanged
+.. automethod:: nf_core.pipelines.lint.PipelineLint.files_unchanged
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/index.md b/docs/api/_src/pipeline_lint_tests/index.md
index c631610d64..3575c08db4 100644
--- a/docs/api/_src/pipeline_lint_tests/index.md
+++ b/docs/api/_src/pipeline_lint_tests/index.md
@@ -1,8 +1,25 @@
-# Pipeline lint tests
+# Pipeline Lint Tests
 
-```{toctree}
-:glob: true
-:maxdepth: 1
-
-*
-```
+    - [actions_awsfulltest](./actions_awsfulltest/)
+    - [actions_awstest](./actions_awstest/)
+    - [actions_ci](./actions_ci/)
+    - [actions_schema_validation](./actions_schema_validation/)
+    - [base_config](./base_config/)
+    - [files_exist](./files_exist/)
+    - [files_unchanged](./files_unchanged/)
+    - [merge_markers](./merge_markers/)
+    - [modules_config](./modules_config/)
+    - [modules_json](./modules_json/)
+    - [modules_structure](./modules_structure/)
+    - [multiqc_config](./multiqc_config/)
+    - [nextflow_config](./nextflow_config/)
+    - [nfcore_yml](./nfcore_yml/)
+    - [pipeline_name_conventions](./pipeline_name_conventions/)
+    - [pipeline_todos](./pipeline_todos/)
+    - [readme](./readme/)
+    - [schema_description](./schema_description/)
+    - [schema_lint](./schema_lint/)
+    - [schema_params](./schema_params/)
+    - [system_exit](./system_exit/)
+    - [template_strings](./template_strings/)
+    - [version_consistency](./version_consistency/)
diff --git a/docs/api/_src/pipeline_lint_tests/merge_markers.md b/docs/api/_src/pipeline_lint_tests/merge_markers.md
index b52fdba1a8..7b620b4af1 100644
--- a/docs/api/_src/pipeline_lint_tests/merge_markers.md
+++ b/docs/api/_src/pipeline_lint_tests/merge_markers.md
@@ -1,5 +1,5 @@
 # merge_markers
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.merge_markers
+.. automethod:: nf_core.pipelines.lint.PipelineLint.merge_markers
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/modules_config.md b/docs/api/_src/pipeline_lint_tests/modules_config.md
index 2a4f51c5a4..c8eac0cf9d 100644
--- a/docs/api/_src/pipeline_lint_tests/modules_config.md
+++ b/docs/api/_src/pipeline_lint_tests/modules_config.md
@@ -1,5 +1,5 @@
 # modules_config
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.modules_config
+.. automethod:: nf_core.pipelines.lint.PipelineLint.modules_config
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/modules_json.md b/docs/api/_src/pipeline_lint_tests/modules_json.md
index 0c0ba71a8f..3070f83f57 100644
--- a/docs/api/_src/pipeline_lint_tests/modules_json.md
+++ b/docs/api/_src/pipeline_lint_tests/modules_json.md
@@ -1,5 +1,5 @@
-# nextflow_config
+# modules_json
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.modules_json
+.. automethod:: nf_core.pipelines.lint.PipelineLint.modules_json
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/modules_structure.md b/docs/api/_src/pipeline_lint_tests/modules_structure.md
index faa39ca77f..8a83918857 100644
--- a/docs/api/_src/pipeline_lint_tests/modules_structure.md
+++ b/docs/api/_src/pipeline_lint_tests/modules_structure.md
@@ -1,5 +1,5 @@
 # modules_structure
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.modules_structure
+.. automethod:: nf_core.pipelines.lint.PipelineLint.modules_structure
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/multiqc_config.md b/docs/api/_src/pipeline_lint_tests/multiqc_config.md
index 311f6b3049..281957749a 100644
--- a/docs/api/_src/pipeline_lint_tests/multiqc_config.md
+++ b/docs/api/_src/pipeline_lint_tests/multiqc_config.md
@@ -1,5 +1,5 @@
 # multiqc_config
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.multiqc_config
+.. automethod:: nf_core.pipelines.lint.PipelineLint.multiqc_config
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/nextflow_config.md b/docs/api/_src/pipeline_lint_tests/nextflow_config.md
index e23e966143..98e8df2574 100644
--- a/docs/api/_src/pipeline_lint_tests/nextflow_config.md
+++ b/docs/api/_src/pipeline_lint_tests/nextflow_config.md
@@ -1,5 +1,5 @@
 # nextflow_config
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.nextflow_config
+.. automethod:: nf_core.pipelines.lint.PipelineLint.nextflow_config
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/nfcore_yml.md b/docs/api/_src/pipeline_lint_tests/nfcore_yml.md
index f7e797a29c..226eb4c948 100644
--- a/docs/api/_src/pipeline_lint_tests/nfcore_yml.md
+++ b/docs/api/_src/pipeline_lint_tests/nfcore_yml.md
@@ -1,5 +1,5 @@
 # nfcore_yml
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.nfcore_yml
+.. automethod:: nf_core.pipelines.lint.PipelineLint.nfcore_yml
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/pipeline_name_conventions.md b/docs/api/_src/pipeline_lint_tests/pipeline_name_conventions.md
index 0034319d3d..09396b6afd 100644
--- a/docs/api/_src/pipeline_lint_tests/pipeline_name_conventions.md
+++ b/docs/api/_src/pipeline_lint_tests/pipeline_name_conventions.md
@@ -1,5 +1,5 @@
 # pipeline_name_conventions
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.pipeline_name_conventions
+.. automethod:: nf_core.pipelines.lint.PipelineLint.pipeline_name_conventions
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/pipeline_todos.md b/docs/api/_src/pipeline_lint_tests/pipeline_todos.md
index 08e456ea22..8292075b91 100644
--- a/docs/api/_src/pipeline_lint_tests/pipeline_todos.md
+++ b/docs/api/_src/pipeline_lint_tests/pipeline_todos.md
@@ -1,5 +1,5 @@
 # pipeline_todos
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.pipeline_todos
+.. automethod:: nf_core.pipelines.lint.PipelineLint.pipeline_todos
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/readme.md b/docs/api/_src/pipeline_lint_tests/readme.md
index 9583a56e0a..bf947bb61e 100644
--- a/docs/api/_src/pipeline_lint_tests/readme.md
+++ b/docs/api/_src/pipeline_lint_tests/readme.md
@@ -1,5 +1,5 @@
 # readme
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.readme
+.. automethod:: nf_core.pipelines.lint.PipelineLint.readme
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/schema_description.md b/docs/api/_src/pipeline_lint_tests/schema_description.md
index 14f756acd2..0429b3cc10 100644
--- a/docs/api/_src/pipeline_lint_tests/schema_description.md
+++ b/docs/api/_src/pipeline_lint_tests/schema_description.md
@@ -1,5 +1,5 @@
 # schema_description
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.schema_description
+.. automethod:: nf_core.pipelines.lint.PipelineLint.schema_description
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/schema_lint.md b/docs/api/_src/pipeline_lint_tests/schema_lint.md
index 39be2ea65c..95bd5cc2fc 100644
--- a/docs/api/_src/pipeline_lint_tests/schema_lint.md
+++ b/docs/api/_src/pipeline_lint_tests/schema_lint.md
@@ -1,5 +1,5 @@
 # schema_lint
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.schema_lint
+.. automethod:: nf_core.pipelines.lint.PipelineLint.schema_lint
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/schema_params.md b/docs/api/_src/pipeline_lint_tests/schema_params.md
index 80a626e880..8c6594c57b 100644
--- a/docs/api/_src/pipeline_lint_tests/schema_params.md
+++ b/docs/api/_src/pipeline_lint_tests/schema_params.md
@@ -1,5 +1,5 @@
 # schema_params
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.schema_params
+.. automethod:: nf_core.pipelines.lint.PipelineLint.schema_params
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/system_exit.md b/docs/api/_src/pipeline_lint_tests/system_exit.md
index 3d0ac20f8d..9ba67d4d2f 100644
--- a/docs/api/_src/pipeline_lint_tests/system_exit.md
+++ b/docs/api/_src/pipeline_lint_tests/system_exit.md
@@ -1,5 +1,5 @@
 # system_exit
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.system_exit
+.. automethod:: nf_core.pipelines.lint.PipelineLint.system_exit
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/template_strings.md b/docs/api/_src/pipeline_lint_tests/template_strings.md
index 3d03bfb256..ee334a2a21 100644
--- a/docs/api/_src/pipeline_lint_tests/template_strings.md
+++ b/docs/api/_src/pipeline_lint_tests/template_strings.md
@@ -1,5 +1,5 @@
 # template_strings
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.template_strings
+.. automethod:: nf_core.pipelines.lint.PipelineLint.template_strings
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/version_consistency.md b/docs/api/_src/pipeline_lint_tests/version_consistency.md
index e8038f8531..868a348704 100644
--- a/docs/api/_src/pipeline_lint_tests/version_consistency.md
+++ b/docs/api/_src/pipeline_lint_tests/version_consistency.md
@@ -1,5 +1,5 @@
 # version_consistency
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.version_consistency
+.. automethod:: nf_core.pipelines.lint.PipelineLint.version_consistency
 ```
diff --git a/docs/api/_src/subworkflow_lint_tests/index.md b/docs/api/_src/subworkflow_lint_tests/index.md
index 0ecf590c0d..da8db49a7b 100644
--- a/docs/api/_src/subworkflow_lint_tests/index.md
+++ b/docs/api/_src/subworkflow_lint_tests/index.md
@@ -1,8 +1,8 @@
-# Subworkflow lint tests
+# Subworkflow Lint Tests
 
-```{toctree}
-:glob: true
-:maxdepth: 1
-
-*
-```
+    - [main_nf](./main_nf/)
+    - [meta_yml](./meta_yml/)
+    - [subworkflow_changes](./subworkflow_changes/)
+    - [subworkflow_tests](./subworkflow_tests/)
+    - [subworkflow_todos](./subworkflow_todos/)
+    - [subworkflow_version](./subworkflow_version/)
diff --git a/docs/api/make_lint_md.py b/docs/api/make_lint_md.py
index 48393094b3..7b823a086e 100644
--- a/docs/api/make_lint_md.py
+++ b/docs/api/make_lint_md.py
@@ -1,53 +1,58 @@
-#!/usr/bin/env python
-
-import fnmatch
-import os
+from pathlib import Path
 
+#!/usr/bin/env python
+import nf_core.commands_pipelines
 import nf_core.modules.lint
 import nf_core.pipelines.lint
 import nf_core.subworkflows.lint
 
 
-def make_docs(docs_basedir, lint_tests, md_template):
-    # Get list of existing .md files
-    existing_docs = []
-    for fn in os.listdir(docs_basedir):
-        if fnmatch.fnmatch(fn, "*.md") and not fnmatch.fnmatch(fn, "index.md"):
-            existing_docs.append(os.path.join(docs_basedir, fn))
+def create_docs(docs_basedir, lint_tests, md_template):
+    docs_basedir.mkdir(parents=True, exist_ok=True)
+    existing_docs = list(docs_basedir.glob("*.md"))
+    existing_docs.remove(docs_basedir / "index.md")
 
     for test_name in lint_tests:
-        fn = os.path.join(docs_basedir, f"{test_name}.md")
-        if os.path.exists(fn):
+        fn = docs_basedir / f"{test_name}.md"
+        if fn.exists():
             existing_docs.remove(fn)
         else:
             with open(fn, "w") as fh:
                 fh.write(md_template.format(test_name))
 
     for fn in existing_docs:
-        os.remove(fn)
+        fn.unlink()
+
+
+def create_index_file(basedir, title):
+    index_file = basedir / "index.md"
+    with open(index_file, "w") as fh:
+        fh.write(f"# {title}\n\n")
+        for fn in sorted(basedir.glob("*.md")):
+            if fn.name != "index.md":
+                fh.write(f"    - [{fn.stem}](./{fn.stem}/)\n")
 
 
 # Create the pipeline docs
-pipeline_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "pipeline_lint_tests")
-make_docs(
-    pipeline_docs_basedir,
+pipeline_lint_docs_basedir = Path(__file__).resolve().parent / "_src" / "pipeline_lint_tests"
+create_docs(
+    pipeline_lint_docs_basedir,
     nf_core.pipelines.lint.PipelineLint._get_all_lint_tests(True),
     """# {0}
 
-```{{eval-rst}}
-.. automethod:: nf_core.pipelines.lint.PipelineLint.{0}
-```
-""",
+    ```{{eval-rst}}
+    .. automethod:: nf_core.pipelines.lint.PipelineLint.{0}
+    ```
+    """,
 )
+create_index_file(pipeline_lint_docs_basedir, "Pipeline Lint Tests")
 
-# Create the modules lint docs
-modules_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "module_lint_tests")
-make_docs(
-    modules_docs_basedir,
-    list(
-        set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)).union(
-            nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=False)
-        )
+# Create the modules docs
+modules_lint_docs_basedir = Path(__file__).resolve().parent / "_src" / "module_lint_tests"
+create_docs(
+    modules_lint_docs_basedir,
+    set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)).union(
+        nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=False)
     ),
     """# {0}
 
@@ -56,15 +61,14 @@ def make_docs(docs_basedir, lint_tests, md_template):
 ```
 """,
 )
+create_index_file(modules_lint_docs_basedir, "Module Lint Tests")
 
-# Create the subworkflows lint docs
-subworkflows_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "subworkflow_lint_tests")
-make_docs(
-    subworkflows_docs_basedir,
-    list(
-        set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True)).union(
-            nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=False)
-        )
+# Create the subworkflow docs
+subworkflow_lint_docs_basedir = Path(__file__).resolve().parent / "_src" / "subworkflow_lint_tests"
+create_docs(
+    subworkflow_lint_docs_basedir,
+    set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True)).union(
+        nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=False)
     ),
     """# {0}
 
@@ -73,3 +77,4 @@ def make_docs(docs_basedir, lint_tests, md_template):
 ```
 """,
 )
+create_index_file(subworkflow_lint_docs_basedir, "Subworkflow Lint Tests")

From e8e2e49d5ab69671d9bcbad4dbe3ddf5733fc09b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 9 Jul 2024 10:55:26 +0200
Subject: [PATCH 032/414] remove unused assets

---
 docs/api/_src/_static/css/custom.css   | 437 -------------------------
 docs/api/_src/_static/js/custom.js     |   0
 docs/api/_src/_static/nf-core-logo.png | Bin 84414 -> 0 bytes
 docs/api/_src/_templates/layout.html   |   4 -
 4 files changed, 441 deletions(-)
 delete mode 100644 docs/api/_src/_static/css/custom.css
 delete mode 100644 docs/api/_src/_static/js/custom.js
 delete mode 100644 docs/api/_src/_static/nf-core-logo.png
 delete mode 100644 docs/api/_src/_templates/layout.html

diff --git a/docs/api/_src/_static/css/custom.css b/docs/api/_src/_static/css/custom.css
deleted file mode 100644
index e892dd9998..0000000000
--- a/docs/api/_src/_static/css/custom.css
+++ /dev/null
@@ -1,437 +0,0 @@
-@media (prefers-color-scheme: light) {
-  a,
-  a:visited {
-    color: #246eb9;
-  }
-  a:hover,
-  a:focus,
-  a:active {
-    color: #c03221;
-  }
-  .wy-nav-side {
-    background-color: #ededed;
-  }
-  .wy-nav-top,
-  .wy-side-nav-search,
-  .wy-menu-vertical a:active {
-    background-color: #32ad65;
-  }
-  .wy-menu-vertical a {
-    color: #343434;
-  }
-  .wy-menu-vertical a:hover {
-    background-color: #abacab85;
-  }
-  .wy-menu-vertical header,
-  .wy-menu-vertical p.caption {
-    color: #32ad65;
-  }
-
-  .wy-side-nav-search input[type="text"] {
-    border: none;
-  }
-
-  code,
-  .rst-content code.literal {
-    background-color: rgba(220, 220, 220, 0.4);
-    color: #c03221;
-    border: none;
-  }
-  .rst-content .note .admonition-title {
-    background-color: #72757bfc;
-  }
-
-  html.writer-html4 .rst-content dl:not(.docutils) > dt,
-  html.writer-html5
-    .rst-content
-    dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple)
-    > dt {
-    background-color: #32ad65;
-    border: none;
-  }
-  .rst-content .method > dt > code {
-    color: #f5f6f7;
-  }
-  .rst-content div[class^="highlight"],
-  .rst-content pre.literal-block {
-    border: none;
-  }
-  .highlight {
-    background-color: #242424;
-    color: #e5e6e7;
-  }
-  .highlight .hll {
-    color: #e5e6e7;
-    background-color: #585b60fc;
-  }
-  .highlight .k,
-  .highlight .nt,
-  .highlight .no {
-    color: #246eb9;
-  }
-  .highlight .s,
-  .highlight .s1,
-  .highlight .s2,
-  .highlight .na {
-    color: #32ad65;
-  }
-  .highlight .nb,
-  .highlight .o,
-  .highlight .cm {
-    color: #ffbe0b;
-  }
-  .highlight .c1 {
-    color: #88898afc;
-  }
-  .highlight .nv,
-  .py > span {
-    color: #c03221;
-  }
-  .py .sig-param,
-  .py .sig-paren,
-  .property .pre {
-    color: #eef0f2;
-  }
-
-  .method > .py .sig-param,
-  .method > .py .sig-paren {
-    color: #32ad65;
-  }
-  .btn.btn-neutral {
-    background-color: #e5e6e7d4 !important;
-  }
-  .rst-content .hint .admonition-title,
-  .rst-content .hint .wy-alert-title,
-  .rst-content .important .admonition-title,
-  .rst-content .important .wy-alert-title,
-  .rst-content .tip .admonition-title,
-  .rst-content .tip .wy-alert-title,
-  .rst-content .wy-alert-success.admonition-todo .admonition-title,
-  .rst-content .wy-alert-success.admonition-todo .wy-alert-title,
-  .rst-content .wy-alert-success.admonition .admonition-title,
-  .rst-content .wy-alert-success.admonition .wy-alert-title,
-  .rst-content .wy-alert-success.attention .admonition-title,
-  .rst-content .wy-alert-success.attention .wy-alert-title,
-  .rst-content .wy-alert-success.caution .admonition-title,
-  .rst-content .wy-alert-success.caution .wy-alert-title,
-  .rst-content .wy-alert-success.danger .admonition-title,
-  .rst-content .wy-alert-success.danger .wy-alert-title,
-  .rst-content .wy-alert-success.error .admonition-title,
-  .rst-content .wy-alert-success.error .wy-alert-title,
-  .rst-content .wy-alert-success.note .admonition-title,
-  .rst-content .wy-alert-success.note .wy-alert-title,
-  .rst-content .wy-alert-success.seealso .admonition-title,
-  .rst-content .wy-alert-success.seealso .wy-alert-title,
-  .rst-content .wy-alert-success.warning .admonition-title,
-  .rst-content .wy-alert-success.warning .wy-alert-title,
-  .rst-content .wy-alert.wy-alert-success .admonition-title,
-  .wy-alert.wy-alert-success .rst-content .admonition-title,
-  .wy-alert.wy-alert-success .wy-alert-title {
-    background-color: #32ad65;
-    color: #e5e6e7;
-  }
-
-  .rst-content .note,
-  .rst-content .seealso,
-  .rst-content .wy-alert-info.admonition,
-  .rst-content .wy-alert-info.admonition-todo,
-  .rst-content .wy-alert-info.attention,
-  .rst-content .wy-alert-info.caution,
-  .rst-content .wy-alert-info.danger,
-  .rst-content .wy-alert-info.error,
-  .rst-content .wy-alert-info.hint,
-  .rst-content .wy-alert-info.important,
-  .rst-content .wy-alert-info.tip,
-  .rst-content .wy-alert-info.warning,
-  .wy-alert.wy-alert-info,
-  .rst-content .hint,
-  .rst-content .important,
-  .rst-content .tip,
-  .rst-content .wy-alert-success.admonition,
-  .rst-content .wy-alert-success.admonition-todo,
-  .rst-content .wy-alert-success.attention,
-  .rst-content .wy-alert-success.caution,
-  .rst-content .wy-alert-success.danger,
-  .rst-content .wy-alert-success.error,
-  .rst-content .wy-alert-success.note,
-  .rst-content .wy-alert-success.seealso,
-  .rst-content .wy-alert-success.warning,
-  .wy-alert.wy-alert-success {
-    color: #343434;
-    background-color: #e3e3e3;
-    border: none;
-  }
-
-  .rst-content .admonition-todo .admonition-title,
-  .rst-content .admonition-todo .wy-alert-title,
-  .rst-content .attention .admonition-title,
-  .rst-content .attention .wy-alert-title,
-  .rst-content .caution .admonition-title,
-  .rst-content .caution .wy-alert-title,
-  .rst-content .warning .admonition-title,
-  .rst-content .warning .wy-alert-title,
-  .rst-content .wy-alert-warning.admonition .admonition-title,
-  .rst-content .wy-alert-warning.admonition .wy-alert-title,
-  .rst-content .wy-alert-warning.danger .admonition-title,
-  .rst-content .wy-alert-warning.danger .wy-alert-title,
-  .rst-content .wy-alert-warning.error .admonition-title,
-  .rst-content .wy-alert-warning.error .wy-alert-title,
-  .rst-content .wy-alert-warning.hint .admonition-title,
-  .rst-content .wy-alert-warning.hint .wy-alert-title,
-  .rst-content .seealso .admonition-title,
-  .rst-content .seealso .wy-alert-title,
-  .rst-content .wy-alert-warning.important .admonition-title,
-  .rst-content .wy-alert-warning.important .wy-alert-title,
-  .rst-content .wy-alert-warning.note .admonition-title,
-  .rst-content .wy-alert-warning.note .wy-alert-title,
-  .rst-content .wy-alert-warning.seealso .admonition-title,
-  .rst-content .wy-alert-warning.seealso .wy-alert-title,
-  .rst-content .wy-alert-warning.tip .admonition-title,
-  .rst-content .wy-alert-warning.tip .wy-alert-title,
-  .rst-content .wy-alert.wy-alert-warning .admonition-title,
-  .wy-alert.wy-alert-warning .rst-content .admonition-title,
-  .wy-alert.wy-alert-warning .wy-alert-title {
-    background-color: #246eb9;
-  }
-  .rst-content .admonition-todo,
-  .rst-content .attention,
-  .rst-content .caution,
-  .rst-content .warning,
-  .rst-content .wy-alert-warning.admonition,
-  .rst-content .wy-alert-warning.danger,
-  .rst-content .wy-alert-warning.error,
-  .rst-content .wy-alert-warning.hint,
-  .rst-content .wy-alert-warning.important,
-  .rst-content .wy-alert-warning.note,
-  .rst-content .wy-alert-warning.seealso,
-  .rst-content .wy-alert-warning.tip,
-  .wy-alert.wy-alert-warning {
-    color: #343434;
-    background-color: #e3e3e3;
-  }
-}
-@media (prefers-color-scheme: dark) {
-  .wy-nav-content-wrap {
-    background-color: #181a1b;
-  }
-  .wy-nav-top,
-  .wy-side-nav-search,
-  .wy-menu-vertical a:active {
-    background-color: #32ad65;
-  }
-  .wy-menu-vertical header,
-  .wy-menu-vertical p.caption {
-    color: #32ad65;
-  }
-  .wy-nav-side {
-    background-color: #2e2e2e;
-  }
-  .wy-nav-content {
-    background-color: #343434;
-    color: #e5e6e7;
-  }
-  a,
-  a:visited {
-    color: #6fb2e8;
-  }
-  a:hover,
-  a:focus,
-  a:active {
-    color: #db9444;
-  }
-  code,
-  .rst-content code.literal {
-    background-color: rgba(220, 220, 220, 0.1);
-    color: #db9444;
-    border: none;
-  }
-  .wy-side-nav-search input[type="text"] {
-    border: none;
-    background-color: #e5e6e7;
-  }
-  .wy-side-nav-search > div.version {
-    color: #e5e6e7c9;
-  }
-  .wy-side-nav-search .wy-dropdown > a,
-  .wy-side-nav-search > a {
-    color: #e5e6e7;
-  }
-
-  html.writer-html4 .rst-content dl:not(.docutils) > dt,
-  html.writer-html5
-    .rst-content
-    dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple)
-    > dt {
-    background-color: #32ad65;
-    border: none;
-  }
-  html.writer-html4 .rst-content dl:not(.docutils) dl:not(.field-list) > dt,
-  html.writer-html5
-    .rst-content
-    dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple)
-    dl:not(.field-list)
-    > dt {
-    background-color: #777;
-    color: #e5e6e7a6;
-  }
-  .rst-content code {
-    color: #e5e6e7d4;
-  }
-  .rst-content .method > dt > code {
-    color: #e5e6e7;
-  }
-  .sig-paren {
-    color: #db9444;
-  }
-  .rst-content .note .admonition-title {
-    background-color: #72757bfc;
-  }
-  .rst-content div[class^="highlight"],
-  .rst-content pre.literal-block {
-    border: none;
-  }
-
-  .highlight {
-    background-color: #242424;
-    color: #e5e6e7;
-  }
-  .highlight .hll {
-    color: #e5e6e7;
-    background-color: #585b60fc;
-  }
-  .highlight .k,
-  .highlight .nt,
-  .highlight .no {
-    color: #6fb2e8;
-  }
-  .highlight .s,
-  .highlight .s1,
-  .highlight .s2,
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-    color: #32ad65;
-  }
-  .highlight .nb,
-  .highlight .o,
-  .highlight .cm {
-    color: #db9444;
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-  .highlight .c1 {
-    color: #88898afc;
-  }
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-    color: #f9d977;
-  }
-  .btn.btn-neutral {
-    background-color: #e5e6e7d4 !important;
-  }
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-  .rst-content .important .wy-alert-title,
-  .rst-content .tip .admonition-title,
-  .rst-content .tip .wy-alert-title,
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-  .rst-content .wy-alert-success.admonition .wy-alert-title,
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-  .rst-content .wy-alert-success.attention .wy-alert-title,
-  .rst-content .wy-alert-success.caution .admonition-title,
-  .rst-content .wy-alert-success.caution .wy-alert-title,
-  .rst-content .wy-alert-success.danger .admonition-title,
-  .rst-content .wy-alert-success.danger .wy-alert-title,
-  .rst-content .wy-alert-success.error .admonition-title,
-  .rst-content .wy-alert-success.error .wy-alert-title,
-  .rst-content .wy-alert-success.note .admonition-title,
-  .rst-content .wy-alert-success.note .wy-alert-title,
-  .rst-content .wy-alert-success.seealso .admonition-title,
-  .rst-content .wy-alert-success.seealso .wy-alert-title,
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-  .rst-content .wy-alert-success.warning .wy-alert-title,
-  .rst-content .wy-alert.wy-alert-success .admonition-title,
-  .wy-alert.wy-alert-success .rst-content .admonition-title,
-  .wy-alert.wy-alert-success .wy-alert-title {
-    background-color: #32ad65;
-    color: #e5e6e7;
-  }
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-  .rst-content .note,
-  .rst-content .seealso,
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-  .rst-content .wy-alert-success.seealso,
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-  .wy-alert.wy-alert-success {
-    color: #343434;
-    background-color: #e3e3e3;
-    border: none;
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-
-  .rst-content .admonition-todo .admonition-title,
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-  .rst-content .wy-alert-warning.admonition .wy-alert-title,
-  .rst-content .wy-alert-warning.danger .admonition-title,
-  .rst-content .wy-alert-warning.danger .wy-alert-title,
-  .rst-content .wy-alert-warning.error .admonition-title,
-  .rst-content .wy-alert-warning.error .wy-alert-title,
-  .rst-content .wy-alert-warning.hint .admonition-title,
-  .rst-content .wy-alert-warning.hint .wy-alert-title,
-  .rst-content .seealso .admonition-title,
-  .rst-content .seealso .wy-alert-title,
-  .rst-content .wy-alert-warning.important .admonition-title,
-  .rst-content .wy-alert-warning.important .wy-alert-title,
-  .rst-content .wy-alert-warning.note .admonition-title,
-  .rst-content .wy-alert-warning.note .wy-alert-title,
-  .rst-content .wy-alert-warning.seealso .admonition-title,
-  .rst-content .wy-alert-warning.seealso .wy-alert-title,
-  .rst-content .wy-alert-warning.tip .admonition-title,
-  .rst-content .wy-alert-warning.tip .wy-alert-title,
-  .rst-content .wy-alert.wy-alert-warning .admonition-title,
-  .wy-alert.wy-alert-warning .rst-content .admonition-title,
-  .wy-alert.wy-alert-warning .wy-alert-title {
-    background-color: #f4a25b;
-  }
-  .rst-content .admonition-todo,
-  .rst-content .attention,
-  .rst-content .caution,
-  .rst-content .warning,
-  .rst-content .wy-alert-warning.admonition,
-  .rst-content .wy-alert-warning.danger,
-  .rst-content .wy-alert-warning.error,
-  .rst-content .wy-alert-warning.hint,
-  .rst-content .wy-alert-warning.important,
-  .rst-content .wy-alert-warning.note,
-  .rst-content .wy-alert-warning.seealso,
-  .rst-content .wy-alert-warning.tip,
-  .wy-alert.wy-alert-warning {
-    color: #343434;
-    background-color: #e3e3e3;
-  }
-}
diff --git a/docs/api/_src/_static/js/custom.js b/docs/api/_src/_static/js/custom.js
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/docs/api/_src/_static/nf-core-logo.png b/docs/api/_src/_static/nf-core-logo.png
deleted file mode 100644
index 91ddb58d8ada2682b8edb9528c09479f248e3010..0000000000000000000000000000000000000000
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zl2F9>5OsM|f{QB%{iH=L&YIMQ$psMok|u}{hF7>(L^KYi;R{?1si2m&eN!!tmd>Ho
z<`0aCn}*$nIDgUKM0KZK2(oU5c}4(U3dm8kG*#7@k#uL1NfEsRUuH_YKRKO^i-tiI
zAaERQ^j!VV7SBw{hQC_>h2<c9_jQE`!*j9!{uhI4|5Ab}KL1kUUrI13!2J8KO#Dj;
rCIy&(|CNb<DZ!)w^Y8z^Ow4!&*eV}g+g((Gj)gm}aV$jzf9L-J#AJD-

diff --git a/docs/api/_src/_templates/layout.html b/docs/api/_src/_templates/layout.html
deleted file mode 100644
index 42341a97c1..0000000000
--- a/docs/api/_src/_templates/layout.html
+++ /dev/null
@@ -1,4 +0,0 @@
-{% extends '!layout.html' %} {% block header %}
-<!-- your html code here -->
-<a href="https://nf-co.re"><img src="./_static/nf-core-logo.png" width="20%" /></a>
-{% endblock %}

From 3f36d108e2da67dd64ac8f25738d17853d9c7622 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 9 Jul 2024 11:14:45 +0200
Subject: [PATCH 033/414] handle mypy warnings

---
 tests/modules/update.py | 32 +++++++++++++++++++-------------
 1 file changed, 19 insertions(+), 13 deletions(-)

diff --git a/tests/modules/update.py b/tests/modules/update.py
index 0fddcc8ba8..b56fc0df1d 100644
--- a/tests/modules/update.py
+++ b/tests/modules/update.py
@@ -90,9 +90,9 @@ def test_install_at_hash_and_update_limit_output(self):
     )
 
     # Copy the module files and check that they are affected by the update
-    tmpdir = tempfile.mkdtemp()
-    trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore")
-    trimgalore_path = os.path.join(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
+    tmpdir = Path(tempfile.mkdtemp())
+    trimgalore_tmpdir = tmpdir / "trimgalore"
+    trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
     shutil.copytree(trimgalore_path, trimgalore_tmpdir)
 
     assert update_obj.update("trimgalore") is True
@@ -112,22 +112,28 @@ def test_install_at_hash_and_update_limit_output(self):
 
     # Check for various scenarios
     for line in log_lines:
-        if re.match(r"'.+' is unchanged", line):
-            # Unchanged files should be reported for both .nf and non-.nf files
-            assert True
-        elif re.match(r"'.+' was created", line):
-            # Created files should be reported for both .nf and non-.nf files
-            assert True
-        elif re.match(r"'.+' was removed", line):
-            # Removed files should be reported for both .nf and non-.nf files
+        if (
+            re.match(r"'.+' is unchanged", line)
+            or re.match(r"'.+' was created", line)
+            or re.match(r"'.+' was removed", line)
+        ):
+            # Unchanged, created, and removed files should be reported for both .nf and non-.nf files
             assert True
         elif re.match(r"Changes in '.+' but not shown", line):
             # Changes not shown should only be for non-.nf files
-            file_path = re.search(r"'(.+)'", line).group(1)
+            match = re.search(r"'(.+)'", line)
+            if match:
+                file_path = match.group(1)
+            else:
+                raise AssertionError("Changes not shown message did not contain a file path")
             assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}"
         elif re.match(r"Changes in '.+':$", line):
             # Changes shown should only be for .nf files
-            file_path = re.search(r"'(.+)'", line).group(1)
+            match = re.search(r"'(.+)'", line)
+            if match:
+                file_path = match.group(1)
+            else:
+                raise AssertionError("Changes shown message did not contain a file path")
             assert Path(file_path).suffix == ".nf", f"Changes in non-.nf file were shown: {line}"
 
     # Clean up

From 18eefb7b05e066f787a99bd74d5f845af0fb53d0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 9 Jul 2024 11:27:05 +0200
Subject: [PATCH 034/414] modernize code

---
 nf_core/modules/modules_json.py |  5 ++-
 tests/modules/update.py         | 67 ++++++++++++++++++---------------
 2 files changed, 40 insertions(+), 32 deletions(-)

diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index b0a4fa661f..42c633ed23 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -862,7 +862,7 @@ def module_present(self, module_name, repo_url, install_dir):
             install_dir, {}
         )
 
-    def get_modules_json(self):
+    def get_modules_json(self) -> dict:
         """
         Returns a copy of the loaded modules.json
 
@@ -871,7 +871,8 @@ def get_modules_json(self):
         """
         if self.modules_json is None:
             self.load()
-        return copy.deepcopy(self.modules_json)
+
+        return copy.deepcopy(self.modules_json)  # type: ignore
 
     def get_component_version(self, component_type, component_name, repo_url, install_dir):
         """
diff --git a/tests/modules/update.py b/tests/modules/update.py
index b56fc0df1d..72766779e3 100644
--- a/tests/modules/update.py
+++ b/tests/modules/update.py
@@ -1,7 +1,6 @@
 import filecmp
 import io
 import logging
-import os
 import re
 import shutil
 import tempfile
@@ -30,15 +29,21 @@
 )
 
 
+def cmp_module(dir1: Path, dir2: Path) -> bool:
+    """Compare two versions of the same module"""
+    files = ["main.nf", "meta.yml"]
+    return all(filecmp.cmp(dir1 / f, dir2 / f, shallow=False) for f in files)
+
+
 def test_install_and_update(self):
     """Installs a module in the pipeline and updates it (no change)"""
     self.mods_install.install("trimgalore")
     update_obj = ModuleUpdate(self.pipeline_dir, show_diff=False)
 
     # Copy the module files and check that they are unaffected by the update
-    tmpdir = tempfile.mkdtemp()
-    trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore")
-    trimgalore_path = os.path.join(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "trimgalore")
+    tmpdir = Path(tempfile.mkdtemp())
+    trimgalore_tmpdir = tmpdir / "trimgalore"
+    trimgalore_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "trimgalore")
     shutil.copytree(trimgalore_path, trimgalore_tmpdir)
 
     assert update_obj.update("trimgalore") is True
@@ -53,9 +58,9 @@ def test_install_at_hash_and_update(self):
     )
 
     # Copy the module files and check that they are affected by the update
-    tmpdir = tempfile.mkdtemp()
-    trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore")
-    trimgalore_path = os.path.join(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
+    tmpdir = Path(tempfile.mkdtemp())
+    trimgalore_tmpdir = tmpdir / "trimgalore"
+    trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
     shutil.copytree(trimgalore_path, trimgalore_tmpdir)
 
     assert update_obj.update("trimgalore") is True
@@ -144,7 +149,7 @@ def test_install_at_hash_and_update_limit_output(self):
 def test_install_at_hash_and_update_and_save_diff_to_file(self):
     """Installs an old version of a module in the pipeline and updates it"""
     self.mods_install_old.install("trimgalore")
-    patch_path = os.path.join(self.pipeline_dir, "trimgalore.patch")
+    patch_path = Path(self.pipeline_dir, "trimgalore.patch")
     update_obj = ModuleUpdate(
         self.pipeline_dir,
         save_diff_fn=patch_path,
@@ -154,9 +159,9 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self):
     )
 
     # Copy the module files and check that they are affected by the update
-    tmpdir = tempfile.mkdtemp()
-    trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore")
-    trimgalore_path = os.path.join(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
+    tmpdir = Path(tempfile.mkdtemp())
+    trimgalore_tmpdir = tmpdir / "trimgalore"
+    trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
     shutil.copytree(trimgalore_path, trimgalore_tmpdir)
 
     assert update_obj.update("trimgalore") is True
@@ -168,7 +173,7 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self):
 def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self):
     """Installs an old version of a module in the pipeline and updates it"""
     self.mods_install_old.install("trimgalore")
-    patch_path = os.path.join(self.pipeline_dir, "trimgalore.patch")
+    patch_path = Path(self.pipeline_dir, "trimgalore.patch")
     update_obj = ModuleUpdate(
         self.pipeline_dir,
         save_diff_fn=patch_path,
@@ -179,16 +184,16 @@ def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self):
     )
 
     # Copy the module files and check that they are affected by the update
-    tmpdir = tempfile.mkdtemp()
-    trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore")
-    trimgalore_path = os.path.join(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
+    tmpdir = Path(tempfile.mkdtemp())
+    trimgalore_tmpdir = tmpdir / "trimgalore"
+    trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
     shutil.copytree(trimgalore_path, trimgalore_tmpdir)
 
     assert update_obj.update("trimgalore") is True
     assert cmp_module(trimgalore_tmpdir, trimgalore_path) is True
 
     # Check that the patch file was created
-    assert os.path.exists(patch_path), f"Patch file was not created at {patch_path}"
+    assert patch_path.exists(), f"Patch file was not created at {patch_path}"
 
     # Read the contents of the patch file
     with open(patch_path) as f:
@@ -202,11 +207,19 @@ def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self):
             assert True
         elif re.match(r"Changes in '.+' but not shown", line):
             # Changes not shown should only be for non-.nf files
-            file_path = re.search(r"'(.+)'", line).group(1)
+            match = re.search(r"'(.+)'", line)
+            if match:
+                file_path = match.group(1)
+            else:
+                raise AssertionError("Changes not shown message did not contain a file path.")
             assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}"
         elif re.match("diff --git", line):
             # Diff should only be shown for .nf files
-            file_path = re.search(r"b/(.+)$", line).group(1)
+            match = re.search(r"'(.+)'", line)
+            if match:
+                file_path = match.group(1)
+            else:
+                raise AssertionError("Changes shown message did not contain a file path.")
             assert Path(file_path).suffix == ".nf", f"Diff shown for non-.nf file: {line}"
 
 
@@ -235,7 +248,7 @@ def test_update_with_config_fixed_version(self):
     update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": OLD_TRIMGALORE_SHA}}}
     config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
     tools_config["update"] = update_config
-    with open(os.path.join(self.pipeline_dir, config_fn), "w") as f:
+    with open(Path(self.pipeline_dir, config_fn), "w") as f:
         yaml.dump(tools_config, f)
 
     # Update all modules in the pipeline
@@ -260,7 +273,7 @@ def test_update_with_config_dont_update(self):
     update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": False}}}
     config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
     tools_config["update"] = update_config
-    with open(os.path.join(self.pipeline_dir, config_fn), "w") as f:
+    with open(Path(self.pipeline_dir, config_fn), "w") as f:
         yaml.dump(tools_config, f)
 
     # Update all modules in the pipeline
@@ -289,7 +302,7 @@ def test_update_with_config_fix_all(self):
     update_config = {GITLAB_URL: OLD_TRIMGALORE_SHA}
     config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
     tools_config["update"] = update_config
-    with open(os.path.join(self.pipeline_dir, config_fn), "w") as f:
+    with open(Path(self.pipeline_dir, config_fn), "w") as f:
         yaml.dump(tools_config, f)
 
     # Update all modules in the pipeline
@@ -313,7 +326,7 @@ def test_update_with_config_no_updates(self):
     update_config = {GITLAB_URL: False}
     config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
     tools_config["update"] = update_config
-    with open(os.path.join(self.pipeline_dir, config_fn), "w") as f:
+    with open(Path(self.pipeline_dir, config_fn), "w") as f:
         yaml.dump(tools_config, f)
 
     # Update all modules in the pipeline
@@ -428,7 +441,7 @@ def test_update_only_show_differences(self, mock_prompt):
     )
     update_old.update()
 
-    tmpdir = tempfile.mkdtemp()
+    tmpdir = Path(tempfile.mkdtemp())
     shutil.rmtree(tmpdir)
     shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir)
 
@@ -476,7 +489,7 @@ def test_update_only_show_differences_when_patch(self, mock_prompt):
     patch_obj = ModulePatch(self.pipeline_dir)
     patch_obj.patch("fastqc")
     # Check that a patch file with the correct name has been created
-    assert "fastqc.diff" in set(os.listdir(module_path))
+    assert "fastqc.diff" in set(Path(module_path).iterdir())
 
     # Update all modules
     assert update_obj.update() is True
@@ -491,12 +504,6 @@ def test_update_only_show_differences_when_patch(self, mock_prompt):
     assert correct_git_sha != current_git_sha
 
 
-def cmp_module(dir1, dir2):
-    """Compare two versions of the same module"""
-    files = ["main.nf", "meta.yml"]
-    return all(filecmp.cmp(os.path.join(dir1, f), os.path.join(dir2, f), shallow=False) for f in files)
-
-
 def test_update_module_with_extra_config_file(self):
     """Try updating a module with a config file"""
     # Install the module

From 9f4323a610cee3b968b2efc7fc18f8c332b3afe4 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 9 Jul 2024 09:28:42 +0000
Subject: [PATCH 035/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 58e9a36bf3..23fcb83362 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -45,6 +45,7 @@
 - Update gitpod/workspace-base Docker digest to 0f38224 ([#3048](https://github.com/nf-core/tools/pull/3048))
 - update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052))
+- update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From 96b50f4739209a4ccb817b5f087e383533a5b4b0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 9 Jul 2024 11:31:56 +0200
Subject: [PATCH 036/414] template: Use filename in code block for `params.yml`

---
 nf_core/pipeline-template/docs/usage.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md
index 6645e0f6cf..ca64377d24 100644
--- a/nf_core/pipeline-template/docs/usage.md
+++ b/nf_core/pipeline-template/docs/usage.md
@@ -89,9 +89,9 @@ The above pipeline run specified with a params file in yaml format:
 nextflow run {{ name }} -profile docker -params-file params.yaml
 ```
 
-with `params.yaml` containing:
+with:
 
-```yaml
+```yaml title="params.yaml"
 input: './samplesheet.csv'
 outdir: './results/'
 genome: 'GRCh37'

From c22888aea2329abf9a658e8a11a6c3514ad72fd0 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 9 Jul 2024 09:33:11 +0000
Subject: [PATCH 037/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 58e9a36bf3..b0b706df1e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@
 - Change paths to test data ([#2985](https://github.com/nf-core/tools/pull/2985))
 - Run awsfulltest on PRs to `master` with two PR approvals ([#3042](https://github.com/nf-core/tools/pull/3042))
 - Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046))
+- Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055))
 
 ### Linting
 

From 2525905655a922bdc0cde8af31062c3354c4cad1 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 9 Jul 2024 11:39:30 +0200
Subject: [PATCH 038/414] fix tests

---
 tests/modules/update.py      | 2 +-
 tests/subworkflows/update.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/modules/update.py b/tests/modules/update.py
index 72766779e3..06ae3a294a 100644
--- a/tests/modules/update.py
+++ b/tests/modules/update.py
@@ -489,7 +489,7 @@ def test_update_only_show_differences_when_patch(self, mock_prompt):
     patch_obj = ModulePatch(self.pipeline_dir)
     patch_obj.patch("fastqc")
     # Check that a patch file with the correct name has been created
-    assert "fastqc.diff" in set(Path(module_path).iterdir())
+    assert "fastqc.diff" in [f.name for f in module_path.glob("*.diff")]
 
     # Update all modules
     assert update_obj.update() is True
diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py
index 7d1a3808dc..42d09aa66a 100644
--- a/tests/subworkflows/update.py
+++ b/tests/subworkflows/update.py
@@ -74,7 +74,7 @@ def test_install_at_hash_and_update_limit_output(self):
     old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
 
     # Copy the subworkflow files and check that they are affected by the update
-    tmpdir = tempfile.mkdtemp()
+    tmpdir = Path(tempfile.mkdtemp())
     sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
     shutil.copytree(sw_path, tmpdir)
 

From 863a8a1063ad756729bf1b3e979d3ce508002a2b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 9 Jul 2024 11:45:04 +0200
Subject: [PATCH 039/414] fix shebang and imports

---
 docs/api/make_lint_md.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/docs/api/make_lint_md.py b/docs/api/make_lint_md.py
index 7b823a086e..432f0d16b6 100644
--- a/docs/api/make_lint_md.py
+++ b/docs/api/make_lint_md.py
@@ -1,7 +1,6 @@
+#!/usr/bin/env python
 from pathlib import Path
 
-#!/usr/bin/env python
-import nf_core.commands_pipelines
 import nf_core.modules.lint
 import nf_core.pipelines.lint
 import nf_core.subworkflows.lint

From 29075d6bf5895f3af97be456413e350dd56a3b31 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 9 Jul 2024 16:36:37 +0200
Subject: [PATCH 040/414] improve per test clean-up, move component comparison
 to utils

---
 nf_core/components/update.py | 14 +++++++++-----
 tests/modules/update.py      | 32 +++++++++++++-------------------
 tests/subworkflows/update.py | 34 +++++++++++-----------------------
 tests/utils.py               | 21 ++++++++++++++-------
 4 files changed, 47 insertions(+), 54 deletions(-)

diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index 37e3f62126..7050b76df8 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -278,11 +278,14 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                     )
 
                     # Ask the user if they want to install the component
-                    dry_run = not questionary.confirm(
-                        f"Update {self.component_type[:-1]} '{component}'?",
-                        default=False,
-                        style=nf_core.utils.nfcore_question_style,
-                    ).unsafe_ask()
+                    if not self.prompt:
+                        dry_run = False
+                    else:
+                        dry_run = not questionary.confirm(
+                            f"Update {self.component_type[:-1]} '{component}'?",
+                            default=False,
+                            style=nf_core.utils.nfcore_question_style,
+                        ).unsafe_ask()
 
             if not dry_run:
                 # Clear the component directory and move the installed files there
@@ -833,6 +836,7 @@ def try_apply_patch(
             for_git=False,
             dsp_from_dir=component_relpath,
             dsp_to_dir=component_relpath,
+            limit_output=self.limit_output,
         )
 
         # Move the patched files to the install dir
diff --git a/tests/modules/update.py b/tests/modules/update.py
index 06ae3a294a..49a261e7b5 100644
--- a/tests/modules/update.py
+++ b/tests/modules/update.py
@@ -1,4 +1,3 @@
-import filecmp
 import io
 import logging
 import re
@@ -26,28 +25,23 @@
     GITLAB_URL,
     OLD_TRIMGALORE_BRANCH,
     OLD_TRIMGALORE_SHA,
+    cmp_component,
 )
 
 
-def cmp_module(dir1: Path, dir2: Path) -> bool:
-    """Compare two versions of the same module"""
-    files = ["main.nf", "meta.yml"]
-    return all(filecmp.cmp(dir1 / f, dir2 / f, shallow=False) for f in files)
-
-
 def test_install_and_update(self):
     """Installs a module in the pipeline and updates it (no change)"""
     self.mods_install.install("trimgalore")
     update_obj = ModuleUpdate(self.pipeline_dir, show_diff=False)
 
     # Copy the module files and check that they are unaffected by the update
-    tmpdir = Path(tempfile.mkdtemp())
+    tmpdir = Path(tempfile.TemporaryDirectory().name)
     trimgalore_tmpdir = tmpdir / "trimgalore"
     trimgalore_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "trimgalore")
     shutil.copytree(trimgalore_path, trimgalore_tmpdir)
 
     assert update_obj.update("trimgalore") is True
-    assert cmp_module(trimgalore_tmpdir, trimgalore_path) is True
+    assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True
 
 
 def test_install_at_hash_and_update(self):
@@ -58,13 +52,13 @@ def test_install_at_hash_and_update(self):
     )
 
     # Copy the module files and check that they are affected by the update
-    tmpdir = Path(tempfile.mkdtemp())
+    tmpdir = Path(tempfile.TemporaryDirectory().name)
     trimgalore_tmpdir = tmpdir / "trimgalore"
     trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
     shutil.copytree(trimgalore_path, trimgalore_tmpdir)
 
     assert update_obj.update("trimgalore") is True
-    assert cmp_module(trimgalore_tmpdir, trimgalore_path) is False
+    assert cmp_component(trimgalore_tmpdir, trimgalore_path) is False
 
     # Check that the modules.json is correctly updated
     mod_json_obj = ModulesJson(self.pipeline_dir)
@@ -95,13 +89,13 @@ def test_install_at_hash_and_update_limit_output(self):
     )
 
     # Copy the module files and check that they are affected by the update
-    tmpdir = Path(tempfile.mkdtemp())
+    tmpdir = Path(tempfile.TemporaryDirectory().name)
     trimgalore_tmpdir = tmpdir / "trimgalore"
     trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
     shutil.copytree(trimgalore_path, trimgalore_tmpdir)
 
     assert update_obj.update("trimgalore") is True
-    assert cmp_module(trimgalore_tmpdir, trimgalore_path) is False
+    assert cmp_component(trimgalore_tmpdir, trimgalore_path) is False
 
     # Check that the modules.json is correctly updated
     mod_json_obj = ModulesJson(self.pipeline_dir)
@@ -159,13 +153,13 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self):
     )
 
     # Copy the module files and check that they are affected by the update
-    tmpdir = Path(tempfile.mkdtemp())
+    tmpdir = Path(tempfile.TemporaryDirectory().name)
     trimgalore_tmpdir = tmpdir / "trimgalore"
     trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
     shutil.copytree(trimgalore_path, trimgalore_tmpdir)
 
     assert update_obj.update("trimgalore") is True
-    assert cmp_module(trimgalore_tmpdir, trimgalore_path) is True
+    assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True
 
     # TODO: Apply the patch to the module
 
@@ -184,13 +178,13 @@ def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self):
     )
 
     # Copy the module files and check that they are affected by the update
-    tmpdir = Path(tempfile.mkdtemp())
+    tmpdir = Path(tempfile.TemporaryDirectory().name)
     trimgalore_tmpdir = tmpdir / "trimgalore"
     trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
     shutil.copytree(trimgalore_path, trimgalore_tmpdir)
 
     assert update_obj.update("trimgalore") is True
-    assert cmp_module(trimgalore_tmpdir, trimgalore_path) is True
+    assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True
 
     # Check that the patch file was created
     assert patch_path.exists(), f"Patch file was not created at {patch_path}"
@@ -441,7 +435,7 @@ def test_update_only_show_differences(self, mock_prompt):
     )
     update_old.update()
 
-    tmpdir = Path(tempfile.mkdtemp())
+    tmpdir = Path(tempfile.TemporaryDirectory().name)
     shutil.rmtree(tmpdir)
     shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir)
 
@@ -455,7 +449,7 @@ def test_update_only_show_differences(self, mock_prompt):
     correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"]
     current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
     assert correct_git_sha != current_git_sha
-    assert cmp_module(Path(tmpdir, mod), Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, mod)) is True
+    assert cmp_component(Path(tmpdir, mod), Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, mod)) is True
 
 
 # Mock questionary answer: do not update module, only show diffs
diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py
index 42d09aa66a..5395d194ae 100644
--- a/tests/subworkflows/update.py
+++ b/tests/subworkflows/update.py
@@ -1,4 +1,3 @@
-import filecmp
 import io
 import logging
 import re
@@ -14,7 +13,7 @@
 from nf_core.modules.update import ModuleUpdate
 from nf_core.subworkflows.update import SubworkflowUpdate
 
-from ..utils import OLD_SUBWORKFLOWS_SHA
+from ..utils import OLD_SUBWORKFLOWS_SHA, cmp_component
 
 
 def test_install_and_update(self):
@@ -23,8 +22,7 @@ def test_install_and_update(self):
     update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False)
 
     # Copy the sw files and check that they are unaffected by the update
-    tmpdir = tempfile.mkdtemp()
-    shutil.rmtree(tmpdir)
+    tmpdir = Path(tempfile.TemporaryDirectory().name)
     sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "bam_stats_samtools")
     shutil.copytree(sw_path, tmpdir)
 
@@ -39,8 +37,8 @@ def test_install_at_hash_and_update(self):
     old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
 
     # Copy the sw files and check that they are affected by the update
-    tmpdir = tempfile.mkdtemp()
-    shutil.rmtree(tmpdir)
+    tmpdir = Path(tempfile.TemporaryDirectory().name)
+
     sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
     shutil.copytree(sw_path, tmpdir)
 
@@ -69,12 +67,13 @@ def test_install_at_hash_and_update_limit_output(self):
     ch = logging.StreamHandler(log_capture)
     logger = logging.getLogger()
     logger.addHandler(ch)
+    logger.setLevel(logging.INFO)
 
     update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False, update_deps=True, limit_output=True)
     old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
 
     # Copy the subworkflow files and check that they are affected by the update
-    tmpdir = Path(tempfile.mkdtemp())
+    tmpdir = Path(tempfile.TemporaryDirectory().name)
     sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
     shutil.copytree(sw_path, tmpdir)
 
@@ -124,7 +123,6 @@ def test_install_at_hash_and_update_limit_output(self):
     # Clean up
     logger.removeHandler(ch)
     log_capture.close()
-    shutil.rmtree(tmpdir)
 
 
 def test_install_at_hash_and_update_and_save_diff_to_file(self):
@@ -134,8 +132,8 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self):
     update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True)
 
     # Copy the sw files and check that they are affected by the update
-    tmpdir = tempfile.mkdtemp()
-    shutil.rmtree(tmpdir)
+    tmpdir = Path(tempfile.TemporaryDirectory().name)
+
     sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
     shutil.copytree(sw_path, tmpdir)
 
@@ -156,8 +154,7 @@ def test_install_at_hash_and_update_and_save_diff_limit_output(self):
     update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True, limit_output=True)
 
     # Copy the sw files and check that they are affected by the update
-    tmpdir = tempfile.mkdtemp()
-    shutil.rmtree(tmpdir)
+    tmpdir = Path(tempfile.TemporaryDirectory().name)
     sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
     shutil.copytree(sw_path, tmpdir)
 
@@ -196,7 +193,6 @@ def test_install_at_hash_and_update_and_save_diff_limit_output(self):
 
     # Clean up
     patch_path.unlink()
-    shutil.rmtree(tmpdir)
 
 
 def test_update_all(self):
@@ -343,8 +339,7 @@ def test_update_all_linked_components_from_subworkflow(self):
     old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
 
     # Copy the sw files and check that they are affected by the update
-    tmpdir = tempfile.mkdtemp()
-    shutil.rmtree(tmpdir)
+    tmpdir = Path(tempfile.TemporaryDirectory().name)
     subworkflows_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME)
     modules_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME)
     shutil.copytree(subworkflows_path, Path(tmpdir, "subworkflows"))
@@ -390,8 +385,7 @@ def test_update_all_subworkflows_from_module(self):
     old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
 
     # Copy the sw files and check that they are affected by the update
-    tmpdir = tempfile.mkdtemp()
-    shutil.rmtree(tmpdir)
+    tmpdir = Path(tempfile.TemporaryDirectory().name)
     sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
     shutil.copytree(sw_path, Path(tmpdir, "fastq_align_bowtie2"))
 
@@ -445,9 +439,3 @@ def test_update_change_of_included_modules(self):
     assert "ensemblvep" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
     assert "ensemblvep/vep" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
     assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "ensemblvep/vep").is_dir()
-
-
-def cmp_component(dir1, dir2):
-    """Compare two versions of the same component"""
-    files = ["main.nf", "meta.yml"]
-    return all(filecmp.cmp(Path(dir1, f), Path(dir2, f), shallow=False) for f in files)
diff --git a/tests/utils.py b/tests/utils.py
index 9a0fd0896f..151655b8f3 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -2,9 +2,10 @@
 Helper functions for tests
 """
 
+import filecmp
 import functools
-import os
 import tempfile
+from pathlib import Path
 from typing import Any, Callable, Tuple
 
 import responses
@@ -93,18 +94,24 @@ def mock_biocontainers_api_calls(rsps: responses.RequestsMock, module: str, vers
     rsps.get(biocontainers_api_url, json=biocontainers_mock, status=200)
 
 
-def create_tmp_pipeline() -> Tuple[str, str, str, str]:
+def create_tmp_pipeline() -> Tuple[Path, Path, str, Path]:
     """Create a new Pipeline for testing"""
 
-    tmp_dir = tempfile.mkdtemp()
-    root_repo_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
-    template_dir = os.path.join(root_repo_dir, "nf_core", "pipeline-template")
+    tmp_dir = Path(tempfile.mkdtemp())
+    root_repo_dir = Path(__file__).resolve().parent.parent
+    template_dir = root_repo_dir / "nf_core" / "pipeline-template"
     pipeline_name = "mypipeline"
-    pipeline_dir = os.path.join(tmp_dir, pipeline_name)
+    pipeline_dir = tmp_dir / pipeline_name
 
     nf_core.pipelines.create.create.PipelineCreate(
-        pipeline_name, "it is mine", "me", no_git=True, outdir=pipeline_dir
+        pipeline_name, "it is mine", "me", no_git=True, outdir=str(pipeline_dir)
     ).init_pipeline()
 
     # return values to instance variables for later use in test methods
     return tmp_dir, template_dir, pipeline_name, pipeline_dir
+
+
+def cmp_component(dir1: Path, dir2: Path) -> bool:
+    """Compare two versions of the same component"""
+    files = ["main.nf", "meta.yml"]
+    return all(filecmp.cmp(dir1 / f, dir2 / f, shallow=False) for f in files)

From c1b955bc12b2becbf92392e673ce3ce619633f88 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 9 Jul 2024 16:44:13 +0200
Subject: [PATCH 041/414] use same output for diff file or print output

---
 nf_core/modules/modules_differ.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py
index 34966b2ffd..e79554f2b6 100644
--- a/nf_core/modules/modules_differ.py
+++ b/nf_core/modules/modules_differ.py
@@ -180,11 +180,18 @@ def write_diff_file(
                 if diff_status == ModulesDiffer.DiffEnum.UNCHANGED:
                     # The files are identical
                     fh.write(f"'{Path(dsp_from_dir, file)}' is unchanged\n")
+                elif diff_status == ModulesDiffer.DiffEnum.CREATED:
+                    # The file was created between the commits
+                    fh.write(f"'{Path(dsp_from_dir, file)}' was created\n")
+                elif diff_status == ModulesDiffer.DiffEnum.REMOVED:
+                    # The file was removed between the commits
+                    fh.write(f"'{Path(dsp_from_dir, file)}' was removed\n")
                 elif limit_output and not file.suffix == ".nf":
                     # Skip printing the diff for files other than main.nf
                     fh.write(f"Changes in '{Path(module, file)}' but not shown\n")
                 else:
                     # The file has changed write the diff lines to the file
+                    fh.write(f"Changes in '{Path(module, file)}':\n")
                     for line in diff:
                         fh.write(line)
                     fh.write("\n")

From 71fe3da619910bc74543a0f75f77a3b24f90b9b8 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 9 Jul 2024 16:56:24 +0200
Subject: [PATCH 042/414] fix module tests

---
 tests/modules/update.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/modules/update.py b/tests/modules/update.py
index 49a261e7b5..12adbeb829 100644
--- a/tests/modules/update.py
+++ b/tests/modules/update.py
@@ -436,7 +436,6 @@ def test_update_only_show_differences(self, mock_prompt):
     update_old.update()
 
     tmpdir = Path(tempfile.TemporaryDirectory().name)
-    shutil.rmtree(tmpdir)
     shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir)
 
     assert update_obj.update() is True

From b5833900284b9da51003295b79fb8e3c9b626cbb Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 10 Jul 2024 16:38:16 +0200
Subject: [PATCH 043/414] fix test

---
 nf_core/components/update.py | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index 7050b76df8..81d897fc79 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -278,14 +278,11 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                     )
 
                     # Ask the user if they want to install the component
-                    if not self.prompt:
-                        dry_run = False
-                    else:
-                        dry_run = not questionary.confirm(
-                            f"Update {self.component_type[:-1]} '{component}'?",
-                            default=False,
-                            style=nf_core.utils.nfcore_question_style,
-                        ).unsafe_ask()
+                    dry_run = not questionary.confirm(
+                        f"Update {self.component_type[:-1]} '{component}'?",
+                        default=False,
+                        style=nf_core.utils.nfcore_question_style,
+                    ).unsafe_ask()
 
             if not dry_run:
                 # Clear the component directory and move the installed files there

From 403af3270cc903d57b273fed22699b59090d361a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 11 Jul 2024 12:15:44 +0200
Subject: [PATCH 044/414] actually test the output

---
 nf_core/components/update.py | 16 +++++++++-------
 tests/modules/update.py      | 11 ++++++++---
 tests/subworkflows/update.py | 22 ++++++++++++----------
 3 files changed, 29 insertions(+), 20 deletions(-)

diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index 81d897fc79..72c6e0254a 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -276,13 +276,15 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                         dsp_to_dir=component_dir,
                         limit_output=self.limit_output,
                     )
-
-                    # Ask the user if they want to install the component
-                    dry_run = not questionary.confirm(
-                        f"Update {self.component_type[:-1]} '{component}'?",
-                        default=False,
-                        style=nf_core.utils.nfcore_question_style,
-                    ).unsafe_ask()
+                    if self.prompt:
+                        # Ask the user if they want to install the component
+                        dry_run = not questionary.confirm(
+                            f"Update {self.component_type[:-1]} '{component}'?",
+                            default=False,
+                            style=nf_core.utils.nfcore_question_style,
+                        ).unsafe_ask()
+                    else:
+                        dry_run = False
 
             if not dry_run:
                 # Clear the component directory and move the installed files there
diff --git a/tests/modules/update.py b/tests/modules/update.py
index 12adbeb829..141a9bed05 100644
--- a/tests/modules/update.py
+++ b/tests/modules/update.py
@@ -78,10 +78,11 @@ def test_install_at_hash_and_update_limit_output(self):
     ch = logging.StreamHandler(log_capture)
     logger = logging.getLogger()
     logger.addHandler(ch)
+    logger.setLevel(logging.INFO)
 
     update_obj = ModuleUpdate(
         self.pipeline_dir,
-        show_diff=False,
+        show_diff=True,
         update_deps=True,
         remote_url=GITLAB_URL,
         branch=OLD_TRIMGALORE_BRANCH,
@@ -98,8 +99,7 @@ def test_install_at_hash_and_update_limit_output(self):
     assert cmp_component(trimgalore_tmpdir, trimgalore_path) is False
 
     # Check that the modules.json is correctly updated
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    mod_json = mod_json_obj.get_modules_json()
+    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
     # Get the up-to-date git_sha for the module from the ModuleRepo object
     correct_git_sha = update_obj.modules_repo.get_latest_component_version("trimgalore", "modules")
     current_git_sha = mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"]
@@ -110,6 +110,7 @@ def test_install_at_hash_and_update_limit_output(self):
     log_lines = log_output.split("\n")
 
     # Check for various scenarios
+    nf_changes_shown = False
     for line in log_lines:
         if (
             re.match(r"'.+' is unchanged", line)
@@ -134,6 +135,10 @@ def test_install_at_hash_and_update_limit_output(self):
             else:
                 raise AssertionError("Changes shown message did not contain a file path")
             assert Path(file_path).suffix == ".nf", f"Changes in non-.nf file were shown: {line}"
+            nf_changes_shown = True
+
+    # Ensure that changes in at least one .nf file were shown
+    assert nf_changes_shown, "No changes in .nf files were shown"
 
     # Clean up
     logger.removeHandler(ch)
diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py
index 5395d194ae..e7328813eb 100644
--- a/tests/subworkflows/update.py
+++ b/tests/subworkflows/update.py
@@ -69,7 +69,7 @@ def test_install_at_hash_and_update_limit_output(self):
     logger.addHandler(ch)
     logger.setLevel(logging.INFO)
 
-    update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False, update_deps=True, limit_output=True)
+    update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=True, update_deps=True, limit_output=True)
     old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
 
     # Copy the subworkflow files and check that they are affected by the update
@@ -98,18 +98,20 @@ def test_install_at_hash_and_update_limit_output(self):
     # Check for various scenarios
     nf_changes_shown = False
     for line in log_lines:
-        if re.match(r"'.+' is unchanged", line):
-            # Unchanged files should be reported for both .nf and non-.nf files
-            assert True
-        elif re.match(r"'.+' was created", line):
-            # Created files should be reported for both .nf and non-.nf files
-            assert True
-        elif re.match(r"'.+' was removed", line):
-            # Removed files should be reported for both .nf and non-.nf files
+        if (
+            re.match(r"'.+' is unchanged", line)
+            or re.match(r"'.+' was created", line)
+            or re.match(r"'.+' was removed", line)
+        ):
+            # Unchanged, created, and removed files should be reported for both .nf and non-.nf files
             assert True
         elif re.match(r"Changes in '.+' but not shown", line):
             # Changes not shown should only be for non-.nf files
-            file_path = re.search(r"'(.+)'", line).group(1)
+            match = re.search(r"'(.+)'", line)
+            if match:
+                file_path = match.group(1)
+            else:
+                raise AssertionError("Changes not shown message did not contain a file path")
             assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}"
         elif re.match(r"Changes in '.+':$", line):
             # Changes shown should only be for .nf files

From 12c166610bf108954a9661241252198e7aa2e239 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 11 Jul 2024 12:16:08 +0200
Subject: [PATCH 045/414] check that limit_output is set only when it makes
 sense

---
 nf_core/components/update.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index 72c6e0254a..a896ef0949 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -77,6 +77,8 @@ def _parameter_checks(self):
 
         if not self.has_valid_directory():
             raise UserWarning("The command was not run in a valid pipeline directory.")
+        if self.limit_output and not (self.save_diff_fn or self.show_diff):
+            raise UserWarning("The '--limit-output' flag can only be used with '--preview' or '--save-diff'.")
 
     def update(self, component=None, silent=False, updated=None, check_diff_exist=True) -> bool:
         """Updates a specified module/subworkflow or all modules/subworkflows in a pipeline.

From cd827e1f5452c0bb6a8615e1cd4ae6aa065bbd3d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 11 Jul 2024 12:16:46 +0200
Subject: [PATCH 046/414] remove short option (`l` might be confused with
 `list` (which we don't have)), fix typo

---
 nf_core/__main__.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 331f536834..f33c63e87c 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -929,12 +929,11 @@ def command_modules_install(ctx, tool, dir, prompt, force, sha):
     help="Prompt for the version of the module",
 )
 @click.option(
-    "-l",
     "--limit-output",
     "limit_output",
     is_flag=True,
     default=False,
-    help="Limit ouput to only the difference in main.nf",
+    help="Limit output to only the difference in main.nf",
 )
 @click.option("-s", "--sha", type=str, metavar="<commit sha>", help="Install module at commit SHA")
 @click.option(

From eb72f09b0923fa325a1935f13fcbc5626c241373 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 11 Jul 2024 14:10:34 +0200
Subject: [PATCH 047/414] update to pytest 8 and move it to dev requirements

---
 requirements-dev.txt | 3 ++-
 requirements.txt     | 2 --
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/requirements-dev.txt b/requirements-dev.txt
index ebfbb530d3..2c7bb0c8cf 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -7,7 +7,6 @@ ruff
 Sphinx
 sphinx-rtd-theme
 textual-dev==1.5.1
-mypy
 types-PyYAML
 types-requests
 types-jsonschema
@@ -16,4 +15,6 @@ types-PyYAML
 types-requests
 types-setuptools
 pytest-textual-snapshot==0.4.0
+pytest-workflow>=2.0.0
+pytest>=8.0.0
 ruff
diff --git a/requirements.txt b/requirements.txt
index ccfc1bc9c1..524b739e89 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -11,8 +11,6 @@ pdiff
 pre-commit
 prompt_toolkit>=3.0.3
 pydantic>=2.2.1
-pytest-workflow>=2.0.0
-pytest>=7.0.0
 pyyaml
 questionary>=1.8.0
 refgenie

From 66c8ca5e9d16435e8fc8a8077666af7d61ff9cbb Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 11 Jul 2024 14:10:42 +0200
Subject: [PATCH 048/414] fix deprecation warning

---
 nf_core/pipelines/download.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py
index 8454f894a2..24de045a68 100644
--- a/nf_core/pipelines/download.py
+++ b/nf_core/pipelines/download.py
@@ -20,7 +20,7 @@
 import rich
 import rich.progress
 from git.exc import GitCommandError, InvalidGitRepositoryError
-from pkg_resources import parse_version as version_parser
+from setuptools._distutils.version import LooseVersion as VersionParser
 
 import nf_core
 import nf_core.pipelines.list
@@ -1693,7 +1693,7 @@ def tidy_tags_and_branches(self):
                     else:
                         # desired revisions may contain arbitrary branch names that do not correspond to valid sematic versioning patterns.
                         valid_versions = [
-                            version_parser(v)
+                            VersionParser(v)
                             for v in desired_revisions
                             if re.match(r"\d+\.\d+(?:\.\d+)*(?:[\w\-_])*", v)
                         ]

From 66be4a0a52390d2637eafda4e702bc97d3016a73 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 11 Jul 2024 14:10:42 +0200
Subject: [PATCH 049/414] fix deprecation warning

---
 nf_core/pipelines/download.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py
index 8454f894a2..43b63d8192 100644
--- a/nf_core/pipelines/download.py
+++ b/nf_core/pipelines/download.py
@@ -20,7 +20,7 @@
 import rich
 import rich.progress
 from git.exc import GitCommandError, InvalidGitRepositoryError
-from pkg_resources import parse_version as version_parser
+from packaging.version import Version
 
 import nf_core
 import nf_core.pipelines.list
@@ -1693,13 +1693,11 @@ def tidy_tags_and_branches(self):
                     else:
                         # desired revisions may contain arbitrary branch names that do not correspond to valid sematic versioning patterns.
                         valid_versions = [
-                            version_parser(v)
-                            for v in desired_revisions
-                            if re.match(r"\d+\.\d+(?:\.\d+)*(?:[\w\-_])*", v)
+                            Version(v) for v in desired_revisions if re.match(r"\d+\.\d+(?:\.\d+)*(?:[\w\-_])*", v)
                         ]
                         # valid versions sorted in ascending order, last will be aliased as "latest".
                         latest = sorted(valid_versions)[-1]
-                        self.repo.create_head("latest", latest)
+                        self.repo.create_head("latest", str(latest))
                         self.checkout(latest)
                     if self.repo.head.is_detached:
                         self.repo.head.reset(index=True, working_tree=True)

From ed64d5415e22def0d6abc8fc4a9b142d00a3f8b7 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 11 Jul 2024 12:31:13 +0000
Subject: [PATCH 050/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7c2f5d99df..706d155d27 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -47,6 +47,7 @@
 - update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052))
 - update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054))
+- Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From e4cfde9aba2567fdc3903f1039caaa995da7a77f Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Mon, 15 Jul 2024 09:05:46 +0000
Subject: [PATCH 051/414] chore(deps): update pre-commit hook
 astral-sh/ruff-pre-commit to v0.5.2

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c1dc7978f6..872bd61e0a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.1
+    rev: v0.5.2
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

From 5b648fba592bf69d864a5ee88e062bad84906f6d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 15 Jul 2024 11:15:23 +0200
Subject: [PATCH 052/414] fix tests by mocking questionary confirm

---
 nf_core/components/update.py | 18 ++++++++----------
 tests/modules/update.py      | 19 ++++++++++---------
 tests/subworkflows/update.py |  6 +++++-
 3 files changed, 23 insertions(+), 20 deletions(-)

diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index a896ef0949..1e31e56271 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -128,7 +128,6 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
         components_info = (
             self.get_all_components_info() if self.update_all else [self.get_single_component_info(component)]
         )
-
         # Save the current state of the modules.json
         old_modules_json = self.modules_json.get_modules_json()
 
@@ -278,15 +277,12 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                         dsp_to_dir=component_dir,
                         limit_output=self.limit_output,
                     )
-                    if self.prompt:
-                        # Ask the user if they want to install the component
-                        dry_run = not questionary.confirm(
-                            f"Update {self.component_type[:-1]} '{component}'?",
-                            default=False,
-                            style=nf_core.utils.nfcore_question_style,
-                        ).unsafe_ask()
-                    else:
-                        dry_run = False
+                    # Ask the user if they want to install the component
+                    dry_run = not questionary.confirm(
+                        f"Update {self.component_type[:-1]} '{component}'?",
+                        default=False,
+                        style=nf_core.utils.nfcore_question_style,
+                    ).unsafe_ask()
 
             if not dry_run:
                 # Clear the component directory and move the installed files there
@@ -397,6 +393,8 @@ def get_single_component_info(self, component):
 
         sha = self.sha
         config_entry = None
+        if self.update_config is None:
+            raise UserWarning("Could not find '.nf-core.yml' file in pipeline directory")
         if any(
             [
                 entry.count("/") == 1
diff --git a/tests/modules/update.py b/tests/modules/update.py
index 141a9bed05..a19067b344 100644
--- a/tests/modules/update.py
+++ b/tests/modules/update.py
@@ -69,7 +69,9 @@ def test_install_at_hash_and_update(self):
     assert correct_git_sha == current_git_sha
 
 
-def test_install_at_hash_and_update_limit_output(self):
+# Mock questionary answer: do not update module, only show diffs
+@mock.patch.object(questionary.Question, "unsafe_ask", return_value=True)
+def test_install_at_hash_and_update_limit_output(self, mock_prompt):
     """Installs an old version of a module in the pipeline and updates it with limited output reporting"""
     assert self.mods_install_old.install("trimgalore")
 
@@ -429,10 +431,8 @@ def test_update_different_branch_mix_modules_branch_test(self):
 @mock.patch.object(questionary.Question, "unsafe_ask", return_value=False)
 def test_update_only_show_differences(self, mock_prompt):
     """Try updating all modules showing differences.
-    Don't update some of them.
+    Only show diffs, don't actually save any updated files.
     Check that the sha in modules.json is not changed."""
-    modules_json = ModulesJson(self.pipeline_dir)
-    update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True)
 
     # Update modules to a fixed old SHA
     update_old = ModuleUpdate(
@@ -443,16 +443,17 @@ def test_update_only_show_differences(self, mock_prompt):
     tmpdir = Path(tempfile.TemporaryDirectory().name)
     shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir)
 
-    assert update_obj.update() is True
+    update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True)
+    assert ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True).update()
 
-    mod_json = modules_json.get_modules_json()
+    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
     # Loop through all modules and check that they are NOT updated (according to the modules.json file)
     # A module that can be updated but shouldn't is fastqc
     # Module multiqc is already up to date so don't check
     mod = "fastqc"
-    correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"]
+    non_updated_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"]
     current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
-    assert correct_git_sha != current_git_sha
+    assert non_updated_git_sha != current_git_sha
     assert cmp_component(Path(tmpdir, mod), Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, mod)) is True
 
 
@@ -469,7 +470,7 @@ def test_update_only_show_differences_when_patch(self, mock_prompt):
     update_old = ModuleUpdate(
         self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905"
     )
-    update_old.update()
+    assert update_old.update()
 
     # Modify fastqc module, it will have a patch which will be applied during update
     # We modify fastqc because it's one of the modules that can be updated and there's another one before it (custom/dumpsoftwareversions)
diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py
index e7328813eb..170b2af660 100644
--- a/tests/subworkflows/update.py
+++ b/tests/subworkflows/update.py
@@ -4,7 +4,9 @@
 import shutil
 import tempfile
 from pathlib import Path
+from unittest import mock
 
+import questionary
 import yaml
 
 import nf_core.utils
@@ -58,7 +60,9 @@ def test_install_at_hash_and_update(self):
     )
 
 
-def test_install_at_hash_and_update_limit_output(self):
+# Mock questionary answer: update components
+@mock.patch.object(questionary.Question, "unsafe_ask", return_value=True)
+def test_install_at_hash_and_update_limit_output(self, mock_prompt):
     """Installs an old version of a subworkflow in the pipeline and updates it with limit_output=True"""
     assert self.subworkflow_install_old.install("fastq_align_bowtie2")
 

From 08a138c8ee6a5f79a1573982927667dc3f0f5782 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 15 Jul 2024 11:15:48 +0200
Subject: [PATCH 053/414] handle new jsonschema error type

---
 nf_core/modules/lint/environment_yml.py | 2 +-
 nf_core/modules/lint/meta_yml.py        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py
index 92281d99c0..e10ef1761d 100644
--- a/nf_core/modules/lint/environment_yml.py
+++ b/nf_core/modules/lint/environment_yml.py
@@ -60,7 +60,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
             hint = ""
             if len(e.path) > 0:
                 hint = f"\nCheck the entry for `{e.path[0]}`."
-            if e.schema.get("message"):
+            if e.schema and isinstance(e.schema, dict) and "message" in e.schema:
                 e.message = e.schema["message"]
             module.failed.append(
                 (
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 481d50b3ef..4c036713c8 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -76,7 +76,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
             hint = f"\nCheck the entry for `{e.path[0]}`."
         if e.message.startswith("None is not of type 'object'") and len(e.path) > 2:
             hint = f"\nCheck that the child entries of {str(e.path[0])+'.'+str(e.path[2])} are indented correctly."
-        if e.schema.get("message"):
+        if e.schema and isinstance(e.schema, dict) and "message" in e.schema:
             e.message = e.schema["message"]
             incorrect_value = meta_yaml
             for key in e.path:

From 4d3f793e7a40b4ead7e5134a070523933946316f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 15 Jul 2024 11:15:48 +0200
Subject: [PATCH 054/414] handle new jsonschema error type

---
 nf_core/modules/lint/environment_yml.py | 2 +-
 nf_core/modules/lint/meta_yml.py        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py
index 92281d99c0..e10ef1761d 100644
--- a/nf_core/modules/lint/environment_yml.py
+++ b/nf_core/modules/lint/environment_yml.py
@@ -60,7 +60,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
             hint = ""
             if len(e.path) > 0:
                 hint = f"\nCheck the entry for `{e.path[0]}`."
-            if e.schema.get("message"):
+            if e.schema and isinstance(e.schema, dict) and "message" in e.schema:
                 e.message = e.schema["message"]
             module.failed.append(
                 (
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 481d50b3ef..4c036713c8 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -76,7 +76,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
             hint = f"\nCheck the entry for `{e.path[0]}`."
         if e.message.startswith("None is not of type 'object'") and len(e.path) > 2:
             hint = f"\nCheck that the child entries of {str(e.path[0])+'.'+str(e.path[2])} are indented correctly."
-        if e.schema.get("message"):
+        if e.schema and isinstance(e.schema, dict) and "message" in e.schema:
             e.message = e.schema["message"]
             incorrect_value = meta_yaml
             for key in e.path:

From 716ead4e61a363dd5340fc6b3b0ede15b872c176 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 15 Jul 2024 09:29:34 +0000
Subject: [PATCH 055/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 706d155d27..fe7fdcc28b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -48,6 +48,7 @@
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052))
 - update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054))
 - Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058))
+- handle new jsonschema error type ([#3061](https://github.com/nf-core/tools/pull/3061))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From e06ebdf422669a405146b57c05c5c59f30395513 Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 15 Jul 2024 11:52:20 +0100
Subject: [PATCH 056/414] Remove Azure specific documentation which is no
 longer required

---
 nf_core/pipeline-template/docs/usage.md | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md
index ca64377d24..bf637219f8 100644
--- a/nf_core/pipeline-template/docs/usage.md
+++ b/nf_core/pipeline-template/docs/usage.md
@@ -207,14 +207,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config
 
 If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
 
-## Azure Resource Requests
-
-To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
-We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required.
-
-Note that the choice of VM size depends on your quota and the overall workload during the analysis.
-For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes).
-
 {% endif -%}
 
 ## Running in the background

From e23869120ce320d3d4d4d58856751c358a2d1dd6 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 15 Jul 2024 14:55:30 +0200
Subject: [PATCH 057/414] move pipelines tests into `pipelines` subdirectory to
 mirror command structure

---
 tests/{ => pipelines}/test_bump_version.py |  0
 tests/{ => pipelines}/test_create.py       |  2 +-
 tests/{ => pipelines}/test_create_app.py   |  0
 tests/{ => pipelines}/test_create_logo.py  |  0
 tests/{ => pipelines}/test_download.py     |  2 +-
 tests/{ => pipelines}/test_launch.py       |  2 +-
 tests/{ => pipelines}/test_lint.py         | 30 +++++++++++-----------
 tests/{ => pipelines}/test_list.py         |  0
 tests/{ => pipelines}/test_params_file.py  |  0
 tests/{ => pipelines}/test_refgenie.py     |  0
 tests/{ => pipelines}/test_schema.py       |  2 +-
 tests/{ => pipelines}/test_sync.py         |  2 +-
 12 files changed, 20 insertions(+), 20 deletions(-)
 rename tests/{ => pipelines}/test_bump_version.py (100%)
 rename tests/{ => pipelines}/test_create.py (99%)
 rename tests/{ => pipelines}/test_create_app.py (100%)
 rename tests/{ => pipelines}/test_create_logo.py (100%)
 rename tests/{ => pipelines}/test_download.py (99%)
 rename tests/{ => pipelines}/test_launch.py (99%)
 rename tests/{ => pipelines}/test_lint.py (90%)
 rename tests/{ => pipelines}/test_list.py (100%)
 rename tests/{ => pipelines}/test_params_file.py (100%)
 rename tests/{ => pipelines}/test_refgenie.py (100%)
 rename tests/{ => pipelines}/test_schema.py (99%)
 rename tests/{ => pipelines}/test_sync.py (99%)

diff --git a/tests/test_bump_version.py b/tests/pipelines/test_bump_version.py
similarity index 100%
rename from tests/test_bump_version.py
rename to tests/pipelines/test_bump_version.py
diff --git a/tests/test_create.py b/tests/pipelines/test_create.py
similarity index 99%
rename from tests/test_create.py
rename to tests/pipelines/test_create.py
index 313b6f5354..d93b26bd1a 100644
--- a/tests/test_create.py
+++ b/tests/pipelines/test_create.py
@@ -9,7 +9,7 @@
 
 import nf_core.pipelines.create.create
 
-from .utils import with_temporary_folder
+from ..utils import with_temporary_folder
 
 TEST_DATA_DIR = Path(__file__).parent / "data"
 PIPELINE_TEMPLATE_YML = TEST_DATA_DIR / "pipeline_create_template.yml"
diff --git a/tests/test_create_app.py b/tests/pipelines/test_create_app.py
similarity index 100%
rename from tests/test_create_app.py
rename to tests/pipelines/test_create_app.py
diff --git a/tests/test_create_logo.py b/tests/pipelines/test_create_logo.py
similarity index 100%
rename from tests/test_create_logo.py
rename to tests/pipelines/test_create_logo.py
diff --git a/tests/test_download.py b/tests/pipelines/test_download.py
similarity index 99%
rename from tests/test_download.py
rename to tests/pipelines/test_download.py
index c3a8c5546a..ebb76fef72 100644
--- a/tests/test_download.py
+++ b/tests/pipelines/test_download.py
@@ -18,7 +18,7 @@
 from nf_core.synced_repo import SyncedRepo
 from nf_core.utils import run_cmd
 
-from .utils import with_temporary_folder
+from ..utils import with_temporary_folder
 
 
 class DownloadTest(unittest.TestCase):
diff --git a/tests/test_launch.py b/tests/pipelines/test_launch.py
similarity index 99%
rename from tests/test_launch.py
rename to tests/pipelines/test_launch.py
index 9774853419..b4b285a3c9 100644
--- a/tests/test_launch.py
+++ b/tests/pipelines/test_launch.py
@@ -11,7 +11,7 @@
 import nf_core.pipelines.create.create
 import nf_core.pipelines.launch
 
-from .utils import create_tmp_pipeline, with_temporary_file, with_temporary_folder
+from ..utils import create_tmp_pipeline, with_temporary_file, with_temporary_folder
 
 
 class TestLaunch(TestCase):
diff --git a/tests/test_lint.py b/tests/pipelines/test_lint.py
similarity index 90%
rename from tests/test_lint.py
rename to tests/pipelines/test_lint.py
index 4e468b7538..460c8f03d8 100644
--- a/tests/test_lint.py
+++ b/tests/pipelines/test_lint.py
@@ -12,7 +12,7 @@
 import nf_core.pipelines.create.create
 import nf_core.pipelines.lint
 
-from .utils import with_temporary_folder
+from ..utils import with_temporary_folder
 
 
 class TestLint(unittest.TestCase):
@@ -179,33 +179,33 @@ def test_sphinx_md_files(self):
     #######################
     # SPECIFIC LINT TESTS #
     #######################
-    from .lint.actions_awsfulltest import (  # type: ignore[misc]
+    from ..lint.actions_awsfulltest import (  # type: ignore[misc]
         test_actions_awsfulltest_fail,
         test_actions_awsfulltest_pass,
         test_actions_awsfulltest_warn,
     )
-    from .lint.actions_awstest import (  # type: ignore[misc]
+    from ..lint.actions_awstest import (  # type: ignore[misc]
         test_actions_awstest_fail,
         test_actions_awstest_pass,
     )
-    from .lint.actions_ci import (  # type: ignore[misc]
+    from ..lint.actions_ci import (  # type: ignore[misc]
         test_actions_ci_fail_wrong_nf,
         test_actions_ci_fail_wrong_trigger,
         test_actions_ci_pass,
     )
-    from .lint.actions_schema_validation import (  # type: ignore[misc]
+    from ..lint.actions_schema_validation import (  # type: ignore[misc]
         test_actions_schema_validation_fails_for_additional_property,
         test_actions_schema_validation_missing_jobs,
         test_actions_schema_validation_missing_on,
     )
-    from .lint.configs import (  # type: ignore[misc]
+    from ..lint.configs import (  # type: ignore[misc]
         test_ignore_base_config,
         test_ignore_modules_config,
         test_superfluous_withname_in_base_config_fails,
         test_superfluous_withname_in_modules_config_fails,
         test_withname_in_modules_config,
     )
-    from .lint.files_exist import (  # type: ignore[misc]
+    from ..lint.files_exist import (  # type: ignore[misc]
         test_files_exist_depreciated_file,
         test_files_exist_fail_conditional,
         test_files_exist_missing_config,
@@ -214,13 +214,13 @@ def test_sphinx_md_files(self):
         test_files_exist_pass_conditional,
         test_files_exist_pass_conditional_nfschema,
     )
-    from .lint.files_unchanged import (  # type: ignore[misc]
+    from ..lint.files_unchanged import (  # type: ignore[misc]
         test_files_unchanged_fail,
         test_files_unchanged_pass,
     )
-    from .lint.merge_markers import test_merge_markers_found  # type: ignore[misc]
-    from .lint.modules_json import test_modules_json_pass  # type: ignore[misc]
-    from .lint.multiqc_config import (  # type: ignore[misc]
+    from ..lint.merge_markers import test_merge_markers_found  # type: ignore[misc]
+    from ..lint.modules_json import test_modules_json_pass  # type: ignore[misc]
+    from ..lint.multiqc_config import (  # type: ignore[misc]
         test_multiqc_config_exists,
         test_multiqc_config_ignore,
         test_multiqc_config_missing_report_section_order,
@@ -229,7 +229,7 @@ def test_sphinx_md_files(self):
         test_multiqc_config_report_comment_release_succeed,
         test_multiqc_incorrect_export_plots,
     )
-    from .lint.nextflow_config import (  # type: ignore[misc]
+    from ..lint.nextflow_config import (  # type: ignore[misc]
         test_allow_params_reference_in_main_nf,
         test_catch_params_assignment_in_main_nf,
         test_default_values_fail,
@@ -242,14 +242,14 @@ def test_sphinx_md_files(self):
         test_nextflow_config_example_pass,
         test_nextflow_config_missing_test_profile_failed,
     )
-    from .lint.nfcore_yml import (  # type: ignore[misc]
+    from ..lint.nfcore_yml import (  # type: ignore[misc]
         test_nfcore_yml_fail_nfcore_version,
         test_nfcore_yml_fail_repo_type,
         test_nfcore_yml_pass,
     )
-    from .lint.template_strings import (  # type: ignore[misc]
+    from ..lint.template_strings import (  # type: ignore[misc]
         test_template_strings,
         test_template_strings_ignore_file,
         test_template_strings_ignored,
     )
-    from .lint.version_consistency import test_version_consistency  # type: ignore[misc]
+    from ..lint.version_consistency import test_version_consistency  # type: ignore[misc]
diff --git a/tests/test_list.py b/tests/pipelines/test_list.py
similarity index 100%
rename from tests/test_list.py
rename to tests/pipelines/test_list.py
diff --git a/tests/test_params_file.py b/tests/pipelines/test_params_file.py
similarity index 100%
rename from tests/test_params_file.py
rename to tests/pipelines/test_params_file.py
diff --git a/tests/test_refgenie.py b/tests/pipelines/test_refgenie.py
similarity index 100%
rename from tests/test_refgenie.py
rename to tests/pipelines/test_refgenie.py
diff --git a/tests/test_schema.py b/tests/pipelines/test_schema.py
similarity index 99%
rename from tests/test_schema.py
rename to tests/pipelines/test_schema.py
index 4cb157c087..633de3db69 100644
--- a/tests/test_schema.py
+++ b/tests/pipelines/test_schema.py
@@ -15,7 +15,7 @@
 import nf_core.pipelines.create.create
 import nf_core.pipelines.schema
 
-from .utils import with_temporary_file, with_temporary_folder
+from ..utils import with_temporary_file, with_temporary_folder
 
 
 class TestSchema(unittest.TestCase):
diff --git a/tests/test_sync.py b/tests/pipelines/test_sync.py
similarity index 99%
rename from tests/test_sync.py
rename to tests/pipelines/test_sync.py
index ca90071d95..d7b73c7ffb 100644
--- a/tests/test_sync.py
+++ b/tests/pipelines/test_sync.py
@@ -14,7 +14,7 @@
 import nf_core.pipelines.create.create
 import nf_core.pipelines.sync
 
-from .utils import with_temporary_folder
+from ..utils import with_temporary_folder
 
 
 class TestModules(unittest.TestCase):

From 7b3d985ff288b6e4e222a9142bed59707d06935f Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 15 Jul 2024 18:02:49 +0200
Subject: [PATCH 058/414] reduce update with limit_output tests

---
 tests/modules/update.py      | 119 ++++++---------------------------
 tests/subworkflows/update.py | 123 ++++++++---------------------------
 tests/test_modules.py        |   5 ++
 tests/test_subworkflows.py   |   5 ++
 4 files changed, 58 insertions(+), 194 deletions(-)

diff --git a/tests/modules/update.py b/tests/modules/update.py
index a19067b344..e02b058fbb 100644
--- a/tests/modules/update.py
+++ b/tests/modules/update.py
@@ -1,6 +1,4 @@
-import io
 import logging
-import re
 import shutil
 import tempfile
 from pathlib import Path
@@ -73,15 +71,9 @@ def test_install_at_hash_and_update(self):
 @mock.patch.object(questionary.Question, "unsafe_ask", return_value=True)
 def test_install_at_hash_and_update_limit_output(self, mock_prompt):
     """Installs an old version of a module in the pipeline and updates it with limited output reporting"""
+    self.caplog.set_level(logging.INFO)
     assert self.mods_install_old.install("trimgalore")
 
-    # Capture the logger output
-    log_capture = io.StringIO()
-    ch = logging.StreamHandler(log_capture)
-    logger = logging.getLogger()
-    logger.addHandler(ch)
-    logger.setLevel(logging.INFO)
-
     update_obj = ModuleUpdate(
         self.pipeline_dir,
         show_diff=True,
@@ -90,61 +82,15 @@ def test_install_at_hash_and_update_limit_output(self, mock_prompt):
         branch=OLD_TRIMGALORE_BRANCH,
         limit_output=True,
     )
+    assert update_obj.update("trimgalore")
 
-    # Copy the module files and check that they are affected by the update
-    tmpdir = Path(tempfile.TemporaryDirectory().name)
-    trimgalore_tmpdir = tmpdir / "trimgalore"
-    trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
-    shutil.copytree(trimgalore_path, trimgalore_tmpdir)
-
-    assert update_obj.update("trimgalore") is True
-    assert cmp_component(trimgalore_tmpdir, trimgalore_path) is False
-
-    # Check that the modules.json is correctly updated
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    # Get the up-to-date git_sha for the module from the ModuleRepo object
-    correct_git_sha = update_obj.modules_repo.get_latest_component_version("trimgalore", "modules")
-    current_git_sha = mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"]
-    assert correct_git_sha == current_git_sha
-
-    # Get the captured log output
-    log_output = log_capture.getvalue()
-    log_lines = log_output.split("\n")
-
-    # Check for various scenarios
-    nf_changes_shown = False
-    for line in log_lines:
-        if (
-            re.match(r"'.+' is unchanged", line)
-            or re.match(r"'.+' was created", line)
-            or re.match(r"'.+' was removed", line)
-        ):
-            # Unchanged, created, and removed files should be reported for both .nf and non-.nf files
-            assert True
-        elif re.match(r"Changes in '.+' but not shown", line):
-            # Changes not shown should only be for non-.nf files
-            match = re.search(r"'(.+)'", line)
-            if match:
-                file_path = match.group(1)
-            else:
-                raise AssertionError("Changes not shown message did not contain a file path")
-            assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}"
-        elif re.match(r"Changes in '.+':$", line):
-            # Changes shown should only be for .nf files
-            match = re.search(r"'(.+)'", line)
-            if match:
-                file_path = match.group(1)
-            else:
-                raise AssertionError("Changes shown message did not contain a file path")
-            assert Path(file_path).suffix == ".nf", f"Changes in non-.nf file were shown: {line}"
-            nf_changes_shown = True
-
-    # Ensure that changes in at least one .nf file were shown
-    assert nf_changes_shown, "No changes in .nf files were shown"
-
-    # Clean up
-    logger.removeHandler(ch)
-    log_capture.close()
+    # Check changes not shown for non-.nf files
+    assert "Changes in 'trimgalore/meta.yml' but not shown" in self.caplog.text
+    # Check changes shown for .nf files
+    assert "Changes in 'trimgalore/main.nf'" in self.caplog.text
+    for line in self.caplog.text.split("\n"):
+        if line.startswith("---"):
+            assert line.endswith("main.nf")
 
 
 def test_install_at_hash_and_update_and_save_diff_to_file(self):
@@ -173,55 +119,32 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self):
 
 def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self):
     """Installs an old version of a module in the pipeline and updates it"""
+    # Install old version of trimgalore
     self.mods_install_old.install("trimgalore")
     patch_path = Path(self.pipeline_dir, "trimgalore.patch")
+    # Update saving the differences to a patch file and with `limit_output`
     update_obj = ModuleUpdate(
         self.pipeline_dir,
         save_diff_fn=patch_path,
-        sha=OLD_TRIMGALORE_SHA,
         remote_url=GITLAB_URL,
         branch=OLD_TRIMGALORE_BRANCH,
         limit_output=True,
     )
-
-    # Copy the module files and check that they are affected by the update
-    tmpdir = Path(tempfile.TemporaryDirectory().name)
-    trimgalore_tmpdir = tmpdir / "trimgalore"
-    trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
-    shutil.copytree(trimgalore_path, trimgalore_tmpdir)
-
-    assert update_obj.update("trimgalore") is True
-    assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True
+    assert update_obj.update("trimgalore")
 
     # Check that the patch file was created
     assert patch_path.exists(), f"Patch file was not created at {patch_path}"
 
     # Read the contents of the patch file
-    with open(patch_path) as f:
-        patch_content = f.read()
-
-    # Check the content of the patch file
-    patch_lines = patch_content.split("\n")
-    for line in patch_lines:
-        if re.match(r"'.+' is unchanged", line):
-            # Unchanged files should be reported for both .nf and non-.nf files
-            assert True
-        elif re.match(r"Changes in '.+' but not shown", line):
-            # Changes not shown should only be for non-.nf files
-            match = re.search(r"'(.+)'", line)
-            if match:
-                file_path = match.group(1)
-            else:
-                raise AssertionError("Changes not shown message did not contain a file path.")
-            assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}"
-        elif re.match("diff --git", line):
-            # Diff should only be shown for .nf files
-            match = re.search(r"'(.+)'", line)
-            if match:
-                file_path = match.group(1)
-            else:
-                raise AssertionError("Changes shown message did not contain a file path.")
-            assert Path(file_path).suffix == ".nf", f"Diff shown for non-.nf file: {line}"
+    with open(patch_path) as fh:
+        patch_content = fh.read()
+        # Check changes not shown for non-.nf files
+        assert "Changes in 'trimgalore/meta.yml' but not shown" in patch_content
+        # Check changes only shown for main.nf
+        assert "Changes in 'trimgalore/main.nf'" in patch_content
+        for line in patch_content:
+            if line.startswith("---"):
+                assert line.endswith("main.nf")
 
 
 def test_update_all(self):
diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py
index 170b2af660..0d3a63c7ef 100644
--- a/tests/subworkflows/update.py
+++ b/tests/subworkflows/update.py
@@ -64,71 +64,23 @@ def test_install_at_hash_and_update(self):
 @mock.patch.object(questionary.Question, "unsafe_ask", return_value=True)
 def test_install_at_hash_and_update_limit_output(self, mock_prompt):
     """Installs an old version of a subworkflow in the pipeline and updates it with limit_output=True"""
+    self.caplog.set_level(logging.INFO)
     assert self.subworkflow_install_old.install("fastq_align_bowtie2")
 
-    # Capture the logger output
-    log_capture = io.StringIO()
-    ch = logging.StreamHandler(log_capture)
-    logger = logging.getLogger()
-    logger.addHandler(ch)
-    logger.setLevel(logging.INFO)
-
     update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=True, update_deps=True, limit_output=True)
-    old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-
-    # Copy the subworkflow files and check that they are affected by the update
-    tmpdir = Path(tempfile.TemporaryDirectory().name)
-    sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
-    shutil.copytree(sw_path, tmpdir)
-
-    assert update_obj.update("fastq_align_bowtie2") is True
-    assert cmp_component(tmpdir, sw_path) is False
 
-    # Check that the modules.json is correctly updated
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    assert (
-        old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
-            "git_sha"
-        ]
-        != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
-            "git_sha"
-        ]
-    )
+    assert update_obj.update("fastq_align_bowtie2")
 
-    # Get the captured log output
-    log_output = log_capture.getvalue()
-    log_lines = log_output.split("\n")
-
-    # Check for various scenarios
-    nf_changes_shown = False
-    for line in log_lines:
-        if (
-            re.match(r"'.+' is unchanged", line)
-            or re.match(r"'.+' was created", line)
-            or re.match(r"'.+' was removed", line)
-        ):
-            # Unchanged, created, and removed files should be reported for both .nf and non-.nf files
-            assert True
-        elif re.match(r"Changes in '.+' but not shown", line):
-            # Changes not shown should only be for non-.nf files
-            match = re.search(r"'(.+)'", line)
-            if match:
-                file_path = match.group(1)
-            else:
-                raise AssertionError("Changes not shown message did not contain a file path")
-            assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}"
-        elif re.match(r"Changes in '.+':$", line):
-            # Changes shown should only be for .nf files
-            file_path = re.search(r"'(.+)'", line).group(1)
-            assert Path(file_path).suffix == ".nf", f"Changes in non-.nf file were shown: {line}"
-            nf_changes_shown = True
-
-    # Ensure that changes in at least one .nf file were shown
-    assert nf_changes_shown, "No changes in .nf files were shown"
-
-    # Clean up
-    logger.removeHandler(ch)
-    log_capture.close()
+    # Check changes not shown for non-.nf files
+    assert "Changes in 'fastq_align_bowtie2/meta.yml' but not shown" in self.caplog.text
+    assert "Changes in 'bam_sort_stats_samtools/meta.yml' but not shown" in self.caplog.text
+    assert "Changes in 'bam_stats_samtools/meta.yml' but not shown" in self.caplog.text
+    assert "Changes in 'samtools/flagstat/meta.yml' but not shown" in self.caplog.text
+    # Check changes only shown for main.nf files
+    assert "Changes in 'fastq_align_bowtie2/main.nf'" in self.caplog.text
+    for line in self.caplog.text.split("\n"):
+        if line.startswith("---"):
+            assert line.endswith("main.nf")
 
 
 def test_install_at_hash_and_update_and_save_diff_to_file(self):
@@ -155,50 +107,29 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self):
 
 def test_install_at_hash_and_update_and_save_diff_limit_output(self):
     """Installs an old version of a sw in the pipeline and updates it. Save differences to a file."""
-    assert self.subworkflow_install_old.install("fastq_align_bowtie2")
+    # Install old version of fastq_align_bowtie2
+    self.subworkflow_install_old.install("fastq_align_bowtie2")
     patch_path = Path(self.pipeline_dir, "fastq_align_bowtie2.patch")
+    # Update saving the differences to a patch file and with `limit_output`
     update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True, limit_output=True)
-
-    # Copy the sw files and check that they are affected by the update
-    tmpdir = Path(tempfile.TemporaryDirectory().name)
-    sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
-    shutil.copytree(sw_path, tmpdir)
-
-    assert update_obj.update("fastq_align_bowtie2") is True
-    assert cmp_component(tmpdir, sw_path) is True
+    assert update_obj.update("fastq_align_bowtie2")
 
     # Check that the patch file was created
     assert patch_path.exists(), f"Patch file was not created at {patch_path}"
 
-    nf_changes_shown = False
-    non_nf_changes_not_shown = False
-
+    # Read the contents of the patch file
     with open(patch_path) as fh:
         content = fh.read()
-
-        # Check the first line
-        assert re.match(
-            r"Changes in module 'nf-core/fastq_align_bowtie2' between \([a-f0-9]+\) and \([a-f0-9]+\)",
-            content.split("\n")[0],
-        ), "Unexpected first line in patch file"
-
-        # Check for .nf file changes shown
-        nf_changes_shown = bool(re.search(r"Changes in '.*\.nf':\n", content))
-
-        # Check for non-.nf file changes not shown
-        non_nf_changes_not_shown = bool(re.search(r"Changes in '.*[^.nf]' but not shown", content))
-
-        # Check that diff content is only for .nf files
-        diff_lines = re.findall(r"diff --git.*", content)
-        for line in diff_lines:
-            assert re.search(r"\.nf$", line), f"Diff shown for non-.nf file: {line}"
-
-    # Ensure that changes in .nf files were shown and non-.nf files were not shown
-    assert nf_changes_shown, "No changes in .nf files were shown in the patch file"
-    assert non_nf_changes_not_shown, "Changes in non-.nf files were not properly limited in the patch file"
-
-    # Clean up
-    patch_path.unlink()
+        # Check changes not shown for non-.nf files
+        assert "Changes in 'fastq_align_bowtie2/meta.yml' but not shown" in content
+        assert "Changes in 'bam_sort_stats_samtools/meta.yml' but not shown" in content
+        assert "Changes in 'bam_stats_samtools/meta.yml' but not shown" in content
+        assert "Changes in 'samtools/flagstat/meta.yml' but not shown" in content
+        # Check changes only shown for main.nf files
+        assert "Changes in 'fastq_align_bowtie2/main.nf'" in content
+        for line in content:
+            if line.startswith("---"):
+                assert line.endswith("main.nf")
 
 
 def test_update_all(self):
diff --git a/tests/test_modules.py b/tests/test_modules.py
index 7dd3132d33..67ba642189 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -5,6 +5,7 @@
 import shutil
 import unittest
 from pathlib import Path
+import pytest
 
 import requests_cache
 import responses
@@ -156,6 +157,10 @@ def test_modulesrepo_class(self):
         assert modrepo.repo_path == "nf-core"
         assert modrepo.branch == "master"
 
+    @pytest.fixture(autouse=True)
+    def _use_caplog(self, caplog):
+        self.caplog = caplog
+
     ############################################
     # Test of the individual modules commands. #
     ############################################
diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py
index b7ebe952db..7b60313110 100644
--- a/tests/test_subworkflows.py
+++ b/tests/test_subworkflows.py
@@ -5,6 +5,7 @@
 import shutil
 import unittest
 from pathlib import Path
+import pytest
 
 import nf_core.modules
 import nf_core.pipelines.create.create
@@ -113,6 +114,10 @@ def tearDown(self):
         if os.path.exists(self.tmp_dir):
             shutil.rmtree(self.tmp_dir)
 
+    @pytest.fixture(autouse=True)
+    def _use_caplog(self, caplog):
+        self.caplog = caplog
+
     ################################################
     # Test of the individual subworkflow commands. #
     ################################################

From 6325769aaef3b2f53b2bc0321455b90f0aa89528 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 16 Jul 2024 08:21:27 +0000
Subject: [PATCH 059/414] [automated] Fix code linting

---
 tests/subworkflows/update.py | 2 --
 tests/test_modules.py        | 2 +-
 tests/test_subworkflows.py   | 1 +
 3 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py
index 0d3a63c7ef..42ed716b1c 100644
--- a/tests/subworkflows/update.py
+++ b/tests/subworkflows/update.py
@@ -1,6 +1,4 @@
-import io
 import logging
-import re
 import shutil
 import tempfile
 from pathlib import Path
diff --git a/tests/test_modules.py b/tests/test_modules.py
index 67ba642189..6e601ce7ad 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -5,8 +5,8 @@
 import shutil
 import unittest
 from pathlib import Path
-import pytest
 
+import pytest
 import requests_cache
 import responses
 import yaml
diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py
index 7b60313110..17bc678cad 100644
--- a/tests/test_subworkflows.py
+++ b/tests/test_subworkflows.py
@@ -5,6 +5,7 @@
 import shutil
 import unittest
 from pathlib import Path
+
 import pytest
 
 import nf_core.modules

From 891d08ab9472e686686561d8b5426be760782268 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 16 Jul 2024 16:21:43 +0200
Subject: [PATCH 060/414] move lint tests into pipeline folder

---
 tests/{lint => pipelines}/__init__.py         |  0
 tests/pipelines/lint/__init__.py              |  0
 .../lint/actions_awsfulltest.py               |  0
 tests/{ => pipelines}/lint/actions_awstest.py |  0
 tests/{ => pipelines}/lint/actions_ci.py      |  0
 .../lint/actions_schema_validation.py         |  0
 tests/{ => pipelines}/lint/configs.py         |  0
 tests/{ => pipelines}/lint/files_exist.py     |  7 +++---
 tests/{ => pipelines}/lint/files_unchanged.py |  0
 tests/{ => pipelines}/lint/merge_markers.py   |  0
 tests/{ => pipelines}/lint/modules_json.py    |  0
 tests/{ => pipelines}/lint/multiqc_config.py  |  0
 tests/{ => pipelines}/lint/nextflow_config.py | 22 +++++++++----------
 tests/{ => pipelines}/lint/nfcore_yml.py      |  0
 .../{ => pipelines}/lint/template_strings.py  |  0
 .../lint/version_consistency.py               |  2 +-
 16 files changed, 15 insertions(+), 16 deletions(-)
 rename tests/{lint => pipelines}/__init__.py (100%)
 create mode 100644 tests/pipelines/lint/__init__.py
 rename tests/{ => pipelines}/lint/actions_awsfulltest.py (100%)
 rename tests/{ => pipelines}/lint/actions_awstest.py (100%)
 rename tests/{ => pipelines}/lint/actions_ci.py (100%)
 rename tests/{ => pipelines}/lint/actions_schema_validation.py (100%)
 rename tests/{ => pipelines}/lint/configs.py (100%)
 rename tests/{ => pipelines}/lint/files_exist.py (95%)
 rename tests/{ => pipelines}/lint/files_unchanged.py (100%)
 rename tests/{ => pipelines}/lint/merge_markers.py (100%)
 rename tests/{ => pipelines}/lint/modules_json.py (100%)
 rename tests/{ => pipelines}/lint/multiqc_config.py (100%)
 rename tests/{ => pipelines}/lint/nextflow_config.py (95%)
 rename tests/{ => pipelines}/lint/nfcore_yml.py (100%)
 rename tests/{ => pipelines}/lint/template_strings.py (100%)
 rename tests/{ => pipelines}/lint/version_consistency.py (93%)

diff --git a/tests/lint/__init__.py b/tests/pipelines/__init__.py
similarity index 100%
rename from tests/lint/__init__.py
rename to tests/pipelines/__init__.py
diff --git a/tests/pipelines/lint/__init__.py b/tests/pipelines/lint/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/tests/lint/actions_awsfulltest.py b/tests/pipelines/lint/actions_awsfulltest.py
similarity index 100%
rename from tests/lint/actions_awsfulltest.py
rename to tests/pipelines/lint/actions_awsfulltest.py
diff --git a/tests/lint/actions_awstest.py b/tests/pipelines/lint/actions_awstest.py
similarity index 100%
rename from tests/lint/actions_awstest.py
rename to tests/pipelines/lint/actions_awstest.py
diff --git a/tests/lint/actions_ci.py b/tests/pipelines/lint/actions_ci.py
similarity index 100%
rename from tests/lint/actions_ci.py
rename to tests/pipelines/lint/actions_ci.py
diff --git a/tests/lint/actions_schema_validation.py b/tests/pipelines/lint/actions_schema_validation.py
similarity index 100%
rename from tests/lint/actions_schema_validation.py
rename to tests/pipelines/lint/actions_schema_validation.py
diff --git a/tests/lint/configs.py b/tests/pipelines/lint/configs.py
similarity index 100%
rename from tests/lint/configs.py
rename to tests/pipelines/lint/configs.py
diff --git a/tests/lint/files_exist.py b/tests/pipelines/lint/files_exist.py
similarity index 95%
rename from tests/lint/files_exist.py
rename to tests/pipelines/lint/files_exist.py
index 679d209876..87508e78a8 100644
--- a/tests/lint/files_exist.py
+++ b/tests/pipelines/lint/files_exist.py
@@ -1,4 +1,3 @@
-import os
 from pathlib import Path
 
 import nf_core.pipelines.lint
@@ -31,12 +30,12 @@ def test_files_exist_missing_main(self):
     assert "File not found: `main.nf`" in results["warned"]
 
 
-def test_files_exist_depreciated_file(self):
-    """Check whether depreciated file issues warning"""
+def test_files_exist_deprecated_file(self):
+    """Check whether deprecated file issues warning"""
     new_pipeline = self._make_pipeline_copy()
 
     nf = Path(new_pipeline, "parameters.settings.json")
-    os.system(f"touch {nf}")
+    nf.touch()
 
     lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
     lint_obj._load()
diff --git a/tests/lint/files_unchanged.py b/tests/pipelines/lint/files_unchanged.py
similarity index 100%
rename from tests/lint/files_unchanged.py
rename to tests/pipelines/lint/files_unchanged.py
diff --git a/tests/lint/merge_markers.py b/tests/pipelines/lint/merge_markers.py
similarity index 100%
rename from tests/lint/merge_markers.py
rename to tests/pipelines/lint/merge_markers.py
diff --git a/tests/lint/modules_json.py b/tests/pipelines/lint/modules_json.py
similarity index 100%
rename from tests/lint/modules_json.py
rename to tests/pipelines/lint/modules_json.py
diff --git a/tests/lint/multiqc_config.py b/tests/pipelines/lint/multiqc_config.py
similarity index 100%
rename from tests/lint/multiqc_config.py
rename to tests/pipelines/lint/multiqc_config.py
diff --git a/tests/lint/nextflow_config.py b/tests/pipelines/lint/nextflow_config.py
similarity index 95%
rename from tests/lint/nextflow_config.py
rename to tests/pipelines/lint/nextflow_config.py
index b90298f542..d9157c90c6 100644
--- a/tests/lint/nextflow_config.py
+++ b/tests/pipelines/lint/nextflow_config.py
@@ -8,7 +8,7 @@
 
 def test_nextflow_config_example_pass(self):
     """Tests that config variable existence test works with good pipeline example"""
-    self.lint_obj._load_pipeline_config()
+    self.lint_obj.load_pipeline_config()
     result = self.lint_obj.nextflow_config()
     assert len(result["failed"]) == 0
     assert len(result["warned"]) == 0
@@ -18,7 +18,7 @@ def test_nextflow_config_bad_name_fail(self):
     """Tests that config variable existence test fails with bad pipeline name"""
     new_pipeline = self._make_pipeline_copy()
     lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load_pipeline_config()
+    lint_obj.load_pipeline_config()
 
     lint_obj.nf_config["manifest.name"] = "bad_name"
     result = lint_obj.nextflow_config()
@@ -30,7 +30,7 @@ def test_nextflow_config_dev_in_release_mode_failed(self):
     """Tests that config variable existence test fails with dev version in release mode"""
     new_pipeline = self._make_pipeline_copy()
     lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load_pipeline_config()
+    lint_obj.load_pipeline_config()
 
     lint_obj.release_mode = True
     lint_obj.nf_config["manifest.version"] = "dev_is_bad_name"
@@ -50,7 +50,7 @@ def test_nextflow_config_missing_test_profile_failed(self):
     with open(nf_conf_file, "w") as f:
         f.write(fail_content)
     lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load_pipeline_config()
+    lint_obj.load_pipeline_config()
     result = lint_obj.nextflow_config()
     assert len(result["failed"]) > 0
     assert len(result["warned"]) == 0
@@ -60,7 +60,7 @@ def test_default_values_match(self):
     """Test that the default values in nextflow.config match the default values defined in the nextflow_schema.json."""
     new_pipeline = self._make_pipeline_copy()
     lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load_pipeline_config()
+    lint_obj.load_pipeline_config()
     result = lint_obj.nextflow_config()
     assert len(result["failed"]) == 0
     assert len(result["warned"]) == 0
@@ -86,7 +86,7 @@ def test_default_values_fail(self):
     with open(nf_schema_file, "w") as f:
         f.write(fail_content)
     lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load_pipeline_config()
+    lint_obj.load_pipeline_config()
     result = lint_obj.nextflow_config()
     assert len(result["failed"]) == 2
     assert (
@@ -107,7 +107,7 @@ def test_catch_params_assignment_in_main_nf(self):
     with open(main_nf_file, "a") as f:
         f.write("params.max_time = 42")
     lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load_pipeline_config()
+    lint_obj.load_pipeline_config()
     result = lint_obj.nextflow_config()
     assert len(result["failed"]) == 1
     assert (
@@ -124,7 +124,7 @@ def test_allow_params_reference_in_main_nf(self):
     with open(main_nf_file, "a") as f:
         f.write("params.max_time == 42")
     lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load_pipeline_config()
+    lint_obj.load_pipeline_config()
     result = lint_obj.nextflow_config()
     assert len(result["failed"]) == 0
 
@@ -139,7 +139,7 @@ def test_default_values_ignored(self):
             "repository_type: pipeline\nlint:\n  nextflow_config:\n    - config_defaults:\n      - params.max_cpus\n"
         )
     lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load_pipeline_config()
+    lint_obj.load_pipeline_config()
     lint_obj._load_lint_config()
     result = lint_obj.nextflow_config()
     assert len(result["failed"]) == 0
@@ -173,7 +173,7 @@ def test_default_values_float(self):
         f.write(fail_content)
 
     lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load_pipeline_config()
+    lint_obj.load_pipeline_config()
     result = lint_obj.nextflow_config()
     assert len(result["failed"]) == 0
     assert len(result["warned"]) == 0
@@ -203,7 +203,7 @@ def test_default_values_float_fail(self):
         f.write(fail_content)
 
     lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load_pipeline_config()
+    lint_obj.load_pipeline_config()
     result = lint_obj.nextflow_config()
 
     assert len(result["failed"]) == 1
diff --git a/tests/lint/nfcore_yml.py b/tests/pipelines/lint/nfcore_yml.py
similarity index 100%
rename from tests/lint/nfcore_yml.py
rename to tests/pipelines/lint/nfcore_yml.py
diff --git a/tests/lint/template_strings.py b/tests/pipelines/lint/template_strings.py
similarity index 100%
rename from tests/lint/template_strings.py
rename to tests/pipelines/lint/template_strings.py
diff --git a/tests/lint/version_consistency.py b/tests/pipelines/lint/version_consistency.py
similarity index 93%
rename from tests/lint/version_consistency.py
rename to tests/pipelines/lint/version_consistency.py
index 1be57969f1..88eadce391 100644
--- a/tests/lint/version_consistency.py
+++ b/tests/pipelines/lint/version_consistency.py
@@ -6,7 +6,7 @@ def test_version_consistency(self):
     """Tests that config variable existence test fails with bad pipeline name"""
     new_pipeline = self._make_pipeline_copy()
     lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load_pipeline_config()
+    lint_obj.load_pipeline_config()
     lint_obj.nextflow_config()
 
     result = lint_obj.version_consistency()

From 11130e64d513969cfe011e8bdec4ae7da62b488b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 16 Jul 2024 16:38:59 +0200
Subject: [PATCH 061/414] make pipeline tests a subclass of TestPipeline

---
 tests/pipelines/test_bump_version.py | 127 ++++++++++-----------------
 tests/pipelines/test_create_logo.py  |  39 +++-----
 tests/pipelines/test_launch.py       |  27 ++----
 tests/test_pipelines.py              |  37 ++++++++
 4 files changed, 104 insertions(+), 126 deletions(-)
 create mode 100644 tests/test_pipelines.py

diff --git a/tests/pipelines/test_bump_version.py b/tests/pipelines/test_bump_version.py
index 260637c064..709e82427d 100644
--- a/tests/pipelines/test_bump_version.py
+++ b/tests/pipelines/test_bump_version.py
@@ -1,86 +1,55 @@
 """Some tests covering the bump_version code."""
 
-import os
-
 import yaml
 
 import nf_core.pipelines.bump_version
-import nf_core.pipelines.create.create
 import nf_core.utils
 
-
-# pass tmp_path as argument, which is a pytest feature
-# see: https://docs.pytest.org/en/latest/how-to/tmp_path.html#the-tmp-path-fixture
-def test_bump_pipeline_version(datafiles, tmp_path):
-    """Test that making a release with the working example files works"""
-
-    # Get a workflow and configs
-    test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline")
-    create_obj = nf_core.pipelines.create.create.PipelineCreate(
-        "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir
-    )
-    create_obj.init_pipeline()
-    pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)
-    pipeline_obj._load()
-
-    # Bump the version number
-    nf_core.pipelines.bump_version.bump_pipeline_version(pipeline_obj, "1.1")
-    new_pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)
-
-    # Check nextflow.config
-    new_pipeline_obj._load_pipeline_config()
-    assert new_pipeline_obj.nf_config["manifest.version"].strip("'\"") == "1.1"
-
-
-def test_dev_bump_pipeline_version(datafiles, tmp_path):
-    """Test that making a release works with a dev name and a leading v"""
-    # Get a workflow and configs
-    test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline")
-    create_obj = nf_core.pipelines.create.create.PipelineCreate(
-        "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir
-    )
-    create_obj.init_pipeline()
-    pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)
-    pipeline_obj._load()
-
-    # Bump the version number
-    nf_core.pipelines.bump_version.bump_pipeline_version(pipeline_obj, "v1.2dev")
-    new_pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)
-
-    # Check the pipeline config
-    new_pipeline_obj._load_pipeline_config()
-    assert new_pipeline_obj.nf_config["manifest.version"].strip("'\"") == "1.2dev"
-
-
-def test_bump_nextflow_version(datafiles, tmp_path):
-    # Get a workflow and configs
-    test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline")
-    create_obj = nf_core.pipelines.create.create.PipelineCreate(
-        "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir
-    )
-    create_obj.init_pipeline()
-    pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)
-    pipeline_obj._load()
-
-    # Bump the version number to a specific version, preferably one
-    # we're not already on
-    version = "22.04.3"
-    nf_core.pipelines.bump_version.bump_nextflow_version(pipeline_obj, version)
-    new_pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)
-
-    # Check nextflow.config
-    new_pipeline_obj._load_pipeline_config()
-    assert new_pipeline_obj.nf_config["manifest.nextflowVersion"].strip("'\"") == f"!>={version}"
-
-    # Check .github/workflows/ci.yml
-    with open(new_pipeline_obj._fp(".github/workflows/ci.yml")) as fh:
-        ci_yaml = yaml.safe_load(fh)
-    assert ci_yaml["jobs"]["test"]["strategy"]["matrix"]["NXF_VER"][0] == version
-
-    # Check README.md
-    with open(new_pipeline_obj._fp("README.md")) as fh:
-        readme = fh.read().splitlines()
-    assert (
-        f"[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A5{version}-23aa62.svg)]"
-        "(https://www.nextflow.io/)" in readme
-    )
+from ..test_pipelines import TestPipelines
+
+
+class TestBumpVersion(TestPipelines):
+    def test_bump_pipeline_version(self):
+        """Test that making a release with the working example files works"""
+
+        # Bump the version number
+        nf_core.pipelines.bump_version.bump_pipeline_version(self.pipeline_obj, "1.1")
+        new_pipeline_obj = nf_core.utils.Pipeline(self.pipeline_dir)
+
+        # Check nextflow.config
+        new_pipeline_obj.load_pipeline_config()
+        assert new_pipeline_obj.nf_config["manifest.version"].strip("'\"") == "1.1"
+
+    def test_dev_bump_pipeline_version(self):
+        """Test that making a release works with a dev name and a leading v"""
+        # Bump the version number
+        nf_core.pipelines.bump_version.bump_pipeline_version(self.pipeline_obj, "v1.2dev")
+        new_pipeline_obj = nf_core.utils.Pipeline(self.pipeline_dir)
+
+        # Check the pipeline config
+        new_pipeline_obj.load_pipeline_config()
+        assert new_pipeline_obj.nf_config["manifest.version"].strip("'\"") == "1.2dev"
+
+    def test_bump_nextflow_version(self):
+        # Bump the version number to a specific version, preferably one
+        # we're not already on
+        version = "22.04.3"
+        nf_core.pipelines.bump_version.bump_nextflow_version(self.pipeline_obj, version)
+        new_pipeline_obj = nf_core.utils.Pipeline(self.pipeline_dir)
+        new_pipeline_obj._load()
+
+        # Check nextflow.config
+        assert new_pipeline_obj.nf_config["manifest.nextflowVersion"].strip("'\"") == f"!>={version}"
+
+        # Check .github/workflows/ci.yml
+        with open(new_pipeline_obj._fp(".github/workflows/ci.yml")) as fh:
+            ci_yaml = yaml.safe_load(fh)
+        assert ci_yaml["jobs"]["test"]["strategy"]["matrix"]["NXF_VER"][0] == version
+
+        # Check README.md
+        with open(new_pipeline_obj._fp("README.md")) as fh:
+            readme = fh.read().splitlines()
+        assert (
+            f"[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A5{version}-23aa62.svg)]"
+            "(https://www.nextflow.io/)" in readme
+        )
diff --git a/tests/pipelines/test_create_logo.py b/tests/pipelines/test_create_logo.py
index 8942894ce2..9ff9fce562 100644
--- a/tests/pipelines/test_create_logo.py
+++ b/tests/pipelines/test_create_logo.py
@@ -1,35 +1,24 @@
 """Test covering the create-logo command."""
 
-import tempfile
-import unittest
 from pathlib import Path
 
 import nf_core.pipelines.create_logo
 
+from ..test_pipelines import TestPipelines
 
-class TestCreateLogo(unittest.TestCase):
-    """Class for create-logo tests"""
-
-    # create tempdir in setup step
-    def setUp(self):
-        self.tempdir = tempfile.TemporaryDirectory()
-        self.tempdir_path = Path(self.tempdir.name)
-
-    # delete tempdir in teardown step
-    def tearDown(self):
-        self.tempdir.cleanup()
 
+class TestCreateLogo(TestPipelines):
     def test_create_logo_png(self):
         """Test that the create-logo command works for PNGs"""
 
         # Create a logo
-        logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path)
+        logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir)
         # Check that the file exists
         self.assertTrue(logo_fn.is_file())
         # Check that the file is a PNG
         self.assertTrue(logo_fn.suffix == ".png")
         # Check that the file is the right size
-        fixture_fn = Path(__file__).parent / "fixtures" / "create_logo.png"
+        fixture_fn = Path(__file__).parent.parent / "fixtures" / "create_logo.png"
         # allow some flexibility in the file size
         self.assertTrue(int(logo_fn.stat().st_size / 1000) == int(fixture_fn.stat().st_size / 1000))
 
@@ -37,13 +26,13 @@ def test_create_logo_png_dark(self):
         """Test that the create-logo command works for dark PNGs"""
 
         # Create a logo
-        logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path, theme="dark")
+        logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir, theme="dark")
         # Check that the file exists
         self.assertTrue(logo_fn.is_file())
         # Check that the file is a PNG
         self.assertTrue(logo_fn.suffix == ".png")
         # Check that the file is the right size
-        fixture_fn = Path(__file__).parent / "fixtures" / "create_logo_dark.png"
+        fixture_fn = Path(__file__).parent.parent / "fixtures" / "create_logo_dark.png"
         # allow some flexibility in the file size
         self.assertTrue(int(logo_fn.stat().st_size / 1000) == int(fixture_fn.stat().st_size / 1000))
 
@@ -51,13 +40,13 @@ def test_create_log_png_width(self):
         """Test that the create-logo command works for PNGs with a custom width"""
 
         # Create a logo
-        logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path, width=100)
+        logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir, width=100)
         # Check that the file exists
         self.assertTrue(logo_fn.is_file())
         # Check that the file is a PNG
         self.assertTrue(logo_fn.suffix == ".png")
         # Check that the file is the right size
-        fixture_fn = Path(__file__).parent / "fixtures" / "create_logo_width100.png"
+        fixture_fn = Path(__file__).parent.parent / "fixtures" / "create_logo_width100.png"
         # allow some flexibility in the file size
         self.assertTrue(int(logo_fn.stat().st_size / 100) == int(fixture_fn.stat().st_size / 100))
 
@@ -65,12 +54,12 @@ def test_create_logo_twice(self):
         """Test that the create-logo command returns an info message when run twice"""
 
         # Create a logo
-        logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path)
+        logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir)
         # Check that the file exists
         self.assertTrue(logo_fn.is_file())
         # Create the logo again and capture the log output
         with self.assertLogs(level="INFO") as log:
-            nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path)
+            nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir)
             # Check that the log message is correct
             self.assertIn("Logo already exists", log.output[0])
 
@@ -79,14 +68,14 @@ def test_create_logo_without_text_fail(self):
 
         # Create a logo
         with self.assertRaises(UserWarning):
-            nf_core.pipelines.create_logo.create_logo("", self.tempdir_path)
+            nf_core.pipelines.create_logo.create_logo("", self.pipeline_dir)
 
     def test_create_logo_with_filename(self):
         """Test that the create-logo command works with a custom filename"""
 
         # Create a logo
         logo_fn = nf_core.pipelines.create_logo.create_logo(
-            "pipes", Path(self.tempdir_path / "custom_dir"), filename="custom"
+            "pipes", Path(self.pipeline_dir / "custom_dir"), filename="custom"
         )
         # Check that the file exists
         self.assertTrue(logo_fn.is_file())
@@ -99,7 +88,7 @@ def test_create_logo_svg(self):
         """Test that the create-logo command works for SVGs"""
 
         # Create a logo
-        logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path, format="svg")
+        logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir, format="svg")
         # Check that the file exists
         self.assertTrue(logo_fn.is_file())
         # Check that the file is a SVG
@@ -115,7 +104,7 @@ def test_create_logo_svg_dark(self):
         """Test that the create-logo command works for svgs and dark theme"""
 
         # Create a logo
-        logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path, format="svg", theme="dark")
+        logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir, format="svg", theme="dark")
         # Check that the file exists
         self.assertTrue(logo_fn.is_file())
         # Check that the file is a SVG
diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py
index b4b285a3c9..c9efa5aa63 100644
--- a/tests/pipelines/test_launch.py
+++ b/tests/pipelines/test_launch.py
@@ -2,36 +2,18 @@
 
 import json
 import os
-import shutil
-from pathlib import Path
-from unittest import TestCase, mock
+from unittest import mock
 
 import pytest
 
 import nf_core.pipelines.create.create
 import nf_core.pipelines.launch
 
-from ..utils import create_tmp_pipeline, with_temporary_file, with_temporary_folder
+from ..test_pipelines import TestPipelines
+from ..utils import with_temporary_file, with_temporary_folder
 
 
-class TestLaunch(TestCase):
-    """Class for launch tests"""
-
-    def setUp(self):
-        """Create a new PipelineSchema and Launch objects"""
-        self.tmp_dir, self.template_dir, self.pipeline_name, self.pipeline_dir = create_tmp_pipeline()
-        self.nf_params_fn = os.path.join(self.tmp_dir, "nf-params.json")
-        self.launcher = nf_core.pipelines.launch.Launch(self.pipeline_dir, params_out=self.nf_params_fn)
-
-    def tearDown(self):
-        """Clean up temporary files and folders"""
-
-        if Path(self.nf_params_fn).exists():
-            Path(self.nf_params_fn).unlink()
-
-        if Path(self.tmp_dir).exists():
-            shutil.rmtree(self.tmp_dir)
-
+class TestLaunch(TestPipelines):
     @mock.patch.object(nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True])
     @mock.patch.object(nf_core.pipelines.launch.Launch, "launch_web_gui")
     def test_launch_pipeline(self, mock_webbrowser, mock_lauch_web_gui):
@@ -43,6 +25,7 @@ def test_launch_file_exists(self, mock_confirm):
         """Test that we detect an existing params file and return"""
         # Make an empty params file to be overwritten
         open(self.nf_params_fn, "a").close()
+
         # Try and to launch, return with error
         assert self.launcher.launch_pipeline() is False
 
diff --git a/tests/test_pipelines.py b/tests/test_pipelines.py
new file mode 100644
index 0000000000..461f046f52
--- /dev/null
+++ b/tests/test_pipelines.py
@@ -0,0 +1,37 @@
+import shutil
+from pathlib import Path
+from unittest import TestCase
+
+from git import Repo
+
+import nf_core.pipelines.launch
+import nf_core.pipelines.lint
+from nf_core.utils import Pipeline
+
+from .utils import create_tmp_pipeline
+
+
+class TestPipelines(TestCase):
+    def setUp(self) -> None:
+        """Create a new Pipeline for testing"""
+        self.tmp_dir, self.template_dir, self.pipeline_name, self.pipeline_dir = create_tmp_pipeline()
+        self.pipeline_obj = Pipeline(self.pipeline_dir)
+        Repo.init(self.pipeline_dir)
+        self.pipeline_obj._load()
+
+        self.nf_params_fn = Path(self.pipeline_dir, "nf-params.json")
+        self.launcher = nf_core.pipelines.launch.Launch(self.pipeline_dir, params_out=self.nf_params_fn)
+
+        self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir)
+
+    def tearDown(self) -> None:
+        """Remove the test pipeline directory"""
+        shutil.rmtree(self.tmp_dir)
+
+    def _make_pipeline_copy(self):
+        """Make a copy of the test pipeline that can be edited
+
+        Returns: Path to new temp directory with pipeline"""
+        new_pipeline = self.tmp_dir / "nf-core-testpipeline-copy"
+        shutil.copytree(self.pipeline_dir, new_pipeline)
+        return new_pipeline

From 20f0ba6ca7f30acb113e5234e60693eba89a410d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 16 Jul 2024 16:40:14 +0200
Subject: [PATCH 062/414] move pytest.ini into pyproject.toml

---
 pyproject.toml | 3 +++
 pytest.ini     | 7 -------
 2 files changed, 3 insertions(+), 7 deletions(-)
 delete mode 100644 pytest.ini

diff --git a/pyproject.toml b/pyproject.toml
index 8168bd7c11..4499324445 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,6 +5,9 @@ requires = ["setuptools>=40.6.0", "wheel"]
 [tool.pytest.ini_options]
 markers = ["datafiles: load datafiles"]
 testpaths = ["tests"]
+python_files = ["test_*.py"]
+# automatically run coroutine tests with asyncio
+asyncio_mode = ["auto"]
 norecursedirs = [
     ".*",
     "build",
diff --git a/pytest.ini b/pytest.ini
deleted file mode 100644
index fcbd03fa45..0000000000
--- a/pytest.ini
+++ /dev/null
@@ -1,7 +0,0 @@
-[pytest]
-testpaths =
-    tests
-python_files = test_*.py
-
-# automatically run coroutine tests with asyncio
-asyncio_mode = auto

From 36050fd44b5dcfb70c6d4fe8b40cb6f45ebc5fd2 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 16 Jul 2024 16:54:32 +0200
Subject: [PATCH 063/414] migrate more tests to pathilb, use commonly shared
 TEST_DATA_DIR var

---
 nf_core/components/lint/__init__.py |  2 +-
 nf_core/modules/modules_json.py     |  8 ++---
 nf_core/pipelines/create/create.py  |  6 ++--
 nf_core/pipelines/download.py       |  7 ++--
 nf_core/pipelines/lint/__init__.py  |  2 +-
 nf_core/pipelines/sync.py           |  5 +--
 nf_core/utils.py                    | 56 +++++++++++++++++------------
 tests/pipelines/test_create.py      |  4 +--
 tests/pipelines/test_download.py    | 12 +++----
 tests/test_utils.py                 |  4 +--
 tests/utils.py                      | 13 +++----
 11 files changed, 66 insertions(+), 53 deletions(-)

diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index 499d31e71e..6d47f1e7a8 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -117,7 +117,7 @@ def __init__(
                     )
                     for comp in self.get_local_components()
                 ]
-            self.config = nf_core.utils.fetch_wf_config(self.dir, cache_config=True)
+            self.config = nf_core.utils.fetch_wf_config(Path(self.dir), cache_config=True)
         else:
             component_dir = Path(
                 self.dir,
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index b0a4fa661f..ca5d9de072 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -38,10 +38,10 @@ def __init__(self, pipeline_dir: str):
         Args:
             pipeline_dir (str): The pipeline directory
         """
-        self.dir = pipeline_dir
-        self.modules_dir = Path(self.dir, "modules")
-        self.subworkflows_dir = Path(self.dir, "subworkflows")
-        self.modules_json_path = Path(self.dir, "modules.json")
+        self.dir = Path(pipeline_dir)
+        self.modules_dir = self.dir / "modules"
+        self.subworkflows_dir = self.dir / "subworkflows"
+        self.modules_json_path = self.dir / "modules.json"
         self.modules_json = None
         self.pipeline_modules = None
         self.pipeline_subworkflows = None
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index bdbbca646f..e9f37306f5 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -50,7 +50,7 @@ def __init__(
         version: str = "1.0.0dev",
         no_git: bool = False,
         force: bool = False,
-        outdir: Optional[str] = None,
+        outdir: Optional[Union[Path, str]] = None,
         template_config: Optional[Union[str, CreateConfig, Path]] = None,
         organisation: str = "nf-core",
         from_config_file: bool = False,
@@ -61,7 +61,7 @@ def __init__(
             self.config = template_config
         elif from_config_file:
             # Try reading config file
-            _, config_yml = nf_core.utils.load_tools_config(outdir if outdir else ".")
+            _, config_yml = nf_core.utils.load_tools_config(str(outdir) if outdir else ".")
             # Obtain a CreateConfig object from `.nf-core.yml` config file
             if "template" in config_yml:
                 self.config = CreateConfig(**config_yml["template"])
@@ -372,6 +372,8 @@ def render_template(self):
             config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir)
             with open(config_fn, "w") as fh:
                 config_yml.update(template=self.config.model_dump())
+                # convert posix path to string for yaml dump
+                config_yml["template"]["outdir"] = str(config_yml["template"]["outdir"])
                 yaml.safe_dump(config_yml, fh)
                 log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
                 run_prettier_on_file(self.outdir / config_fn)
diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py
index 43b63d8192..f16430b0a8 100644
--- a/nf_core/pipelines/download.py
+++ b/nf_core/pipelines/download.py
@@ -10,6 +10,7 @@
 import tarfile
 import textwrap
 from datetime import datetime
+from pathlib import Path
 from typing import List, Optional, Tuple
 from zipfile import ZipFile
 
@@ -697,7 +698,7 @@ def wf_use_local_configs(self, revision_dirname):
         with open(nfconfig_fn, "w") as nfconfig_fh:
             nfconfig_fh.write(nfconfig)
 
-    def find_container_images(self, workflow_directory):
+    def find_container_images(self, workflow_directory: str) -> None:
         """Find container image names for workflow.
 
         Starts by using `nextflow config` to pull out any process.container
@@ -716,7 +717,7 @@ def find_container_images(self, workflow_directory):
         module_findings = []
 
         # Use linting code to parse the pipeline nextflow config
-        self.nf_config = nf_core.utils.fetch_wf_config(workflow_directory)
+        self.nf_config = nf_core.utils.fetch_wf_config(Path(workflow_directory))
 
         # Find any config variables that look like a container
         for k, v in self.nf_config.items():
@@ -1007,7 +1008,7 @@ def gather_registries(self, workflow_directory: str) -> None:
 
         # should exist, because find_container_images() is always called before
         if not self.nf_config:
-            self.nf_config = nf_core.utils.fetch_wf_config(workflow_directory)
+            self.nf_config = nf_core.utils.fetch_wf_config(Path(workflow_directory))
 
         # Select registries defined in pipeline config
         configured_registries = [
diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
index cf5ba3913f..b40f0ee292 100644
--- a/nf_core/pipelines/lint/__init__.py
+++ b/nf_core/pipelines/lint/__init__.py
@@ -559,7 +559,7 @@ def run_linting(
 
     # Load the various pipeline configs
     lint_obj._load_lint_config()
-    lint_obj._load_pipeline_config()
+    lint_obj.load_pipeline_config()
     lint_obj._list_files()
 
     # Create the modules lint object
diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index f9a874c7e4..a309fa8c3b 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -5,6 +5,7 @@
 import os
 import re
 import shutil
+from pathlib import Path
 
 import git
 import questionary
@@ -69,7 +70,7 @@ def __init__(
     ):
         """Initialise syncing object"""
 
-        self.pipeline_dir = os.path.abspath(pipeline_dir)
+        self.pipeline_dir = Path(pipeline_dir).resolve()
         self.from_branch = from_branch
         self.original_branch = None
         self.original_merge_branch = f"nf-core-template-merge-{nf_core.__version__}"
@@ -209,7 +210,7 @@ def get_wf_config(self):
 
         # Fetch workflow variables
         log.debug("Fetching workflow config variables")
-        self.wf_config = nf_core.utils.fetch_wf_config(self.pipeline_dir)
+        self.wf_config = nf_core.utils.fetch_wf_config(Path(self.pipeline_dir))
 
         # Check that we have the required variables
         for rvar in self.required_config_vars:
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 48d1c3ca3d..cf624935b3 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -141,7 +141,7 @@ def __init__(self, wf_path):
         self.files = []
         self.git_sha = None
         self.minNextflowVersion = None
-        self.wf_path = wf_path
+        self.wf_path = Path(wf_path)
         self.pipeline_name = None
         self.pipeline_prefix = None
         self.schema_obj = None
@@ -156,13 +156,15 @@ def __init__(self, wf_path):
         if os.environ.get("GITHUB_PR_COMMIT", "") != "":
             self.git_sha = os.environ["GITHUB_PR_COMMIT"]
 
-    def _load(self):
+    def __repr__(self) -> str:
+        return f"<Pipeline '{self.pipeline_name}' at {self.wf_path}>"
+
+    def _load(self) -> bool:
         """Run core load functions"""
-        self._list_files()
-        self._load_pipeline_config()
-        self._load_conda_environment()
 
-    def _list_files(self):
+        return self._list_files() and self.load_pipeline_config() and self._load_conda_environment()
+
+    def _list_files(self) -> bool:
         """Get a list of all files in the pipeline"""
         try:
             # First, try to get the list of files using git
@@ -174,18 +176,36 @@ def _list_files(self):
                     self.files.append(full_fn)
                 else:
                     log.debug(f"`git ls-files` returned '{full_fn}' but could not open it!")
+            return True
         except subprocess.CalledProcessError as e:
             # Failed, so probably not initialised as a git repository - just a list of all files
             log.debug(f"Couldn't call 'git ls-files': {e}")
             self.files = []
             for subdir, _, files in os.walk(self.wf_path):
                 for fn in files:
-                    self.files.append(Path(subdir) / fn)
+                    self.files.append(Path(subdir, str(fn)))
+            if len(self.files) > 0:
+                return True
+            return False
+
+    def _load_conda_environment(self) -> bool:
+        """Try to load the pipeline environment.yml file, if it exists"""
+        try:
+            with open(Path(self.wf_path, "environment.yml")) as fh:
+                self.conda_config = yaml.safe_load(fh)
+            return True
+        except FileNotFoundError:
+            log.debug("No conda `environment.yml` file found.")
+            return False
 
-    def _load_pipeline_config(self):
+    def _fp(self, fn):
+        """Convenience function to get full path to a file in the pipeline"""
+        return os.path.join(self.wf_path, fn)
+
+    def load_pipeline_config(self) -> bool:
         """Get the nextflow config for this pipeline
 
-        Once loaded, set a few convienence reference class attributes
+        Once loaded, set a few convenience reference class attributes
         """
         self.nf_config = fetch_wf_config(self.wf_path)
 
@@ -194,18 +214,8 @@ def _load_pipeline_config(self):
         nextflow_version_match = re.search(r"[0-9\.]+(-edge)?", self.nf_config.get("manifest.nextflowVersion", ""))
         if nextflow_version_match:
             self.minNextflowVersion = nextflow_version_match.group(0)
-
-    def _load_conda_environment(self):
-        """Try to load the pipeline environment.yml file, if it exists"""
-        try:
-            with open(os.path.join(self.wf_path, "environment.yml")) as fh:
-                self.conda_config = yaml.safe_load(fh)
-        except FileNotFoundError:
-            log.debug("No conda `environment.yml` file found.")
-
-    def _fp(self, fn):
-        """Convenience function to get full path to a file in the pipeline"""
-        return os.path.join(self.wf_path, fn)
+            return True
+        return False
 
 
 def is_pipeline_directory(wf_path):
@@ -229,7 +239,7 @@ def is_pipeline_directory(wf_path):
             raise UserWarning(warning)
 
 
-def fetch_wf_config(wf_path: str, cache_config: bool = True) -> dict:
+def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict:
     """Uses Nextflow to retrieve the the configuration variables
     from a Nextflow workflow.
 
@@ -263,7 +273,7 @@ def fetch_wf_config(wf_path: str, cache_config: bool = True) -> dict:
     concat_hash = ""
     for fn in ["nextflow.config", "main.nf"]:
         try:
-            with open(Path(wf_path, fn), "rb") as fh:
+            with open(wf_path / fn, "rb") as fh:
                 concat_hash += hashlib.sha256(fh.read()).hexdigest()
         except FileNotFoundError:
             pass
diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py
index d93b26bd1a..bb27445e70 100644
--- a/tests/pipelines/test_create.py
+++ b/tests/pipelines/test_create.py
@@ -2,16 +2,14 @@
 
 import os
 import unittest
-from pathlib import Path
 
 import git
 import yaml
 
 import nf_core.pipelines.create.create
 
-from ..utils import with_temporary_folder
+from ..utils import TEST_DATA_DIR, with_temporary_folder
 
-TEST_DATA_DIR = Path(__file__).parent / "data"
 PIPELINE_TEMPLATE_YML = TEST_DATA_DIR / "pipeline_create_template.yml"
 PIPELINE_TEMPLATE_YML_SKIP = TEST_DATA_DIR / "pipeline_create_template_skip.yml"
 
diff --git a/tests/pipelines/test_download.py b/tests/pipelines/test_download.py
index ebb76fef72..7ed6de3fa7 100644
--- a/tests/pipelines/test_download.py
+++ b/tests/pipelines/test_download.py
@@ -18,7 +18,7 @@
 from nf_core.synced_repo import SyncedRepo
 from nf_core.utils import run_cmd
 
-from ..utils import with_temporary_folder
+from ..utils import TEST_DATA_DIR, with_temporary_folder
 
 
 class DownloadTest(unittest.TestCase):
@@ -139,12 +139,12 @@ def test_wf_use_local_configs(self, tmp_path):
 
         with tempfile.TemporaryDirectory() as test_outdir:
             download_obj = DownloadWorkflow(pipeline="dummy", revision="1.2.0", outdir=test_outdir)
-            shutil.copytree(test_pipeline_dir, os.path.join(test_outdir, "workflow"))
+            shutil.copytree(test_pipeline_dir, Path(test_outdir, "workflow"))
             download_obj.download_configs()
 
             # Test the function
             download_obj.wf_use_local_configs("workflow")
-            wf_config = nf_core.utils.fetch_wf_config(os.path.join(test_outdir, "workflow"), cache_config=False)
+            wf_config = nf_core.utils.fetch_wf_config(Path(test_outdir, "workflow"), cache_config=False)
             assert wf_config["params.custom_config_base"] == f"{test_outdir}/workflow/../configs/"
 
     #
@@ -173,7 +173,7 @@ def test_find_container_images_config_basic(self, tmp_path, mock_fetch_wf_config
     @mock.patch("nf_core.utils.fetch_wf_config")
     def test__find_container_images_config_nextflow(self, tmp_path, mock_fetch_wf_config):
         download_obj = DownloadWorkflow(pipeline="dummy", outdir=tmp_path)
-        result = run_cmd("nextflow", f"config -flat {Path(__file__).resolve().parent / 'data/mock_config_containers'}")
+        result = run_cmd("nextflow", f"config -flat {TEST_DATA_DIR}'/mock_config_containers'")
         if result is not None:
             nfconfig_raw, _ = result
             config = {}
@@ -203,7 +203,7 @@ def test__find_container_images_config_nextflow(self, tmp_path, mock_fetch_wf_co
     def test_find_container_images_modules(self, tmp_path, mock_fetch_wf_config):
         download_obj = DownloadWorkflow(pipeline="dummy", outdir=tmp_path)
         mock_fetch_wf_config.return_value = {}
-        download_obj.find_container_images(Path(__file__).resolve().parent / "data/mock_module_containers")
+        download_obj.find_container_images(TEST_DATA_DIR / "mock_module_containers")
 
         # mock_docker_single_quay_io.nf
         assert "quay.io/biocontainers/singlequay:1.9--pyh9f0ad1d_0" in download_obj.containers
@@ -546,7 +546,7 @@ def test_remote_container_functionality(self, tmp_dir):
             outdir=os.path.join(tmp_dir, "new"),
             revision="3.9",
             compress_type="none",
-            container_cache_index=Path(__file__).resolve().parent / "data/testdata_remote_containers.txt",
+            container_cache_index=TEST_DATA_DIR / "data/testdata_remote_containers.txt",
         )
 
         download_obj.include_configs = False  # suppress prompt, because stderr.is_interactive doesn't.
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 89ba0444ff..7afe1a532f 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -95,9 +95,9 @@ def test_rich_force_colours_true(self):
         os.environ.pop("PY_COLORS", None)
         assert nf_core.utils.rich_force_colors() is True
 
-    def test_load_pipeline_config(self):
+    def testload_pipeline_config(self):
         """Load the pipeline Nextflow config"""
-        self.pipeline_obj._load_pipeline_config()
+        self.pipeline_obj.load_pipeline_config()
         assert self.pipeline_obj.nf_config["dag.enabled"] == "true"
 
     # TODO nf-core: Assess and strip out if no longer required for DSL2
diff --git a/tests/utils.py b/tests/utils.py
index 9a0fd0896f..7be0799d6f 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -3,8 +3,8 @@
 """
 
 import functools
-import os
 import tempfile
+from pathlib import Path
 from typing import Any, Callable, Tuple
 
 import responses
@@ -12,6 +12,7 @@
 import nf_core.modules
 import nf_core.pipelines.create.create
 
+TEST_DATA_DIR = Path(__file__).parent / "data"
 OLD_TRIMGALORE_SHA = "9b7a3bdefeaad5d42324aa7dd50f87bea1b04386"
 OLD_TRIMGALORE_BRANCH = "mimic-old-trimgalore"
 GITLAB_URL = "https://gitlab.com/nf-core/modules-test.git"
@@ -93,14 +94,14 @@ def mock_biocontainers_api_calls(rsps: responses.RequestsMock, module: str, vers
     rsps.get(biocontainers_api_url, json=biocontainers_mock, status=200)
 
 
-def create_tmp_pipeline() -> Tuple[str, str, str, str]:
+def create_tmp_pipeline() -> Tuple[Path, Path, str, Path]:
     """Create a new Pipeline for testing"""
 
-    tmp_dir = tempfile.mkdtemp()
-    root_repo_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
-    template_dir = os.path.join(root_repo_dir, "nf_core", "pipeline-template")
+    tmp_dir = Path(tempfile.TemporaryDirectory().name)
+    root_repo_dir = Path(__file__).resolve().parent.parent
+    template_dir = Path(root_repo_dir, "nf_core", "pipeline-template")
     pipeline_name = "mypipeline"
-    pipeline_dir = os.path.join(tmp_dir, pipeline_name)
+    pipeline_dir = Path(tmp_dir, pipeline_name)
 
     nf_core.pipelines.create.create.PipelineCreate(
         pipeline_name, "it is mine", "me", no_git=True, outdir=pipeline_dir

From fb274107d592b16e7634cc64db149a6b514e88db Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 16 Jul 2024 16:55:00 +0200
Subject: [PATCH 064/414] use testpipeline class in test_lint

---
 tests/pipelines/test_lint.py | 83 +++++++++++-------------------------
 1 file changed, 26 insertions(+), 57 deletions(-)

diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py
index 460c8f03d8..8530fea5ad 100644
--- a/tests/pipelines/test_lint.py
+++ b/tests/pipelines/test_lint.py
@@ -3,51 +3,20 @@
 import fnmatch
 import json
 import os
-import shutil
-import tempfile
-import unittest
+from pathlib import Path
 
 import yaml
 
 import nf_core.pipelines.create.create
 import nf_core.pipelines.lint
 
+from ..test_pipelines import TestPipelines
 from ..utils import with_temporary_folder
 
 
-class TestLint(unittest.TestCase):
+class TestLint(TestPipelines):
     """Class for lint tests"""
 
-    def setUp(self):
-        """Function that runs at start of tests for common resources
-
-        Use nf_core.pipelines.create() to make a pipeline that we can use for testing
-        """
-
-        self.tmp_dir = tempfile.mkdtemp()
-        self.test_pipeline_dir = os.path.join(self.tmp_dir, "nf-core-testpipeline")
-        self.create_obj = nf_core.pipelines.create.create.PipelineCreate(
-            "testpipeline", "This is a test pipeline", "Test McTestFace", outdir=self.test_pipeline_dir
-        )
-        self.create_obj.init_pipeline()
-
-        # Base lint object on this directory
-        self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.test_pipeline_dir)
-
-    def tearDown(self):
-        """Clean up temporary files and folders"""
-
-        if os.path.exists(self.tmp_dir):
-            shutil.rmtree(self.tmp_dir)
-
-    def _make_pipeline_copy(self):
-        """Make a copy of the test pipeline that can be edited
-
-        Returns: Path to new temp directory with pipeline"""
-        new_pipeline = os.path.join(self.tmp_dir, "nf-core-testpipeline-copy")
-        shutil.copytree(self.test_pipeline_dir, new_pipeline)
-        return new_pipeline
-
     ##########################
     # CORE lint.py FUNCTIONS #
     ##########################
@@ -56,7 +25,7 @@ def test_run_linting_function(self):
 
         We don't really check any of this code as it's just a series of function calls
         and we're testing each of those individually. This is mostly to check for syntax errors."""
-        nf_core.pipelines.lint.run_linting(self.test_pipeline_dir, False)
+        nf_core.pipelines.lint.run_linting(self.pipeline_dir, False)
 
     def test_init_pipeline_lint(self):
         """Simply create a PipelineLint object.
@@ -64,11 +33,11 @@ def test_init_pipeline_lint(self):
         This checks that all of the lint test imports are working properly,
         we also check that the git sha was found and that the release flag works properly
         """
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.test_pipeline_dir, True)
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir, True)
 
         # Tests that extra test is added for release mode
         assert "version_consistency" in lint_obj.lint_tests
-
+        assert lint_obj.git_sha
         # Tests that parent nf_core.utils.Pipeline class __init__() is working to find git hash
         assert len(lint_obj.git_sha) > 0
 
@@ -86,7 +55,7 @@ def test_load_lint_config_ignore_all_tests(self):
 
         # Make a config file listing all test names
         config_dict = {"lint": {test_name: False for test_name in lint_obj.lint_tests}}
-        with open(os.path.join(new_pipeline, ".nf-core.yml"), "w") as fh:
+        with open(Path(new_pipeline, ".nf-core.yml"), "w") as fh:
             yaml.dump(config_dict, fh)
 
         # Load the new lint config file and check
@@ -130,7 +99,7 @@ def test_json_output(self, tmp_dir):
         self.lint_obj.warned.append(("test_three", "This test gave a warning"))
 
         # Make a temp dir for the JSON output
-        json_fn = os.path.join(tmp_dir, "lint_results.json")
+        json_fn = Path(tmp_dir, "lint_results.json")
         self.lint_obj._save_json_results(json_fn)
 
         # Load created JSON file and check its contents
@@ -156,7 +125,7 @@ def test_sphinx_md_files(self):
         """Check that we have .md files for all lint module code,
         and that there are no unexpected files (eg. deleted lint tests)"""
 
-        docs_basedir = os.path.join(
+        docs_basedir = Path(
             os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "docs", "api", "_src", "pipeline_lint_tests"
         )
 
@@ -164,12 +133,12 @@ def test_sphinx_md_files(self):
         existing_docs = []
         for fn in os.listdir(docs_basedir):
             if fnmatch.fnmatch(fn, "*.md") and not fnmatch.fnmatch(fn, "index.md"):
-                existing_docs.append(os.path.join(docs_basedir, fn))
+                existing_docs.append(Path(docs_basedir, fn))
 
         # Check .md files against each test name
         lint_obj = nf_core.pipelines.lint.PipelineLint("", True)
         for test_name in lint_obj.lint_tests:
-            fn = os.path.join(docs_basedir, f"{test_name}.md")
+            fn = Path(docs_basedir, f"{test_name}.md")
             assert os.path.exists(fn), f"Could not find lint docs .md file: {fn}"
             existing_docs.remove(fn)
 
@@ -179,34 +148,34 @@ def test_sphinx_md_files(self):
     #######################
     # SPECIFIC LINT TESTS #
     #######################
-    from ..lint.actions_awsfulltest import (  # type: ignore[misc]
+    from .lint.actions_awsfulltest import (  # type: ignore[misc]
         test_actions_awsfulltest_fail,
         test_actions_awsfulltest_pass,
         test_actions_awsfulltest_warn,
     )
-    from ..lint.actions_awstest import (  # type: ignore[misc]
+    from .lint.actions_awstest import (  # type: ignore[misc]
         test_actions_awstest_fail,
         test_actions_awstest_pass,
     )
-    from ..lint.actions_ci import (  # type: ignore[misc]
+    from .lint.actions_ci import (  # type: ignore[misc]
         test_actions_ci_fail_wrong_nf,
         test_actions_ci_fail_wrong_trigger,
         test_actions_ci_pass,
     )
-    from ..lint.actions_schema_validation import (  # type: ignore[misc]
+    from .lint.actions_schema_validation import (  # type: ignore[misc]
         test_actions_schema_validation_fails_for_additional_property,
         test_actions_schema_validation_missing_jobs,
         test_actions_schema_validation_missing_on,
     )
-    from ..lint.configs import (  # type: ignore[misc]
+    from .lint.configs import (  # type: ignore[misc]
         test_ignore_base_config,
         test_ignore_modules_config,
         test_superfluous_withname_in_base_config_fails,
         test_superfluous_withname_in_modules_config_fails,
         test_withname_in_modules_config,
     )
-    from ..lint.files_exist import (  # type: ignore[misc]
-        test_files_exist_depreciated_file,
+    from .lint.files_exist import (  # type: ignore[misc]
+        test_files_exist_deprecated_file,
         test_files_exist_fail_conditional,
         test_files_exist_missing_config,
         test_files_exist_missing_main,
@@ -214,13 +183,13 @@ def test_sphinx_md_files(self):
         test_files_exist_pass_conditional,
         test_files_exist_pass_conditional_nfschema,
     )
-    from ..lint.files_unchanged import (  # type: ignore[misc]
+    from .lint.files_unchanged import (  # type: ignore[misc]
         test_files_unchanged_fail,
         test_files_unchanged_pass,
     )
-    from ..lint.merge_markers import test_merge_markers_found  # type: ignore[misc]
-    from ..lint.modules_json import test_modules_json_pass  # type: ignore[misc]
-    from ..lint.multiqc_config import (  # type: ignore[misc]
+    from .lint.merge_markers import test_merge_markers_found  # type: ignore[misc]
+    from .lint.modules_json import test_modules_json_pass  # type: ignore[misc]
+    from .lint.multiqc_config import (  # type: ignore[misc]
         test_multiqc_config_exists,
         test_multiqc_config_ignore,
         test_multiqc_config_missing_report_section_order,
@@ -229,7 +198,7 @@ def test_sphinx_md_files(self):
         test_multiqc_config_report_comment_release_succeed,
         test_multiqc_incorrect_export_plots,
     )
-    from ..lint.nextflow_config import (  # type: ignore[misc]
+    from .lint.nextflow_config import (  # type: ignore[misc]
         test_allow_params_reference_in_main_nf,
         test_catch_params_assignment_in_main_nf,
         test_default_values_fail,
@@ -242,14 +211,14 @@ def test_sphinx_md_files(self):
         test_nextflow_config_example_pass,
         test_nextflow_config_missing_test_profile_failed,
     )
-    from ..lint.nfcore_yml import (  # type: ignore[misc]
+    from .lint.nfcore_yml import (  # type: ignore[misc]
         test_nfcore_yml_fail_nfcore_version,
         test_nfcore_yml_fail_repo_type,
         test_nfcore_yml_pass,
     )
-    from ..lint.template_strings import (  # type: ignore[misc]
+    from .lint.template_strings import (  # type: ignore[misc]
         test_template_strings,
         test_template_strings_ignore_file,
         test_template_strings_ignored,
     )
-    from ..lint.version_consistency import test_version_consistency  # type: ignore[misc]
+    from .lint.version_consistency import test_version_consistency  # type: ignore[misc]

From 1d2076b511665034153d2ed3010508479f1e8e27 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 16 Jul 2024 17:56:42 +0200
Subject: [PATCH 065/414] fix tests

---
 nf_core/utils.py                 | 24 ++++++++++++------------
 tests/pipelines/test_download.py |  4 ++--
 tests/pipelines/test_lint.py     |  4 +---
 tests/pipelines/test_list.py     | 28 ++++++++++++++--------------
 tests/test_pipelines.py          |  3 ---
 5 files changed, 29 insertions(+), 34 deletions(-)

diff --git a/nf_core/utils.py b/nf_core/utils.py
index cf624935b3..9b3775d62d 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -19,7 +19,7 @@
 import time
 from contextlib import contextmanager
 from pathlib import Path
-from typing import Generator, Tuple, Union
+from typing import Dict, Generator, List, Optional, Tuple, Union
 
 import git
 import prompt_toolkit
@@ -135,22 +135,22 @@ class Pipeline:
 
     def __init__(self, wf_path):
         """Initialise pipeline object"""
-        self.conda_config = {}
-        self.conda_package_info = {}
-        self.nf_config = {}
-        self.files = []
-        self.git_sha = None
-        self.minNextflowVersion = None
+        self.conda_config: Dict = {}
+        self.conda_package_info: Dict = {}
+        self.nf_config: Dict = {}
+        self.files: List[Path] = []
+        self.git_sha: Optional[str] = None
+        self.minNextflowVersion: Optional[str] = None
         self.wf_path = Path(wf_path)
-        self.pipeline_name = None
-        self.pipeline_prefix = None
-        self.schema_obj = None
+        self.pipeline_name: Optional[str] = None
+        self.pipeline_prefix: Optional[str] = None
+        self.schema_obj: Optional[Dict] = None
 
         try:
             repo = git.Repo(self.wf_path)
             self.git_sha = repo.head.object.hexsha
-        except Exception:
-            log.debug(f"Could not find git hash for pipeline: {self.wf_path}")
+        except Exception as e:
+            log.debug(f"Could not find git hash for pipeline: {self.wf_path}. {e}")
 
         # Overwrite if we have the last commit from the PR - otherwise we get a merge commit hash
         if os.environ.get("GITHUB_PR_COMMIT", "") != "":
diff --git a/tests/pipelines/test_download.py b/tests/pipelines/test_download.py
index 7ed6de3fa7..d571b82cee 100644
--- a/tests/pipelines/test_download.py
+++ b/tests/pipelines/test_download.py
@@ -203,7 +203,7 @@ def test__find_container_images_config_nextflow(self, tmp_path, mock_fetch_wf_co
     def test_find_container_images_modules(self, tmp_path, mock_fetch_wf_config):
         download_obj = DownloadWorkflow(pipeline="dummy", outdir=tmp_path)
         mock_fetch_wf_config.return_value = {}
-        download_obj.find_container_images(TEST_DATA_DIR / "mock_module_containers")
+        download_obj.find_container_images(str(Path(TEST_DATA_DIR, "mock_module_containers")))
 
         # mock_docker_single_quay_io.nf
         assert "quay.io/biocontainers/singlequay:1.9--pyh9f0ad1d_0" in download_obj.containers
@@ -546,7 +546,7 @@ def test_remote_container_functionality(self, tmp_dir):
             outdir=os.path.join(tmp_dir, "new"),
             revision="3.9",
             compress_type="none",
-            container_cache_index=TEST_DATA_DIR / "data/testdata_remote_containers.txt",
+            container_cache_index=str(Path(TEST_DATA_DIR, "testdata_remote_containers.txt")),
         )
 
         download_obj.include_configs = False  # suppress prompt, because stderr.is_interactive doesn't.
diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py
index 8530fea5ad..80d7e1e018 100644
--- a/tests/pipelines/test_lint.py
+++ b/tests/pipelines/test_lint.py
@@ -125,9 +125,7 @@ def test_sphinx_md_files(self):
         """Check that we have .md files for all lint module code,
         and that there are no unexpected files (eg. deleted lint tests)"""
 
-        docs_basedir = Path(
-            os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "docs", "api", "_src", "pipeline_lint_tests"
-        )
+        docs_basedir = Path(Path(__file__).parent.parent.parent, "docs", "api", "_src", "pipeline_lint_tests")
 
         # Get list of existing .md files
         existing_docs = []
diff --git a/tests/pipelines/test_list.py b/tests/pipelines/test_list.py
index 21d239287d..32970ae076 100644
--- a/tests/pipelines/test_list.py
+++ b/tests/pipelines/test_list.py
@@ -14,15 +14,17 @@
 
 import nf_core.pipelines.list
 
-# create a temporary directory that can be used by the tests in this file
-tmp = Path(tempfile.mkdtemp())
-tmp_nxf = tmp / "nxf"
-tmp_nxf_str = str(tmp_nxf)
-
 
 class TestList(unittest.TestCase):
     """Class for list tests"""
 
+    def setUp(self) -> None:
+        # create a temporary directory that can be used by the tests in this file
+        tmp = Path(tempfile.TemporaryDirectory().name)
+        self.tmp_nxf = tmp / "nxf"
+        self.tmp_nxf_str = str(self.tmp_nxf)
+        os.environ["NXF_ASSETS"] = self.tmp_nxf_str
+
     @mock.patch("subprocess.check_output")
     def test_working_listcall(self, mock_subprocess):
         """Test that listing pipelines works"""
@@ -105,28 +107,26 @@ def test_local_workflows_compare_and_fail_silently(self):
 
         rwf_ex.releases = None
 
-    @mock.patch.dict(os.environ, {"NXF_ASSETS": tmp_nxf_str})
     @mock.patch("nf_core.pipelines.list.LocalWorkflow")
     def test_parse_local_workflow_and_succeed(self, mock_local_wf):
-        test_path = tmp_nxf / "nf-core"
+        test_path = self.tmp_nxf / "nf-core"
         if not os.path.isdir(test_path):
             os.makedirs(test_path)
-        assert os.environ["NXF_ASSETS"] == tmp_nxf_str
-        with open(tmp_nxf / "nf-core/dummy-wf", "w") as f:
+        assert os.environ["NXF_ASSETS"] == self.tmp_nxf_str
+        with open(self.tmp_nxf / "nf-core/dummy-wf", "w") as f:
             f.write("dummy")
         workflows_obj = nf_core.pipelines.list.Workflows()
         workflows_obj.get_local_nf_workflows()
         assert len(workflows_obj.local_workflows) == 1
 
-    @mock.patch.dict(os.environ, {"NXF_ASSETS": tmp_nxf_str})
     @mock.patch("nf_core.pipelines.list.LocalWorkflow")
     @mock.patch("subprocess.check_output")
     def test_parse_local_workflow_home(self, mock_local_wf, mock_subprocess):
-        test_path = tmp_nxf / "nf-core"
+        test_path = self.tmp_nxf / "nf-core"
         if not os.path.isdir(test_path):
             os.makedirs(test_path)
-        assert os.environ["NXF_ASSETS"] == tmp_nxf_str
-        with open(tmp_nxf / "nf-core/dummy-wf", "w") as f:
+        assert os.environ["NXF_ASSETS"] == self.tmp_nxf_str
+        with open(self.tmp_nxf / "nf-core/dummy-wf", "w") as f:
             f.write("dummy")
         workflows_obj = nf_core.pipelines.list.Workflows()
         workflows_obj.get_local_nf_workflows()
@@ -135,7 +135,7 @@ def test_parse_local_workflow_home(self, mock_local_wf, mock_subprocess):
     @mock.patch("git.Repo")
     def test_local_workflow_investigation(self, mock_repo, mock_stat):
         local_wf = nf_core.pipelines.list.LocalWorkflow("dummy")
-        local_wf.local_path = tmp
+        local_wf.local_path = self.tmp_nxf.parent
         mock_repo.head.commit.hexsha = "h00r4y"
         mock_stat.st_mode = 1
         local_wf.get_local_nf_workflow_details()
diff --git a/tests/test_pipelines.py b/tests/test_pipelines.py
index 461f046f52..899c4641ea 100644
--- a/tests/test_pipelines.py
+++ b/tests/test_pipelines.py
@@ -2,8 +2,6 @@
 from pathlib import Path
 from unittest import TestCase
 
-from git import Repo
-
 import nf_core.pipelines.launch
 import nf_core.pipelines.lint
 from nf_core.utils import Pipeline
@@ -16,7 +14,6 @@ def setUp(self) -> None:
         """Create a new Pipeline for testing"""
         self.tmp_dir, self.template_dir, self.pipeline_name, self.pipeline_dir = create_tmp_pipeline()
         self.pipeline_obj = Pipeline(self.pipeline_dir)
-        Repo.init(self.pipeline_dir)
         self.pipeline_obj._load()
 
         self.nf_params_fn = Path(self.pipeline_dir, "nf-params.json")

From 65084dd6143d3be44121689b84ec3a00fa857356 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 16 Jul 2024 18:48:35 +0000
Subject: [PATCH 066/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fe7fdcc28b..6bc07e2a7d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@
 
 - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976))
 - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014))
+- Rrestructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070))
 
 ### Download
 

From 45fdfb9ddd06e0b75fef592475ce166ee89894da Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 09:57:57 +0200
Subject: [PATCH 067/414] more fine-grained setup steps

---
 nf_core/pipelines/create/create.py |  2 +-
 nf_core/utils.py                   |  2 +-
 tests/pipelines/test_launch.py     | 13 +++++++++----
 tests/pipelines/test_lint.py       |  4 ++++
 tests/pipelines/test_list.py       |  5 ++---
 tests/test_pipelines.py            |  8 --------
 6 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index e9f37306f5..8cfa09491f 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -61,7 +61,7 @@ def __init__(
             self.config = template_config
         elif from_config_file:
             # Try reading config file
-            _, config_yml = nf_core.utils.load_tools_config(str(outdir) if outdir else ".")
+            _, config_yml = nf_core.utils.load_tools_config(outdir if outdir else ".")
             # Obtain a CreateConfig object from `.nf-core.yml` config file
             if "template" in config_yml:
                 self.config = CreateConfig(**config_yml["template"])
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 9b3775d62d..ead871aed1 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -133,7 +133,7 @@ class Pipeline:
         schema_obj (obj): A :class:`PipelineSchema` object
     """
 
-    def __init__(self, wf_path):
+    def __init__(self, wf_path: Path) -> None:
         """Initialise pipeline object"""
         self.conda_config: Dict = {}
         self.conda_package_info: Dict = {}
diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py
index c9efa5aa63..03bc0e98be 100644
--- a/tests/pipelines/test_launch.py
+++ b/tests/pipelines/test_launch.py
@@ -1,7 +1,7 @@
 """Tests covering the pipeline launch code."""
 
 import json
-import os
+from pathlib import Path
 from unittest import mock
 
 import pytest
@@ -14,6 +14,11 @@
 
 
 class TestLaunch(TestPipelines):
+    def setUp(self) -> None:
+        super().setUp()
+        self.nf_params_fn = Path(self.pipeline_dir, "nf-params.json")
+        self.launcher = nf_core.pipelines.launch.Launch(self.pipeline_dir, params_out=self.nf_params_fn)
+
     @mock.patch.object(nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True])
     @mock.patch.object(nf_core.pipelines.launch.Launch, "launch_web_gui")
     def test_launch_pipeline(self, mock_webbrowser, mock_lauch_web_gui):
@@ -47,12 +52,12 @@ def test_get_pipeline_schema(self):
     @with_temporary_folder
     def test_make_pipeline_schema(self, tmp_path):
         """Create a workflow, but delete the schema file, then try to load it"""
-        test_pipeline_dir = os.path.join(tmp_path, "wf")
+        test_pipeline_dir = Path(tmp_path, "wf")
         create_obj = nf_core.pipelines.create.create.PipelineCreate(
             "testpipeline", "a description", "Me", outdir=test_pipeline_dir, no_git=True
         )
         create_obj.init_pipeline()
-        os.remove(os.path.join(test_pipeline_dir, "nextflow_schema.json"))
+        Path(test_pipeline_dir, "nextflow_schema.json").unlink()
         self.launcher = nf_core.pipelines.launch.Launch(test_pipeline_dir, params_out=self.nf_params_fn)
         self.launcher.get_pipeline_schema()
         assert len(self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]) > 2
@@ -300,7 +305,7 @@ def test_build_command_params(self):
         # Check command
         assert (
             self.launcher.nextflow_cmd
-            == f'nextflow run {self.pipeline_dir} -params-file "{os.path.relpath(self.nf_params_fn)}"'
+            == f'nextflow run {self.pipeline_dir} -params-file "{Path(self.nf_params_fn).relative_to(Path.cwd())}"'
         )
         # Check saved parameters file
         with open(self.nf_params_fn) as fh:
diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py
index 80d7e1e018..800ffa16b3 100644
--- a/tests/pipelines/test_lint.py
+++ b/tests/pipelines/test_lint.py
@@ -17,6 +17,10 @@
 class TestLint(TestPipelines):
     """Class for lint tests"""
 
+    def setUp(self) -> None:
+        super().setUp()
+        self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir)
+
     ##########################
     # CORE lint.py FUNCTIONS #
     ##########################
diff --git a/tests/pipelines/test_list.py b/tests/pipelines/test_list.py
index 32970ae076..aacc3805e8 100644
--- a/tests/pipelines/test_list.py
+++ b/tests/pipelines/test_list.py
@@ -4,10 +4,9 @@
 import os
 import tempfile
 import time
-import unittest
 from datetime import datetime
 from pathlib import Path
-from unittest import mock
+from unittest import TestCase, mock
 
 import pytest
 from rich.console import Console
@@ -15,7 +14,7 @@
 import nf_core.pipelines.list
 
 
-class TestList(unittest.TestCase):
+class TestList(TestCase):
     """Class for list tests"""
 
     def setUp(self) -> None:
diff --git a/tests/test_pipelines.py b/tests/test_pipelines.py
index 899c4641ea..656ccbef55 100644
--- a/tests/test_pipelines.py
+++ b/tests/test_pipelines.py
@@ -1,9 +1,6 @@
 import shutil
-from pathlib import Path
 from unittest import TestCase
 
-import nf_core.pipelines.launch
-import nf_core.pipelines.lint
 from nf_core.utils import Pipeline
 
 from .utils import create_tmp_pipeline
@@ -16,11 +13,6 @@ def setUp(self) -> None:
         self.pipeline_obj = Pipeline(self.pipeline_dir)
         self.pipeline_obj._load()
 
-        self.nf_params_fn = Path(self.pipeline_dir, "nf-params.json")
-        self.launcher = nf_core.pipelines.launch.Launch(self.pipeline_dir, params_out=self.nf_params_fn)
-
-        self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir)
-
     def tearDown(self) -> None:
         """Remove the test pipeline directory"""
         shutil.rmtree(self.tmp_dir)

From 189015f1b12809bce71744801823c6fa4a956c58 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 10:00:53 +0200
Subject: [PATCH 068/414] don't run list_files on every init, only needed for
 one linting step

---
 nf_core/pipelines/lint/__init__.py         |  1 -
 nf_core/pipelines/lint/template_strings.py |  3 +-
 nf_core/utils.py                           | 53 +++++++++++-----------
 tests/test_utils.py                        |  4 +-
 4 files changed, 31 insertions(+), 30 deletions(-)

diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
index b40f0ee292..d731cb018d 100644
--- a/nf_core/pipelines/lint/__init__.py
+++ b/nf_core/pipelines/lint/__init__.py
@@ -560,7 +560,6 @@ def run_linting(
     # Load the various pipeline configs
     lint_obj._load_lint_config()
     lint_obj.load_pipeline_config()
-    lint_obj._list_files()
 
     # Create the modules lint object
     module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress)
diff --git a/nf_core/pipelines/lint/template_strings.py b/nf_core/pipelines/lint/template_strings.py
index 9b015bc209..90c47203f6 100644
--- a/nf_core/pipelines/lint/template_strings.py
+++ b/nf_core/pipelines/lint/template_strings.py
@@ -39,10 +39,11 @@ def template_strings(self):
     ignored = []
     # Files that should be ignored according to the linting config
     ignore_files = self.lint_config.get("template_strings", [])
+    files = self.list_files()
 
     # Loop through files, searching for string
     num_matches = 0
-    for fn in self.files:
+    for fn in files:
         if str(fn.relative_to(self.wf_path)) in ignore_files:
             ignored.append(f"Ignoring Jinja template strings in file `{fn}`")
             continue
diff --git a/nf_core/utils.py b/nf_core/utils.py
index ead871aed1..b5719a2b15 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -162,31 +162,7 @@ def __repr__(self) -> str:
     def _load(self) -> bool:
         """Run core load functions"""
 
-        return self._list_files() and self.load_pipeline_config() and self._load_conda_environment()
-
-    def _list_files(self) -> bool:
-        """Get a list of all files in the pipeline"""
-        try:
-            # First, try to get the list of files using git
-            git_ls_files = subprocess.check_output(["git", "ls-files"], cwd=self.wf_path).splitlines()
-            self.files = []
-            for fn in git_ls_files:
-                full_fn = Path(self.wf_path) / fn.decode("utf-8")
-                if full_fn.is_file():
-                    self.files.append(full_fn)
-                else:
-                    log.debug(f"`git ls-files` returned '{full_fn}' but could not open it!")
-            return True
-        except subprocess.CalledProcessError as e:
-            # Failed, so probably not initialised as a git repository - just a list of all files
-            log.debug(f"Couldn't call 'git ls-files': {e}")
-            self.files = []
-            for subdir, _, files in os.walk(self.wf_path):
-                for fn in files:
-                    self.files.append(Path(subdir, str(fn)))
-            if len(self.files) > 0:
-                return True
-            return False
+        return self.load_pipeline_config() and self._load_conda_environment()
 
     def _load_conda_environment(self) -> bool:
         """Try to load the pipeline environment.yml file, if it exists"""
@@ -202,6 +178,31 @@ def _fp(self, fn):
         """Convenience function to get full path to a file in the pipeline"""
         return os.path.join(self.wf_path, fn)
 
+    def list_files(self) -> List[Path]:
+        """Get a list of all files in the pipeline"""
+        files = []
+        try:
+            # First, try to get the list of files using git
+            git_ls_files = subprocess.check_output(["git", "ls-files"], cwd=self.wf_path).splitlines()
+            for fn in git_ls_files:
+                full_fn = Path(self.wf_path) / fn.decode("utf-8")
+                if full_fn.is_file():
+                    files.append(full_fn)
+                else:
+                    log.debug(f"`git ls-files` returned '{full_fn}' but could not open it!")
+        except subprocess.CalledProcessError as e:
+            # Failed, so probably not initialised as a git repository - just a list of all files
+            log.debug(f"Couldn't call 'git ls-files': {e}")
+            files = []
+            for file_path in self.wf_path.rglob("*"):
+                if file_path.is_file():
+                    # Append the file path to the list
+                    files.append(file_path.relative_to(self.wf_path))
+            if len(files) == 0:
+                log.debug(f"No files found in pipeline: {self.wf_path}")
+
+        return files
+
     def load_pipeline_config(self) -> bool:
         """Get the nextflow config for this pipeline
 
@@ -1082,7 +1083,7 @@ def determine_base_dir(directory="."):
     return directory if (base_dir == start_dir or str(base_dir) == base_dir.root) else base_dir
 
 
-def get_first_available_path(directory, paths):
+def get_first_available_path(directory: Union[Path, str], paths: List[str]) -> Union[Path, None]:
     for p in paths:
         if Path(directory, p).is_file():
             return Path(directory, p)
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 7afe1a532f..f61f3584e2 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -109,7 +109,7 @@ def testload_pipeline_config(self):
 
     def test_list_files_git(self):
         """Test listing pipeline files using `git ls`"""
-        self.pipeline_obj._list_files()
+        self.pipeline_obj.list_files()
         assert Path(self.test_pipeline_dir, "main.nf") in self.pipeline_obj.files
 
     @with_temporary_folder
@@ -119,7 +119,7 @@ def test_list_files_no_git(self, tmpdir):
         tmp_fn = Path(tmpdir, "testfile")
         tmp_fn.touch()
         pipeline_obj = nf_core.utils.Pipeline(tmpdir)
-        pipeline_obj._list_files()
+        pipeline_obj.list_files()
         assert tmp_fn in pipeline_obj.files
 
     @mock.patch("os.path.exists")

From 2ddc860183729642bd69169b3d948fa3ec273d46 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 10:01:29 +0200
Subject: [PATCH 069/414] create git repo with testpipeline

---
 tests/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/utils.py b/tests/utils.py
index 38a10fa810..ef8f334669 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -105,7 +105,7 @@ def create_tmp_pipeline() -> Tuple[Path, Path, str, Path]:
     pipeline_dir = tmp_dir / pipeline_name
 
     nf_core.pipelines.create.create.PipelineCreate(
-        pipeline_name, "it is mine", "me", no_git=True, outdir=str(pipeline_dir)
+        pipeline_name, "it is mine", "me", no_git=False, outdir=str(pipeline_dir)
     ).init_pipeline()
 
     # return values to instance variables for later use in test methods

From c313fed6a08c0e157a93a19a14d4d77946ad6d50 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 10:25:45 +0200
Subject: [PATCH 070/414] update textual snapshots to new location

---
 .editorconfig                                 |  2 +-
 .../__snapshots__/test_create_app.ambr        |  0
 tests/pipelines/test_create_app.py            | 26 ++++++++++---------
 3 files changed, 15 insertions(+), 13 deletions(-)
 rename tests/{ => pipelines}/__snapshots__/test_create_app.ambr (100%)

diff --git a/.editorconfig b/.editorconfig
index 5aa8697d30..f266805d6e 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -21,7 +21,7 @@ indent_style = unset
 [**/Makefile]
 indent_style = unset
 
-[tests/__snapshots__/*]
+[tests/pipelines/__snapshots__/*]
 charset = unset
 end_of_line = unset
 insert_final_newline = unset
diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
similarity index 100%
rename from tests/__snapshots__/test_create_app.ambr
rename to tests/pipelines/__snapshots__/test_create_app.ambr
diff --git a/tests/pipelines/test_create_app.py b/tests/pipelines/test_create_app.py
index 8c89b92cba..9a02f04f00 100644
--- a/tests/pipelines/test_create_app.py
+++ b/tests/pipelines/test_create_app.py
@@ -4,6 +4,8 @@
 
 from nf_core.pipelines.create import PipelineCreateApp
 
+INIT_FILE = "../../nf_core/pipelines/create/__init__.py"
+
 
 async def test_app_bindings():
     """Test that the app bindings work."""
@@ -23,7 +25,7 @@ async def test_app_bindings():
 
 def test_welcome(snap_compare):
     """Test snapshot for the first screen in the app. The welcome screen."""
-    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50))
+    assert snap_compare(INIT_FILE, terminal_size=(100, 50))
 
 
 def test_choose_type(snap_compare):
@@ -36,7 +38,7 @@ def test_choose_type(snap_compare):
     async def run_before(pilot) -> None:
         await pilot.click("#start")
 
-    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+    assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before)
 
 
 def test_basic_details_nfcore(snap_compare):
@@ -51,7 +53,7 @@ async def run_before(pilot) -> None:
         await pilot.click("#start")
         await pilot.click("#type_nfcore")
 
-    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+    assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before)
 
 
 def test_basic_details_custom(snap_compare):
@@ -66,7 +68,7 @@ async def run_before(pilot) -> None:
         await pilot.click("#start")
         await pilot.click("#type_custom")
 
-    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+    assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before)
 
 
 def test_type_nfcore(snap_compare):
@@ -89,7 +91,7 @@ async def run_before(pilot) -> None:
         await pilot.press("M", "e")
         await pilot.click("#next")
 
-    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+    assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before)
 
 
 def test_type_nfcore_validation(snap_compare):
@@ -108,7 +110,7 @@ async def run_before(pilot) -> None:
         await pilot.click("#next")
         await pilot.pause()
 
-    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+    assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before)
 
 
 def test_type_custom(snap_compare):
@@ -132,7 +134,7 @@ async def run_before(pilot) -> None:
         await pilot.press("M", "e")
         await pilot.click("#next")
 
-    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+    assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before)
 
 
 def test_final_details(snap_compare):
@@ -157,7 +159,7 @@ async def run_before(pilot) -> None:
         await pilot.click("#next")
         await pilot.click("#continue")
 
-    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+    assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before)
 
 
 def test_customisation_help(snap_compare):
@@ -184,7 +186,7 @@ async def run_before(pilot) -> None:
         await pilot.press("tab")
         await pilot.press("enter")
 
-    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+    assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before)
 
 
 def test_github_question(tmpdir, snap_compare):
@@ -216,7 +218,7 @@ async def run_before(pilot) -> None:
         await pilot.app.workers.wait_for_complete()
         await pilot.click("#close_screen")
 
-    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+    assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before)
 
 
 @mock.patch("nf_core.pipelines.create.githubrepo.GithubRepo._get_github_credentials")
@@ -255,7 +257,7 @@ async def run_before(pilot) -> None:
         await pilot.click("#close_screen")
         await pilot.click("#github_repo")
 
-    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+    assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before)
 
 
 def test_github_exit_message(tmpdir, snap_compare):
@@ -291,4 +293,4 @@ async def run_before(pilot) -> None:
         await pilot.click("#github_repo")
         await pilot.click("#exit")
 
-    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+    assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before)

From d6560656873b8bc448cde44975c78fb0abc39e02 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 11:19:49 +0200
Subject: [PATCH 071/414] fix tests

---
 nf_core/pipelines/launch.py    | 5 +++--
 nf_core/utils.py               | 2 +-
 tests/pipelines/test_launch.py | 5 +----
 tests/test_utils.py            | 8 ++++----
 tests/utils.py                 | 2 +-
 5 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/nf_core/pipelines/launch.py b/nf_core/pipelines/launch.py
index 3a5f97e78f..e03982a25a 100644
--- a/nf_core/pipelines/launch.py
+++ b/nf_core/pipelines/launch.py
@@ -7,6 +7,7 @@
 import re
 import subprocess
 import webbrowser
+from pathlib import Path
 
 import questionary
 from rich.console import Console
@@ -46,7 +47,7 @@ def __init__(
         self.schema_obj = None
         self.use_params_file = False if command_only else True
         self.params_in = params_in
-        self.params_out = params_out if params_out else os.path.join(os.getcwd(), "nf-params.json")
+        self.params_out = params_out if params_out else Path.cwd() / "nf-params.json"
         self.save_all = save_all
         self.show_hidden = show_hidden
         self.web_schema_launch_url = url if url else "https://nf-co.re/launch"
@@ -697,7 +698,7 @@ def build_command(self):
             # Write the user selection to a file and run nextflow with that
             if self.use_params_file:
                 dump_json_with_prettier(self.params_out, self.schema_obj.input_params)
-                self.nextflow_cmd += f' -params-file "{os.path.relpath(self.params_out)}"'
+                self.nextflow_cmd += f' -params-file "{Path(self.params_out)}"'
 
             # Call nextflow with a list of command line flags
             else:
diff --git a/nf_core/utils.py b/nf_core/utils.py
index b5719a2b15..0cd812cb04 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -197,7 +197,7 @@ def list_files(self) -> List[Path]:
             for file_path in self.wf_path.rglob("*"):
                 if file_path.is_file():
                     # Append the file path to the list
-                    files.append(file_path.relative_to(self.wf_path))
+                    files.append(file_path)
             if len(files) == 0:
                 log.debug(f"No files found in pipeline: {self.wf_path}")
 
diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py
index 03bc0e98be..da7618d486 100644
--- a/tests/pipelines/test_launch.py
+++ b/tests/pipelines/test_launch.py
@@ -303,10 +303,7 @@ def test_build_command_params(self):
         self.launcher.schema_obj.input_params.update({"input": "custom_input"})
         self.launcher.build_command()
         # Check command
-        assert (
-            self.launcher.nextflow_cmd
-            == f'nextflow run {self.pipeline_dir} -params-file "{Path(self.nf_params_fn).relative_to(Path.cwd())}"'
-        )
+        assert self.launcher.nextflow_cmd == f'nextflow run {self.pipeline_dir} -params-file "{self.nf_params_fn}"'
         # Check saved parameters file
         with open(self.nf_params_fn) as fh:
             try:
diff --git a/tests/test_utils.py b/tests/test_utils.py
index f61f3584e2..860cba5ba6 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -109,8 +109,8 @@ def testload_pipeline_config(self):
 
     def test_list_files_git(self):
         """Test listing pipeline files using `git ls`"""
-        self.pipeline_obj.list_files()
-        assert Path(self.test_pipeline_dir, "main.nf") in self.pipeline_obj.files
+        files = self.pipeline_obj.list_files()
+        assert Path(self.test_pipeline_dir, "main.nf") in files
 
     @with_temporary_folder
     def test_list_files_no_git(self, tmpdir):
@@ -119,8 +119,8 @@ def test_list_files_no_git(self, tmpdir):
         tmp_fn = Path(tmpdir, "testfile")
         tmp_fn.touch()
         pipeline_obj = nf_core.utils.Pipeline(tmpdir)
-        pipeline_obj.list_files()
-        assert tmp_fn in pipeline_obj.files
+        files = pipeline_obj.list_files()
+        assert tmp_fn in files
 
     @mock.patch("os.path.exists")
     @mock.patch("os.makedirs")
diff --git a/tests/utils.py b/tests/utils.py
index ef8f334669..90c4ae0418 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -105,7 +105,7 @@ def create_tmp_pipeline() -> Tuple[Path, Path, str, Path]:
     pipeline_dir = tmp_dir / pipeline_name
 
     nf_core.pipelines.create.create.PipelineCreate(
-        pipeline_name, "it is mine", "me", no_git=False, outdir=str(pipeline_dir)
+        pipeline_name, "it is mine", "me", no_git=False, outdir=pipeline_dir
     ).init_pipeline()
 
     # return values to instance variables for later use in test methods

From 21cdbbdd2871fe74d337ee755e83680c2ad820f6 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 12:07:12 +0200
Subject: [PATCH 072/414] remove asyncio mode (and see what happens)

---
 pyproject.toml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4499324445..775f04c9a1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,8 +6,6 @@ requires = ["setuptools>=40.6.0", "wheel"]
 markers = ["datafiles: load datafiles"]
 testpaths = ["tests"]
 python_files = ["test_*.py"]
-# automatically run coroutine tests with asyncio
-asyncio_mode = ["auto"]
 norecursedirs = [
     ".*",
     "build",

From e0a82d51bf231dfc04629bf32105cacc10c8556c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 12:08:14 +0200
Subject: [PATCH 073/414] fix refgenie tests

---
 nf_core/pipelines/create/create.py    |  9 ++++++---
 nf_core/pipelines/create_logo.py      |  1 -
 nf_core/pipelines/lint/files_exist.py |  2 +-
 nf_core/pipelines/refgenie.py         |  2 +-
 requirements.txt                      |  4 ++--
 tests/pipelines/lint/files_exist.py   |  2 +-
 tests/pipelines/test_refgenie.py      | 20 ++++++++++----------
 7 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 8cfa09491f..c5af956690 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -355,7 +355,6 @@ def render_template(self):
         # Remove all unused parameters in the nextflow schema
         if not self.jinja_params["igenomes"] or not self.jinja_params["nf_core_configs"]:
             self.update_nextflow_schema()
-
         if self.config.is_nfcore:
             # Make a logo and save it, if it is a nf-core pipeline
             self.make_pipeline_logo()
@@ -513,11 +512,15 @@ def fix_linting(self):
     def make_pipeline_logo(self):
         """Fetch a logo for the new pipeline from the nf-core website"""
         email_logo_path = Path(self.outdir) / "assets"
-        create_logo(text=self.jinja_params["short_name"], dir=email_logo_path, theme="light", force=self.force)
+        create_logo(text=self.jinja_params["short_name"], dir=email_logo_path, theme="light", force=bool(self.force))
         for theme in ["dark", "light"]:
             readme_logo_path = Path(self.outdir) / "docs" / "images"
             create_logo(
-                text=self.jinja_params["short_name"], dir=readme_logo_path, width=600, theme=theme, force=self.force
+                text=self.jinja_params["short_name"],
+                dir=readme_logo_path,
+                width=600,
+                theme=theme,
+                force=bool(self.force),
             )
 
     def git_init_pipeline(self):
diff --git a/nf_core/pipelines/create_logo.py b/nf_core/pipelines/create_logo.py
index 1e96b7032c..780bafd7f5 100644
--- a/nf_core/pipelines/create_logo.py
+++ b/nf_core/pipelines/create_logo.py
@@ -20,7 +20,6 @@ def create_logo(
     force: bool = False,
 ) -> Path:
     """Create a logo for a pipeline."""
-
     if not text:
         raise UserWarning("Please provide the name of the text to put on the logo.")
     dir = Path(dir)
diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index c6f622b3e0..edad62aab8 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -5,7 +5,7 @@
 log = logging.getLogger(__name__)
 
 
-def files_exist(self) -> Dict[str, Union[List[str], bool]]:
+def files_exist(self) -> Dict[str, List[str]]:
     """Checks a given pipeline directory for required files.
 
     Iterates through the pipeline's directory content and checks that specified
diff --git a/nf_core/pipelines/refgenie.py b/nf_core/pipelines/refgenie.py
index de9201bcd6..19ef4b5121 100644
--- a/nf_core/pipelines/refgenie.py
+++ b/nf_core/pipelines/refgenie.py
@@ -183,7 +183,7 @@ def update_config(rgc):
 
     # Save the updated genome config
     try:
-        with open(refgenie_genomes_config_file, "w+") as fh:
+        with open(str(refgenie_genomes_config_file), "w+") as fh:
             fh.write(refgenie_genomes)
         log.info(f"Updated nf-core genomes config: {refgenie_genomes_config_file}")
     except FileNotFoundError:
diff --git a/requirements.txt b/requirements.txt
index 524b739e89..fb658be2fb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -9,10 +9,10 @@ packaging
 pillow
 pdiff
 pre-commit
-prompt_toolkit>=3.0.3
+prompt_toolkit<=3.0.36
 pydantic>=2.2.1
 pyyaml
-questionary>=1.8.0
+questionary>=2.0.1
 refgenie
 requests
 requests_cache
diff --git a/tests/pipelines/lint/files_exist.py b/tests/pipelines/lint/files_exist.py
index 87508e78a8..4ae167b1d0 100644
--- a/tests/pipelines/lint/files_exist.py
+++ b/tests/pipelines/lint/files_exist.py
@@ -14,7 +14,7 @@ def test_files_exist_missing_config(self):
     lint_obj.nf_config["manifest.name"] = "nf-core/testpipeline"
 
     results = lint_obj.files_exist()
-    assert results["failed"] == ["File not found: `CHANGELOG.md`"]
+    assert "File not found: `CHANGELOG.md`" in results["failed"]
 
 
 def test_files_exist_missing_main(self):
diff --git a/tests/pipelines/test_refgenie.py b/tests/pipelines/test_refgenie.py
index 23cc0dd14a..734a2368bd 100644
--- a/tests/pipelines/test_refgenie.py
+++ b/tests/pipelines/test_refgenie.py
@@ -5,6 +5,7 @@
 import subprocess
 import tempfile
 import unittest
+from pathlib import Path
 
 
 class TestRefgenie(unittest.TestCase):
@@ -14,36 +15,35 @@ def setUp(self):
         """
         Prepare a refgenie config file
         """
-        self.tmp_dir = tempfile.mkdtemp()
-        self.NXF_HOME = os.path.join(self.tmp_dir, ".nextflow")
-        self.NXF_REFGENIE_PATH = os.path.join(self.NXF_HOME, "nf-core", "refgenie_genomes.config")
-        self.REFGENIE = os.path.join(self.tmp_dir, "genomes_config.yaml")
-        self.translation_file = os.path.join(self.tmp_dir, "alias_translations.yaml")
+        self.tmp_dir = Path(tempfile.TemporaryDirectory().name)
+        self.NXF_HOME = self.tmp_dir / ".nextflow"
+        self.NXF_REFGENIE_PATH = self.NXF_HOME / "nf-core" / "refgenie_genomes.config"
+        self.REFGENIE = self.tmp_dir / "genomes_config.yaml"
+        self.translation_file = self.tmp_dir / "alias_translations.yaml"
         # Set NXF_HOME environment variable
         # avoids adding includeConfig statement to config file outside the current tmpdir
         try:
             self.NXF_HOME_ORIGINAL = os.environ["NXF_HOME"]
         except Exception:
             self.NXF_HOME_ORIGINAL = None
-        os.environ["NXF_HOME"] = self.NXF_HOME
+        os.environ["NXF_HOME"] = str(self.NXF_HOME)
 
         # create NXF_HOME and nf-core directories
-        os.makedirs(os.path.join(self.NXF_HOME, "nf-core"), exist_ok=True)
+        nf_core_dir = self.NXF_HOME / "nf-core"
+        nf_core_dir.mkdir(parents=True, exist_ok=True)
 
         # Initialize a refgenie config
         os.system(f"refgenie init -c {self.REFGENIE}")
 
         # Add NXF_REFGENIE_PATH to refgenie config
         with open(self.REFGENIE, "a") as fh:
-            fh.write(f"nextflow_config: {os.path.join(self.NXF_REFGENIE_PATH)}\n")
+            fh.write(f"nextflow_config: {self.NXF_REFGENIE_PATH}\n")
 
         # Add an alias translation to YAML file
         with open(self.translation_file, "a") as fh:
             fh.write("ensembl_gtf: gtf\n")
 
     def tearDown(self) -> None:
-        # Remove the tempdir again
-        os.system(f"rm -rf {self.tmp_dir}")
         # Reset NXF_HOME environment variable
         if self.NXF_HOME_ORIGINAL is None:
             del os.environ["NXF_HOME"]

From 1fde6ca6e70866d0a8b7a7a79ade75afefcf36bb Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 13:12:43 +0200
Subject: [PATCH 074/414] add cleanup step to some download tests

---
 nf_core/pipelines/download.py    |  2 +-
 tests/pipelines/test_download.py | 16 ++++++++++++++++
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py
index f16430b0a8..797909636c 100644
--- a/nf_core/pipelines/download.py
+++ b/nf_core/pipelines/download.py
@@ -231,7 +231,7 @@ def download_workflow(self):
             summary_log.append(f"Enabled for Seqera Platform: '{self.platform}'")
 
         # Check that the outdir doesn't already exist
-        if os.path.exists(self.outdir):
+        if self.outdir is not None and os.path.exists(self.outdir):
             if not self.force:
                 raise DownloadError(
                     f"Output directory '{self.outdir}' already exists (use [red]--force[/] to overwrite)"
diff --git a/tests/pipelines/test_download.py b/tests/pipelines/test_download.py
index d571b82cee..a898d37b70 100644
--- a/tests/pipelines/test_download.py
+++ b/tests/pipelines/test_download.py
@@ -13,6 +13,7 @@
 import pytest
 
 import nf_core.pipelines.create.create
+import nf_core.pipelines.list
 import nf_core.utils
 from nf_core.pipelines.download import ContainerError, DownloadWorkflow, WorkflowRepo
 from nf_core.synced_repo import SyncedRepo
@@ -643,6 +644,11 @@ def test_download_workflow_for_platform(self, tmp_dir, _):
             in download_obj.containers
         )  # indirect definition via $container variable.
 
+        # clean-up
+        # remove "nf-core-rnaseq*" directories
+        for path in Path().cwd().glob("nf-core-rnaseq*"):
+            shutil.rmtree(path)
+
     #
     # Brief test adding a single custom tag to Seqera Platform download
     #
@@ -659,6 +665,11 @@ def test_download_workflow_for_platform_with_one_custom_tag(self, _, tmp_dir):
         )
         assert isinstance(download_obj.additional_tags, list) and len(download_obj.additional_tags) == 1
 
+        # clean-up
+        # remove "nf-core-rnaseq*" directories
+        for path in Path().cwd().glob("nf-core-rnaseq*"):
+            shutil.rmtree(path)
+
     #
     # Test adding custom tags to Seqera Platform download (full test)
     #
@@ -727,3 +738,8 @@ def test_download_workflow_for_platform_with_custom_tags(self, _, tmp_dir):
                     "[red]Could not apply invalid `--tag` specification[/]: 'What is this?'",
                 }
             )
+
+            # clean-up
+            # remove "nf-core-rnaseq*" directories
+            for path in Path().cwd().glob("nf-core-rnaseq*"):
+                shutil.rmtree(path)

From a0f788dc1d7a8059e8077ca3413397f9f38cc3be Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 13:40:39 +0200
Subject: [PATCH 075/414] start converting linting tests to new subclass
 structure

---
 nf_core/pipelines/create_logo.py              | 13 ++--
 tests/pipelines/lint/actions_awsfulltest.py   | 60 ------------------
 .../lint/test_actions_awsfulltest.py          | 61 +++++++++++++++++++
 tests/pipelines/test_lint.py                  | 20 +++---
 4 files changed, 77 insertions(+), 77 deletions(-)
 delete mode 100644 tests/pipelines/lint/actions_awsfulltest.py
 create mode 100644 tests/pipelines/lint/test_actions_awsfulltest.py

diff --git a/nf_core/pipelines/create_logo.py b/nf_core/pipelines/create_logo.py
index 780bafd7f5..0643d2e295 100644
--- a/nf_core/pipelines/create_logo.py
+++ b/nf_core/pipelines/create_logo.py
@@ -90,11 +90,14 @@ def create_logo(
             color = theme == "dark" and (250, 250, 250) or (5, 5, 5)
             draw.text((110, 465), text, color, font=font)
 
-            # Crop to max width
-            img = img.crop((0, 0, max_width, height))
-
-            # Resize
-            img = img.resize((width, int((width / max_width) * height)))
+            if img is not None:
+                # Crop to max width
+                img = img.crop((0, 0, max_width, height))
+
+                # Resize
+                img = img.resize((width, int((width / max_width) * height)))
+            else:
+                log.error("Failed to create logo, no image object created.")
 
             # Save to cache
             Path(cache_path.parent).mkdir(parents=True, exist_ok=True)
diff --git a/tests/pipelines/lint/actions_awsfulltest.py b/tests/pipelines/lint/actions_awsfulltest.py
deleted file mode 100644
index d1479bb1e1..0000000000
--- a/tests/pipelines/lint/actions_awsfulltest.py
+++ /dev/null
@@ -1,60 +0,0 @@
-from pathlib import Path
-
-import yaml
-
-import nf_core.pipelines.lint
-
-
-def test_actions_awsfulltest_warn(self):
-    """Lint test: actions_awsfulltest - PASS"""
-    self.lint_obj._load()
-    results = self.lint_obj.actions_awsfulltest()
-    assert "`.github/workflows/awsfulltest.yml` is triggered correctly" in results["passed"]
-    assert len(results.get("failed", [])) == 0
-    assert len(results.get("ignored", [])) == 0
-
-
-def test_actions_awsfulltest_pass(self):
-    """Lint test: actions_awsfulltest - WARN"""
-
-    # Edit .github/workflows/awsfulltest.yml to use -profile test_full
-    new_pipeline = self._make_pipeline_copy()
-    with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
-        awsfulltest_yml = fh.read()
-    awsfulltest_yml = awsfulltest_yml.replace("-profile test ", "-profile test_full ")
-    with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
-        fh.write(awsfulltest_yml)
-
-    # Make lint object
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-
-    results = lint_obj.actions_awsfulltest()
-    assert results["passed"] == [
-        "`.github/workflows/awsfulltest.yml` is triggered correctly",
-        "`.github/workflows/awsfulltest.yml` does not use `-profile test`",
-    ]
-    assert len(results.get("warned", [])) == 0
-    assert len(results.get("failed", [])) == 0
-    assert len(results.get("ignored", [])) == 0
-
-
-def test_actions_awsfulltest_fail(self):
-    """Lint test: actions_awsfulltest - FAIL"""
-
-    # Edit .github/workflows/awsfulltest.yml to use -profile test_full
-    new_pipeline = self._make_pipeline_copy()
-    with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
-        awsfulltest_yml = yaml.safe_load(fh)
-    del awsfulltest_yml[True]["pull_request_review"]
-    with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
-        yaml.dump(awsfulltest_yml, fh)
-
-    # Make lint object
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-
-    results = lint_obj.actions_awsfulltest()
-    assert results["failed"] == ["`.github/workflows/awsfulltest.yml` is not triggered correctly"]
-    assert "`.github/workflows/awsfulltest.yml` does not use `-profile test`" in results["passed"]
-    assert len(results.get("ignored", [])) == 0
diff --git a/tests/pipelines/lint/test_actions_awsfulltest.py b/tests/pipelines/lint/test_actions_awsfulltest.py
new file mode 100644
index 0000000000..5c070fd5cf
--- /dev/null
+++ b/tests/pipelines/lint/test_actions_awsfulltest.py
@@ -0,0 +1,61 @@
+from pathlib import Path
+
+import yaml
+
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintActionsAwsfulltest(TestLint):
+    def test_actions_awsfulltest_warn(self):
+        """Lint test: actions_awsfulltest - PASS"""
+        self.lint_obj._load()
+        results = self.lint_obj.actions_awsfulltest()
+        assert "`.github/workflows/awsfulltest.yml` is triggered correctly" in results["passed"]
+        assert len(results.get("failed", [])) == 0
+        assert len(results.get("ignored", [])) == 0
+
+    def test_actions_awsfulltest_pass(self):
+        """Lint test: actions_awsfulltest - WARN"""
+
+        # Edit .github/workflows/awsfulltest.yml to use -profile test_full
+        new_pipeline = self._make_pipeline_copy()
+        with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
+            awsfulltest_yml = fh.read()
+        awsfulltest_yml = awsfulltest_yml.replace("-profile test ", "-profile test_full ")
+        with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
+            fh.write(awsfulltest_yml)
+
+        # Make lint object
+        lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
+        lint_obj._load()
+
+        results = lint_obj.actions_awsfulltest()
+        assert results["passed"] == [
+            "`.github/workflows/awsfulltest.yml` is triggered correctly",
+            "`.github/workflows/awsfulltest.yml` does not use `-profile test`",
+        ]
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("failed", [])) == 0
+        assert len(results.get("ignored", [])) == 0
+
+    def test_actions_awsfulltest_fail(self):
+        """Lint test: actions_awsfulltest - FAIL"""
+
+        # Edit .github/workflows/awsfulltest.yml to use -profile test_full
+        new_pipeline = self._make_pipeline_copy()
+        with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh:
+            awsfulltest_yml = yaml.safe_load(fh)
+        del awsfulltest_yml[True]["pull_request_review"]
+        with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh:
+            yaml.dump(awsfulltest_yml, fh)
+
+        # Make lint object
+        lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
+        lint_obj._load()
+
+        results = lint_obj.actions_awsfulltest()
+        assert results["failed"] == ["`.github/workflows/awsfulltest.yml` is not triggered correctly"]
+        assert "`.github/workflows/awsfulltest.yml` does not use `-profile test`" in results["passed"]
+        assert len(results.get("ignored", [])) == 0
diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py
index 800ffa16b3..54279cd064 100644
--- a/tests/pipelines/test_lint.py
+++ b/tests/pipelines/test_lint.py
@@ -1,8 +1,6 @@
 """Some tests covering the linting code."""
 
-import fnmatch
 import json
-import os
 from pathlib import Path
 
 import yaml
@@ -133,16 +131,18 @@ def test_sphinx_md_files(self):
 
         # Get list of existing .md files
         existing_docs = []
-        for fn in os.listdir(docs_basedir):
-            if fnmatch.fnmatch(fn, "*.md") and not fnmatch.fnmatch(fn, "index.md"):
-                existing_docs.append(Path(docs_basedir, fn))
+        existing_docs = [
+            str(Path(docs_basedir, fn))
+            for fn in Path(docs_basedir).iterdir()
+            if fn.match("*.md") and not fn.match("index.md")
+        ]
 
         # Check .md files against each test name
         lint_obj = nf_core.pipelines.lint.PipelineLint("", True)
         for test_name in lint_obj.lint_tests:
             fn = Path(docs_basedir, f"{test_name}.md")
-            assert os.path.exists(fn), f"Could not find lint docs .md file: {fn}"
-            existing_docs.remove(fn)
+            assert fn.exists(), f"Could not find lint docs .md file: {fn}"
+            existing_docs.remove(str(fn))
 
         # Check that we have no remaining .md files that we didn't expect
         assert len(existing_docs) == 0, f"Unexpected lint docs .md files found: {', '.join(existing_docs)}"
@@ -150,11 +150,7 @@ def test_sphinx_md_files(self):
     #######################
     # SPECIFIC LINT TESTS #
     #######################
-    from .lint.actions_awsfulltest import (  # type: ignore[misc]
-        test_actions_awsfulltest_fail,
-        test_actions_awsfulltest_pass,
-        test_actions_awsfulltest_warn,
-    )
+
     from .lint.actions_awstest import (  # type: ignore[misc]
         test_actions_awstest_fail,
         test_actions_awstest_pass,

From 13be56f73d50e753d941301ed9a84424d3fa3022 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 13:41:25 +0200
Subject: [PATCH 076/414] update prettier version

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c1dc7978f6..bcf7ff65ce 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -10,7 +10,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.2.5
+          - prettier@3.3.3
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"

From da155abe4945be13eaa5beb3654dd342dc9d5b19 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 13:54:53 +0200
Subject: [PATCH 077/414] import linting tests correctly to avoid "module is
 not callable" warnings

---
 nf_core/pipelines/lint/__init__.py | 73 +++++++++++++++++++-----------
 1 file changed, 47 insertions(+), 26 deletions(-)

diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
index d731cb018d..93f6523709 100644
--- a/nf_core/pipelines/lint/__init__.py
+++ b/nf_core/pipelines/lint/__init__.py
@@ -30,6 +30,29 @@
 from nf_core.utils import plural_s as _s
 from nf_core.utils import strip_ansi_codes
 
+from .actions_awsfulltest import actions_awsfulltest
+from .actions_awstest import actions_awstest
+from .actions_ci import actions_ci
+from .actions_schema_validation import actions_schema_validation
+from .configs import base_config, modules_config
+from .files_exist import files_exist
+from .files_unchanged import files_unchanged
+from .merge_markers import merge_markers
+from .modules_json import modules_json
+from .modules_structure import modules_structure
+from .multiqc_config import multiqc_config
+from .nextflow_config import nextflow_config
+from .nfcore_yml import nfcore_yml
+from .pipeline_name_conventions import pipeline_name_conventions
+from .pipeline_todos import pipeline_todos
+from .readme import readme
+from .schema_description import schema_description
+from .schema_lint import schema_lint
+from .schema_params import schema_params
+from .system_exit import system_exit
+from .template_strings import template_strings
+from .version_consistency import version_consistency
+
 log = logging.getLogger(__name__)
 
 
@@ -52,32 +75,30 @@ class PipelineLint(nf_core.utils.Pipeline):
         warned (list): A list of tuples of the form: ``(<warned no>, <reason>)``
     """
 
-    from .actions_awsfulltest import actions_awsfulltest  # type: ignore[misc]
-    from .actions_awstest import actions_awstest  # type: ignore[misc]
-    from .actions_ci import actions_ci  # type: ignore[misc]
-    from .actions_schema_validation import (  # type: ignore[misc]
-        actions_schema_validation,
-    )
-    from .configs import base_config, modules_config  # type: ignore[misc]
-    from .files_exist import files_exist  # type: ignore[misc]
-    from .files_unchanged import files_unchanged  # type: ignore[misc]
-    from .merge_markers import merge_markers  # type: ignore[misc]
-    from .modules_json import modules_json  # type: ignore[misc]
-    from .modules_structure import modules_structure  # type: ignore[misc]
-    from .multiqc_config import multiqc_config  # type: ignore[misc]
-    from .nextflow_config import nextflow_config  # type: ignore[misc]
-    from .nfcore_yml import nfcore_yml  # type: ignore[misc]
-    from .pipeline_name_conventions import (  # type: ignore[misc]
-        pipeline_name_conventions,
-    )
-    from .pipeline_todos import pipeline_todos  # type: ignore[misc]
-    from .readme import readme  # type: ignore[misc]
-    from .schema_description import schema_description  # type: ignore[misc]
-    from .schema_lint import schema_lint  # type: ignore[misc]
-    from .schema_params import schema_params  # type: ignore[misc]
-    from .system_exit import system_exit  # type: ignore[misc]
-    from .template_strings import template_strings  # type: ignore[misc]
-    from .version_consistency import version_consistency  # type: ignore[misc]
+    # Import all linting tests as methods for this class
+    actions_awsfulltest = actions_awsfulltest
+    actions_awstest = actions_awstest
+    actions_ci = actions_ci
+    actions_schema_validation = actions_schema_validation
+    base_config = base_config
+    modules_config = modules_config
+    files_exist = files_exist
+    files_unchanged = files_unchanged
+    merge_markers = merge_markers
+    modules_json = modules_json
+    modules_structure = modules_structure
+    multiqc_config = multiqc_config
+    nextflow_config = nextflow_config
+    nfcore_yml = nfcore_yml
+    pipeline_name_conventions = pipeline_name_conventions
+    pipeline_todos = pipeline_todos
+    readme = readme
+    schema_description = schema_description
+    schema_lint = schema_lint
+    schema_params = schema_params
+    system_exit = system_exit
+    template_strings = template_strings
+    version_consistency = version_consistency
 
     def __init__(
         self, wf_path, release_mode=False, fix=(), key=None, fail_ignored=False, fail_warned=False, hide_progress=False

From 4c77621e8816a0ec5da9d9096efc89e77e5951f6 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 14:31:33 +0200
Subject: [PATCH 078/414] convert rest of the lint test to new subclass
 structure

---
 tests/pipelines/lint/actions_awstest.py       |  37 --
 tests/pipelines/lint/actions_ci.py            |  49 ---
 .../lint/actions_schema_validation.py         |  66 ----
 tests/pipelines/lint/configs.py               |  89 -----
 tests/pipelines/lint/files_exist.py           |  97 -----
 tests/pipelines/lint/files_unchanged.py       |  26 --
 tests/pipelines/lint/merge_markers.py         |  22 --
 tests/pipelines/lint/modules_json.py          |   6 -
 tests/pipelines/lint/multiqc_config.py        | 129 -------
 tests/pipelines/lint/nextflow_config.py       | 211 -----------
 tests/pipelines/lint/nfcore_yml.py            |  53 ---
 tests/pipelines/lint/template_strings.py      |  53 ---
 tests/pipelines/lint/test_actions_awstest.py  |  39 ++
 tests/pipelines/lint/test_actions_ci.py       |  50 +++
 .../lint/test_actions_schema_validation.py    |  62 +++
 tests/pipelines/lint/test_configs.py          |  91 +++++
 tests/pipelines/lint/test_files_exist.py      |  91 +++++
 tests/pipelines/lint/test_files_unchanged.py  |  28 ++
 tests/pipelines/lint/test_merge_markers.py    |  25 ++
 tests/pipelines/lint/test_modules_json.py     |  10 +
 tests/pipelines/lint/test_multiqc_config.py   | 127 +++++++
 tests/pipelines/lint/test_nextflow_config.py  | 200 ++++++++++
 tests/pipelines/lint/test_nfcore_yml.py       |  57 +++
 tests/pipelines/lint/test_template_strings.py |  55 +++
 .../lint/test_version_consistency.py          |  19 +
 tests/pipelines/lint/version_consistency.py   |  14 -
 tests/pipelines/test_lint.py                  | 354 ++++++++----------
 27 files changed, 1012 insertions(+), 1048 deletions(-)
 delete mode 100644 tests/pipelines/lint/actions_awstest.py
 delete mode 100644 tests/pipelines/lint/actions_ci.py
 delete mode 100644 tests/pipelines/lint/actions_schema_validation.py
 delete mode 100644 tests/pipelines/lint/configs.py
 delete mode 100644 tests/pipelines/lint/files_exist.py
 delete mode 100644 tests/pipelines/lint/files_unchanged.py
 delete mode 100644 tests/pipelines/lint/merge_markers.py
 delete mode 100644 tests/pipelines/lint/modules_json.py
 delete mode 100644 tests/pipelines/lint/multiqc_config.py
 delete mode 100644 tests/pipelines/lint/nextflow_config.py
 delete mode 100644 tests/pipelines/lint/nfcore_yml.py
 delete mode 100644 tests/pipelines/lint/template_strings.py
 create mode 100644 tests/pipelines/lint/test_actions_awstest.py
 create mode 100644 tests/pipelines/lint/test_actions_ci.py
 create mode 100644 tests/pipelines/lint/test_actions_schema_validation.py
 create mode 100644 tests/pipelines/lint/test_configs.py
 create mode 100644 tests/pipelines/lint/test_files_exist.py
 create mode 100644 tests/pipelines/lint/test_files_unchanged.py
 create mode 100644 tests/pipelines/lint/test_merge_markers.py
 create mode 100644 tests/pipelines/lint/test_modules_json.py
 create mode 100644 tests/pipelines/lint/test_multiqc_config.py
 create mode 100644 tests/pipelines/lint/test_nextflow_config.py
 create mode 100644 tests/pipelines/lint/test_nfcore_yml.py
 create mode 100644 tests/pipelines/lint/test_template_strings.py
 create mode 100644 tests/pipelines/lint/test_version_consistency.py
 delete mode 100644 tests/pipelines/lint/version_consistency.py

diff --git a/tests/pipelines/lint/actions_awstest.py b/tests/pipelines/lint/actions_awstest.py
deleted file mode 100644
index 259bf866bf..0000000000
--- a/tests/pipelines/lint/actions_awstest.py
+++ /dev/null
@@ -1,37 +0,0 @@
-import os
-
-import yaml
-
-import nf_core.pipelines.lint
-
-
-def test_actions_awstest_pass(self):
-    """Lint test: actions_awstest - PASS"""
-    self.lint_obj._load()
-    results = self.lint_obj.actions_awstest()
-    assert results["passed"] == ["'.github/workflows/awstest.yml' is triggered correctly"]
-    assert len(results.get("warned", [])) == 0
-    assert len(results.get("failed", [])) == 0
-    assert len(results.get("ignored", [])) == 0
-
-
-def test_actions_awstest_fail(self):
-    """Lint test: actions_awsfulltest - FAIL"""
-
-    # Edit .github/workflows/awsfulltest.yml to use -profile test_full
-    new_pipeline = self._make_pipeline_copy()
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml")) as fh:
-        awstest_yml = yaml.safe_load(fh)
-    awstest_yml[True]["push"] = ["master"]
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml"), "w") as fh:
-        yaml.dump(awstest_yml, fh)
-
-    # Make lint object
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-
-    results = lint_obj.actions_awstest()
-    assert results["failed"] == ["'.github/workflows/awstest.yml' is not triggered correctly"]
-    assert len(results.get("warned", [])) == 0
-    assert len(results.get("passed", [])) == 0
-    assert len(results.get("ignored", [])) == 0
diff --git a/tests/pipelines/lint/actions_ci.py b/tests/pipelines/lint/actions_ci.py
deleted file mode 100644
index eb438b881d..0000000000
--- a/tests/pipelines/lint/actions_ci.py
+++ /dev/null
@@ -1,49 +0,0 @@
-import os
-
-import yaml
-
-import nf_core.pipelines.lint
-
-
-def test_actions_ci_pass(self):
-    """Lint test: actions_ci - PASS"""
-    self.lint_obj._load()
-    results = self.lint_obj.actions_ci()
-    assert results["passed"] == [
-        "'.github/workflows/ci.yml' is triggered on expected events",
-        "'.github/workflows/ci.yml' checks minimum NF version",
-    ]
-    assert len(results.get("warned", [])) == 0
-    assert len(results.get("failed", [])) == 0
-    assert len(results.get("ignored", [])) == 0
-
-
-def test_actions_ci_fail_wrong_nf(self):
-    """Lint test: actions_ci - FAIL - wrong minimum version of Nextflow tested"""
-    self.lint_obj._load()
-    self.lint_obj.minNextflowVersion = "1.2.3"
-    results = self.lint_obj.actions_ci()
-    assert results["failed"] == ["Minimum pipeline NF version '1.2.3' is not tested in '.github/workflows/ci.yml'"]
-
-
-def test_actions_ci_fail_wrong_trigger(self):
-    """Lint test: actions_actions_ci - FAIL - workflow triggered incorrectly, NF ver not checked at all"""
-
-    # Edit .github/workflows/actions_ci.yml to mess stuff up!
-    new_pipeline = self._make_pipeline_copy()
-    with open(os.path.join(new_pipeline, ".github", "workflows", "ci.yml")) as fh:
-        ci_yml = yaml.safe_load(fh)
-    ci_yml[True]["push"] = ["dev", "patch"]
-    ci_yml["jobs"]["test"]["strategy"]["matrix"] = {"nxf_versionnn": ["foo", ""]}
-    with open(os.path.join(new_pipeline, ".github", "workflows", "ci.yml"), "w") as fh:
-        yaml.dump(ci_yml, fh)
-
-    # Make lint object
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-
-    results = lint_obj.actions_ci()
-    assert results["failed"] == [
-        "'.github/workflows/ci.yml' is not triggered on expected events",
-        "'.github/workflows/ci.yml' does not check minimum NF version",
-    ]
diff --git a/tests/pipelines/lint/actions_schema_validation.py b/tests/pipelines/lint/actions_schema_validation.py
deleted file mode 100644
index 4b00e7bf40..0000000000
--- a/tests/pipelines/lint/actions_schema_validation.py
+++ /dev/null
@@ -1,66 +0,0 @@
-from pathlib import Path
-
-import yaml
-
-import nf_core.pipelines.lint
-
-
-def test_actions_schema_validation_missing_jobs(self):
-    """Missing 'jobs' field should result in failure"""
-    new_pipeline = self._make_pipeline_copy()
-
-    awstest_yml_path = Path(new_pipeline) / ".github" / "workflows" / "awstest.yml"
-    with open(awstest_yml_path) as fh:
-        awstest_yml = yaml.safe_load(fh)
-    awstest_yml.pop("jobs")
-    with open(awstest_yml_path, "w") as fh:
-        yaml.dump(awstest_yml, fh)
-
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-
-    results = lint_obj.actions_schema_validation()
-
-    assert "Workflow validation failed for awstest.yml: 'jobs' is a required property" in results["failed"][0]
-
-
-def test_actions_schema_validation_missing_on(self):
-    """Missing 'on' field should result in failure"""
-    new_pipeline = self._make_pipeline_copy()
-
-    awstest_yml_path = Path(new_pipeline) / ".github" / "workflows" / "awstest.yml"
-    with open(awstest_yml_path) as fh:
-        awstest_yml = yaml.safe_load(fh)
-    awstest_yml.pop(True)
-    with open(awstest_yml_path, "w") as fh:
-        yaml.dump(awstest_yml, fh)
-
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-
-    results = lint_obj.actions_schema_validation()
-
-    assert results["failed"][0] == "Missing 'on' keyword in awstest.yml"
-    assert "Workflow validation failed for awstest.yml: 'on' is a required property" in results["failed"][1]
-
-
-def test_actions_schema_validation_fails_for_additional_property(self):
-    """Missing 'jobs' field should result in failure"""
-    new_pipeline = self._make_pipeline_copy()
-
-    awstest_yml_path = Path(new_pipeline) / ".github" / "workflows" / "awstest.yml"
-    with open(awstest_yml_path) as fh:
-        awstest_yml = yaml.safe_load(fh)
-    awstest_yml["not_jobs"] = awstest_yml["jobs"]
-    with open(awstest_yml_path, "w") as fh:
-        yaml.dump(awstest_yml, fh)
-
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-
-    results = lint_obj.actions_schema_validation()
-
-    assert (
-        "Workflow validation failed for awstest.yml: Additional properties are not allowed ('not_jobs' was unexpected)"
-        in results["failed"][0]
-    )
diff --git a/tests/pipelines/lint/configs.py b/tests/pipelines/lint/configs.py
deleted file mode 100644
index 3ca35cab8c..0000000000
--- a/tests/pipelines/lint/configs.py
+++ /dev/null
@@ -1,89 +0,0 @@
-from pathlib import Path
-
-import yaml
-
-import nf_core.pipelines.create
-import nf_core.pipelines.lint
-
-
-def test_withname_in_modules_config(self):
-    """Tests finding withName in modules.config passes linting."""
-
-    new_pipeline = self._make_pipeline_copy()
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    result = lint_obj.modules_config()
-    assert len(result["failed"]) == 0
-    assert any(
-        ["`FASTQC` found in `conf/modules.config` and Nextflow scripts." in passed for passed in result["passed"]]
-    )
-
-
-def test_superfluous_withname_in_modules_config_fails(self):
-    """Tests finding withName in modules.config fails linting."""
-    new_pipeline = self._make_pipeline_copy()
-    # Add withName to modules.config
-    modules_config = Path(new_pipeline) / "conf" / "modules.config"
-    with open(modules_config, "a") as f:
-        f.write("\nwithName: 'BPIPE' {\n cache = false \n}")
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline, hide_progress=False)
-    lint_obj._load()
-    result = lint_obj.modules_config()
-    assert len(result["failed"]) == 1
-    assert result["failed"][0].startswith("`conf/modules.config` contains `withName:BPIPE`")
-
-
-def test_ignore_modules_config(self):
-    """Tests ignoring the modules.config passes linting."""
-    new_pipeline = self._make_pipeline_copy()
-    # ignore modules.config in linting
-    with open(Path(new_pipeline) / ".nf-core.yml") as f:
-        content = yaml.safe_load(f)
-        old_content = content.copy()
-        content["lint"] = {"modules_config": False}
-    with open(Path(new_pipeline) / ".nf-core.yml", "w") as f:
-        yaml.dump(content, f)
-    Path(new_pipeline, "conf", "modules.config").unlink()
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    result = lint_obj.modules_config()
-    assert len(result["ignored"]) == 1
-    assert result["ignored"][0].startswith("`conf/modules.config` not found, but it is ignored.")
-    # cleanup
-    with open(Path(new_pipeline) / ".nf-core.yml", "w") as f:
-        yaml.dump(old_content, f)
-
-
-def test_superfluous_withname_in_base_config_fails(self):
-    """Tests finding withName in base.config fails linting."""
-    new_pipeline = self._make_pipeline_copy()
-    # Add withName to base.config
-    base_config = Path(new_pipeline) / "conf" / "base.config"
-    with open(base_config, "a") as f:
-        f.write("\nwithName:CUSTOM_DUMPSOFTWAREVERSIONS {\n cache = false \n}")
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    result = lint_obj.base_config()
-    assert len(result["failed"]) == 1
-    assert result["failed"][0].startswith("`conf/base.config` contains `withName:CUSTOM_DUMPSOFTWAREVERSIONS`")
-
-
-def test_ignore_base_config(self):
-    """Tests ignoring the base.config passes linting."""
-    new_pipeline = self._make_pipeline_copy()
-    # ignore base.config in linting
-    with open(Path(new_pipeline) / ".nf-core.yml") as f:
-        content = yaml.safe_load(f)
-        old_content = content.copy()
-        content["lint"] = {"base_config": False}
-    with open(Path(new_pipeline) / ".nf-core.yml", "w") as f:
-        yaml.dump(content, f)
-    Path(new_pipeline, "conf", "base.config").unlink()
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    result = lint_obj.base_config()
-    assert len(result["ignored"]) == 1
-    assert result["ignored"][0].startswith("`conf/base.config` not found, but it is ignored.")
-    # cleanup
-    with open(Path(new_pipeline) / ".nf-core.yml", "w") as f:
-        yaml.dump(old_content, f)
diff --git a/tests/pipelines/lint/files_exist.py b/tests/pipelines/lint/files_exist.py
deleted file mode 100644
index 4ae167b1d0..0000000000
--- a/tests/pipelines/lint/files_exist.py
+++ /dev/null
@@ -1,97 +0,0 @@
-from pathlib import Path
-
-import nf_core.pipelines.lint
-
-
-def test_files_exist_missing_config(self):
-    """Lint test: critical files missing FAIL"""
-    new_pipeline = self._make_pipeline_copy()
-
-    Path(new_pipeline, "CHANGELOG.md").unlink()
-
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    lint_obj.nf_config["manifest.name"] = "nf-core/testpipeline"
-
-    results = lint_obj.files_exist()
-    assert "File not found: `CHANGELOG.md`" in results["failed"]
-
-
-def test_files_exist_missing_main(self):
-    """Check if missing main issues warning"""
-    new_pipeline = self._make_pipeline_copy()
-
-    Path(new_pipeline, "main.nf").unlink()
-
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-
-    results = lint_obj.files_exist()
-    assert "File not found: `main.nf`" in results["warned"]
-
-
-def test_files_exist_deprecated_file(self):
-    """Check whether deprecated file issues warning"""
-    new_pipeline = self._make_pipeline_copy()
-
-    nf = Path(new_pipeline, "parameters.settings.json")
-    nf.touch()
-
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-
-    results = lint_obj.files_exist()
-    assert results["failed"] == ["File must be removed: `parameters.settings.json`"]
-
-
-def test_files_exist_pass(self):
-    """Lint check should pass if all files are there"""
-
-    new_pipeline = self._make_pipeline_copy()
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-
-    results = lint_obj.files_exist()
-    assert results["failed"] == []
-
-
-def test_files_exist_pass_conditional(self):
-    new_pipeline = self._make_pipeline_copy()
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    lint_obj.nf_config["plugins"] = []
-    lib_dir = Path(new_pipeline, "lib")
-    lib_dir.mkdir()
-    (lib_dir / "nfcore_external_java_deps.jar").touch()
-    results = lint_obj.files_exist()
-    assert results["failed"] == []
-    assert results["ignored"] == []
-
-
-def test_files_exist_fail_conditional(self):
-    new_pipeline = self._make_pipeline_copy()
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    lib_dir = Path(new_pipeline, "lib")
-    lib_dir.mkdir()
-    (lib_dir / "nfcore_external_java_deps.jar").touch()
-    results = lint_obj.files_exist()
-    assert results["failed"] == ["File must be removed: `lib/nfcore_external_java_deps.jar`"]
-    assert results["ignored"] == []
-
-
-def test_files_exist_pass_conditional_nfschema(self):
-    new_pipeline = self._make_pipeline_copy()
-    # replace nf-validation with nf-schema in nextflow.config
-    with open(Path(new_pipeline, "nextflow.config")) as f:
-        config = f.read()
-    config = config.replace("nf-validation", "nf-schema")
-    with open(Path(new_pipeline, "nextflow.config"), "w") as f:
-        f.write(config)
-
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    lint_obj.nf_config["manifest.schema"] = "nf-core"
-    results = lint_obj.files_exist()
-    assert results["failed"] == []
-    assert results["ignored"] == []
diff --git a/tests/pipelines/lint/files_unchanged.py b/tests/pipelines/lint/files_unchanged.py
deleted file mode 100644
index 07a7229191..0000000000
--- a/tests/pipelines/lint/files_unchanged.py
+++ /dev/null
@@ -1,26 +0,0 @@
-from pathlib import Path
-
-import nf_core.pipelines.lint
-
-
-def test_files_unchanged_pass(self):
-    self.lint_obj._load()
-    results = self.lint_obj.files_unchanged()
-    assert len(results.get("warned", [])) == 0
-    assert len(results.get("failed", [])) == 0
-    assert len(results.get("ignored", [])) == 0
-    assert not results.get("could_fix", True)
-
-
-def test_files_unchanged_fail(self):
-    failing_file = Path(".github", "CONTRIBUTING.md")
-    new_pipeline = self._make_pipeline_copy()
-    with open(Path(new_pipeline, failing_file), "a") as fh:
-        fh.write("THIS SHOULD NOT BE HERE")
-
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    results = lint_obj.files_unchanged()
-    assert len(results["failed"]) > 0
-    assert str(failing_file) in results["failed"][0]
-    assert results["could_fix"]
diff --git a/tests/pipelines/lint/merge_markers.py b/tests/pipelines/lint/merge_markers.py
deleted file mode 100644
index 0e3699e190..0000000000
--- a/tests/pipelines/lint/merge_markers.py
+++ /dev/null
@@ -1,22 +0,0 @@
-import os
-
-import nf_core.pipelines.lint
-
-
-def test_merge_markers_found(self):
-    """Missing 'jobs' field should result in failure"""
-    new_pipeline = self._make_pipeline_copy()
-
-    with open(os.path.join(new_pipeline, "main.nf")) as fh:
-        main_nf_content = fh.read()
-    main_nf_content = ">>>>>>>\n" + main_nf_content
-    with open(os.path.join(new_pipeline, "main.nf"), "w") as fh:
-        fh.write(main_nf_content)
-
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-
-    results = lint_obj.merge_markers()
-    assert len(results["failed"]) > 0
-    assert len(results["passed"]) == 0
-    assert "Merge marker '>>>>>>>' in " in results["failed"][0]
diff --git a/tests/pipelines/lint/modules_json.py b/tests/pipelines/lint/modules_json.py
deleted file mode 100644
index f025daa7f1..0000000000
--- a/tests/pipelines/lint/modules_json.py
+++ /dev/null
@@ -1,6 +0,0 @@
-def test_modules_json_pass(self):
-    self.lint_obj._load()
-    results = self.lint_obj.modules_json()
-    assert len(results.get("warned", [])) == 0
-    assert len(results.get("failed", [])) == 0
-    assert len(results.get("passed", [])) > 0
diff --git a/tests/pipelines/lint/multiqc_config.py b/tests/pipelines/lint/multiqc_config.py
deleted file mode 100644
index 7f1fdbd67c..0000000000
--- a/tests/pipelines/lint/multiqc_config.py
+++ /dev/null
@@ -1,129 +0,0 @@
-from pathlib import Path
-
-import yaml
-
-import nf_core.pipelines.lint
-
-
-def test_multiqc_config_exists(self):
-    """Test that linting fails if the multiqc_config.yml file is missing"""
-    # Delete the file
-    new_pipeline = self._make_pipeline_copy()
-    Path(Path(new_pipeline, "assets", "multiqc_config.yml")).unlink()
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    result = lint_obj.multiqc_config()
-    assert result["failed"] == ["`assets/multiqc_config.yml` not found."]
-
-
-def test_multiqc_config_ignore(self):
-    """Test that linting succeeds if the multiqc_config.yml file is missing but ignored"""
-    # Delete the file
-    new_pipeline = self._make_pipeline_copy()
-    Path(Path(new_pipeline, "assets", "multiqc_config.yml")).unlink()
-    with open(Path(new_pipeline, ".nf-core.yml")) as f:
-        content = yaml.safe_load(f)
-        old_content = content.copy()
-        content["lint"] = {"multiqc_config": False}
-    with open(Path(new_pipeline, ".nf-core.yml"), "w") as f:
-        yaml.dump(content, f)
-
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    result = lint_obj.multiqc_config()
-    assert result["ignored"] == ["`assets/multiqc_config.yml` not found, but it is ignored."]
-
-    # cleanup
-    with open(Path(new_pipeline, ".nf-core.yml"), "w") as f:
-        yaml.dump(old_content, f)
-
-
-def test_multiqc_config_missing_report_section_order(self):
-    """Test that linting fails if the multiqc_config.yml file is missing the report_section_order"""
-    new_pipeline = self._make_pipeline_copy()
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml")) as fh:
-        mqc_yml = yaml.safe_load(fh)
-    mqc_yml_tmp = mqc_yml.copy()
-    mqc_yml.pop("report_section_order")
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
-        yaml.safe_dump(mqc_yml, fh)
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    result = lint_obj.multiqc_config()
-    # Reset the file
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
-        yaml.safe_dump(mqc_yml_tmp, fh)
-    assert result["failed"] == ["`assets/multiqc_config.yml` does not contain `report_section_order`"]
-
-
-def test_multiqc_incorrect_export_plots(self):
-    """Test that linting fails if the multiqc_config.yml file has an incorrect value for export_plots"""
-    new_pipeline = self._make_pipeline_copy()
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml")) as fh:
-        mqc_yml = yaml.safe_load(fh)
-    mqc_yml_tmp = mqc_yml.copy()
-    mqc_yml["export_plots"] = False
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
-        yaml.safe_dump(mqc_yml, fh)
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    result = lint_obj.multiqc_config()
-    # Reset the file
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
-        yaml.safe_dump(mqc_yml_tmp, fh)
-    assert result["failed"] == ["`assets/multiqc_config.yml` does not contain 'export_plots: true'."]
-
-
-def test_multiqc_config_report_comment_fail(self):
-    """Test that linting fails if the multiqc_config.yml file has an incorrect report_comment"""
-    new_pipeline = self._make_pipeline_copy()
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml")) as fh:
-        mqc_yml = yaml.safe_load(fh)
-    mqc_yml_tmp = mqc_yml.copy()
-    mqc_yml["report_comment"] = "This is a test"
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
-        yaml.safe_dump(mqc_yml, fh)
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    result = lint_obj.multiqc_config()
-    # Reset the file
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
-        yaml.safe_dump(mqc_yml_tmp, fh)
-    assert len(result["failed"]) == 1
-    assert result["failed"][0].startswith("`assets/multiqc_config.yml` does not contain a matching 'report_comment'.")
-
-
-def test_multiqc_config_report_comment_release_fail(self):
-    """Test that linting fails if the multiqc_config.yml file has an incorrect report_comment for a release version"""
-    new_pipeline = self._make_pipeline_copy()
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml")) as fh:
-        mqc_yml = yaml.safe_load(fh)
-    mqc_yml_tmp = mqc_yml.copy()
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
-        yaml.safe_dump(mqc_yml, fh)
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    # bump version
-    lint_obj.nf_config["manifest.version"] = "1.0"
-    result = lint_obj.multiqc_config()
-    # Reset the file
-    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
-        yaml.safe_dump(mqc_yml_tmp, fh)
-    assert len(result["failed"]) == 1
-    assert result["failed"][0].startswith("`assets/multiqc_config.yml` does not contain a matching 'report_comment'.")
-
-
-def test_multiqc_config_report_comment_release_succeed(self):
-    """Test that linting fails if the multiqc_config.yml file has a correct report_comment for a release version"""
-
-    import nf_core.pipelines.bump_version
-
-    new_pipeline = self._make_pipeline_copy()
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    # bump version using the bump_version function
-    nf_core.pipelines.bump_version.bump_pipeline_version(lint_obj, "1.0")
-    # lint again
-    lint_obj._load()
-    result = lint_obj.multiqc_config()
-    assert "`assets/multiqc_config.yml` contains a matching 'report_comment'." in result["passed"]
diff --git a/tests/pipelines/lint/nextflow_config.py b/tests/pipelines/lint/nextflow_config.py
deleted file mode 100644
index d9157c90c6..0000000000
--- a/tests/pipelines/lint/nextflow_config.py
+++ /dev/null
@@ -1,211 +0,0 @@
-import os
-import re
-from pathlib import Path
-
-import nf_core.pipelines.create.create
-import nf_core.pipelines.lint
-
-
-def test_nextflow_config_example_pass(self):
-    """Tests that config variable existence test works with good pipeline example"""
-    self.lint_obj.load_pipeline_config()
-    result = self.lint_obj.nextflow_config()
-    assert len(result["failed"]) == 0
-    assert len(result["warned"]) == 0
-
-
-def test_nextflow_config_bad_name_fail(self):
-    """Tests that config variable existence test fails with bad pipeline name"""
-    new_pipeline = self._make_pipeline_copy()
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj.load_pipeline_config()
-
-    lint_obj.nf_config["manifest.name"] = "bad_name"
-    result = lint_obj.nextflow_config()
-    assert len(result["failed"]) > 0
-    assert len(result["warned"]) == 0
-
-
-def test_nextflow_config_dev_in_release_mode_failed(self):
-    """Tests that config variable existence test fails with dev version in release mode"""
-    new_pipeline = self._make_pipeline_copy()
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj.load_pipeline_config()
-
-    lint_obj.release_mode = True
-    lint_obj.nf_config["manifest.version"] = "dev_is_bad_name"
-    result = lint_obj.nextflow_config()
-    assert len(result["failed"]) > 0
-    assert len(result["warned"]) == 0
-
-
-def test_nextflow_config_missing_test_profile_failed(self):
-    """Test failure if config file does not contain `test` profile."""
-    new_pipeline = self._make_pipeline_copy()
-    # Change the name of the test profile so there is no such profile
-    nf_conf_file = os.path.join(new_pipeline, "nextflow.config")
-    with open(nf_conf_file) as f:
-        content = f.read()
-        fail_content = re.sub(r"\btest\b", "testfail", content)
-    with open(nf_conf_file, "w") as f:
-        f.write(fail_content)
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj.load_pipeline_config()
-    result = lint_obj.nextflow_config()
-    assert len(result["failed"]) > 0
-    assert len(result["warned"]) == 0
-
-
-def test_default_values_match(self):
-    """Test that the default values in nextflow.config match the default values defined in the nextflow_schema.json."""
-    new_pipeline = self._make_pipeline_copy()
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj.load_pipeline_config()
-    result = lint_obj.nextflow_config()
-    assert len(result["failed"]) == 0
-    assert len(result["warned"]) == 0
-    assert "Config default value correct: params.max_cpus" in str(result["passed"])
-    assert "Config default value correct: params.validate_params" in str(result["passed"])
-
-
-def test_default_values_fail(self):
-    """Test linting fails if the default values in nextflow.config do not match the ones defined in the nextflow_schema.json."""
-    new_pipeline = self._make_pipeline_copy()
-    # Change the default value of max_cpus in nextflow.config
-    nf_conf_file = Path(new_pipeline) / "nextflow.config"
-    with open(nf_conf_file) as f:
-        content = f.read()
-        fail_content = re.sub(r"\bmax_cpus\s*=\s*16\b", "max_cpus = 0", content)
-    with open(nf_conf_file, "w") as f:
-        f.write(fail_content)
-    # Change the default value of max_memory in nextflow_schema.json
-    nf_schema_file = Path(new_pipeline) / "nextflow_schema.json"
-    with open(nf_schema_file) as f:
-        content = f.read()
-        fail_content = re.sub(r'"default": "128.GB"', '"default": "18.GB"', content)
-    with open(nf_schema_file, "w") as f:
-        f.write(fail_content)
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj.load_pipeline_config()
-    result = lint_obj.nextflow_config()
-    assert len(result["failed"]) == 2
-    assert (
-        "Config default value incorrect: `params.max_cpus` is set as `16` in `nextflow_schema.json` but is `0` in `nextflow.config`."
-        in result["failed"]
-    )
-    assert (
-        "Config default value incorrect: `params.max_memory` is set as `18.GB` in `nextflow_schema.json` but is `128.GB` in `nextflow.config`."
-        in result["failed"]
-    )
-
-
-def test_catch_params_assignment_in_main_nf(self):
-    """Test linting fails if main.nf contains an assignment to a parameter from nextflow_schema.json."""
-    new_pipeline = self._make_pipeline_copy()
-    # Add parameter assignment in main.nf
-    main_nf_file = Path(new_pipeline) / "main.nf"
-    with open(main_nf_file, "a") as f:
-        f.write("params.max_time = 42")
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj.load_pipeline_config()
-    result = lint_obj.nextflow_config()
-    assert len(result["failed"]) == 1
-    assert (
-        result["failed"][0]
-        == "Config default value incorrect: `params.max_time` is set as `240.h` in `nextflow_schema.json` but is `null` in `nextflow.config`."
-    )
-
-
-def test_allow_params_reference_in_main_nf(self):
-    """Test linting allows for references like `params.aligner == 'bwa'` in main.nf. The test will detect if the bug mentioned in GitHub-issue #2833 reemerges."""
-    new_pipeline = self._make_pipeline_copy()
-    # Add parameter reference in main.nf
-    main_nf_file = Path(new_pipeline) / "main.nf"
-    with open(main_nf_file, "a") as f:
-        f.write("params.max_time == 42")
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj.load_pipeline_config()
-    result = lint_obj.nextflow_config()
-    assert len(result["failed"]) == 0
-
-
-def test_default_values_ignored(self):
-    """Test ignoring linting of default values."""
-    new_pipeline = self._make_pipeline_copy()
-    # Add max_cpus to the ignore list
-    nf_core_yml = Path(new_pipeline) / ".nf-core.yml"
-    with open(nf_core_yml, "w") as f:
-        f.write(
-            "repository_type: pipeline\nlint:\n  nextflow_config:\n    - config_defaults:\n      - params.max_cpus\n"
-        )
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj.load_pipeline_config()
-    lint_obj._load_lint_config()
-    result = lint_obj.nextflow_config()
-    assert len(result["failed"]) == 0
-    assert len(result["ignored"]) == 1
-    assert "Config default value correct: params.max_cpu" not in str(result["passed"])
-    assert "Config default ignored: params.max_cpus" in str(result["ignored"])
-
-
-def test_default_values_float(self):
-    """Test comparing two float values."""
-    new_pipeline = self._make_pipeline_copy()
-    # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params`
-    nf_conf_file = Path(new_pipeline) / "nextflow.config"
-    with open(nf_conf_file) as f:
-        content = f.read()
-        fail_content = re.sub(
-            r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content
-        )
-    with open(nf_conf_file, "w") as f:
-        f.write(fail_content)
-    # Add a float value `dummy` to the nextflow_schema.json
-    nf_schema_file = Path(new_pipeline) / "nextflow_schema.json"
-    with open(nf_schema_file) as f:
-        content = f.read()
-        fail_content = re.sub(
-            r'"validate_params": {',
-            '    "dummy": {"type": "number","default":0.000000001},\n"validate_params": {',
-            content,
-        )
-    with open(nf_schema_file, "w") as f:
-        f.write(fail_content)
-
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj.load_pipeline_config()
-    result = lint_obj.nextflow_config()
-    assert len(result["failed"]) == 0
-    assert len(result["warned"]) == 0
-    assert "Config default value correct: params.dummy" in str(result["passed"])
-
-
-def test_default_values_float_fail(self):
-    """Test comparing two float values."""
-    new_pipeline = self._make_pipeline_copy()
-    # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params`
-    nf_conf_file = Path(new_pipeline) / "nextflow.config"
-    with open(nf_conf_file) as f:
-        content = f.read()
-        fail_content = re.sub(
-            r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content
-        )
-    with open(nf_conf_file, "w") as f:
-        f.write(fail_content)
-    # Add a float value `dummy` to the nextflow_schema.json
-    nf_schema_file = Path(new_pipeline) / "nextflow_schema.json"
-    with open(nf_schema_file) as f:
-        content = f.read()
-        fail_content = re.sub(
-            r'"validate_params": {', '    "dummy": {"type": "float","default":0.000001},\n"validate_params": {', content
-        )
-    with open(nf_schema_file, "w") as f:
-        f.write(fail_content)
-
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj.load_pipeline_config()
-    result = lint_obj.nextflow_config()
-
-    assert len(result["failed"]) == 1
-    assert len(result["warned"]) == 0
-    assert "Config default value incorrect: `params.dummy" in str(result["failed"])
diff --git a/tests/pipelines/lint/nfcore_yml.py b/tests/pipelines/lint/nfcore_yml.py
deleted file mode 100644
index 94d2870e11..0000000000
--- a/tests/pipelines/lint/nfcore_yml.py
+++ /dev/null
@@ -1,53 +0,0 @@
-import re
-from pathlib import Path
-
-import nf_core.pipelines.create
-import nf_core.pipelines.lint
-
-
-def test_nfcore_yml_pass(self):
-    """Lint test: nfcore_yml - PASS"""
-    self.lint_obj._load()
-    results = self.lint_obj.nfcore_yml()
-
-    assert "Repository type in `.nf-core.yml` is valid" in str(results["passed"])
-    assert "nf-core version in `.nf-core.yml` is set to the latest version" in str(results["passed"])
-    assert len(results.get("warned", [])) == 0
-    assert len(results.get("failed", [])) == 0
-    assert len(results.get("ignored", [])) == 0
-
-
-def test_nfcore_yml_fail_repo_type(self):
-    """Lint test: nfcore_yml - FAIL - repository type not set"""
-    new_pipeline = self._make_pipeline_copy()
-    nf_core_yml = Path(new_pipeline) / ".nf-core.yml"
-    with open(nf_core_yml) as fh:
-        content = fh.read()
-        new_content = content.replace("repository_type: pipeline", "repository_type: foo")
-    with open(nf_core_yml, "w") as fh:
-        fh.write(new_content)
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    results = lint_obj.nfcore_yml()
-    assert "Repository type in `.nf-core.yml` is not valid." in str(results["failed"])
-    assert len(results.get("warned", [])) == 0
-    assert len(results.get("passed", [])) >= 0
-    assert len(results.get("ignored", [])) == 0
-
-
-def test_nfcore_yml_fail_nfcore_version(self):
-    """Lint test: nfcore_yml - FAIL - nf-core version not set"""
-    new_pipeline = self._make_pipeline_copy()
-    nf_core_yml = Path(new_pipeline) / ".nf-core.yml"
-    with open(nf_core_yml) as fh:
-        content = fh.read()
-        new_content = re.sub(r"nf_core_version:.+", "nf_core_version: foo", content)
-    with open(nf_core_yml, "w") as fh:
-        fh.write(new_content)
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    results = lint_obj.nfcore_yml()
-    assert "nf-core version in `.nf-core.yml` is not set to the latest version." in str(results["warned"])
-    assert len(results.get("failed", [])) == 0
-    assert len(results.get("passed", [])) >= 0
-    assert len(results.get("ignored", [])) == 0
diff --git a/tests/pipelines/lint/template_strings.py b/tests/pipelines/lint/template_strings.py
deleted file mode 100644
index 2db9e20a3f..0000000000
--- a/tests/pipelines/lint/template_strings.py
+++ /dev/null
@@ -1,53 +0,0 @@
-import subprocess
-from pathlib import Path
-
-import nf_core.pipelines.create
-import nf_core.pipelines.lint
-
-
-def test_template_strings(self):
-    """Tests finding a template string in a file fails linting."""
-    new_pipeline = self._make_pipeline_copy()
-    # Add template string to a file
-    txt_file = Path(new_pipeline) / "docs" / "test.txt"
-    with open(txt_file, "w") as f:
-        f.write("my {{ template_string }}")
-    subprocess.check_output(["git", "add", "docs"], cwd=new_pipeline)
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    result = lint_obj.template_strings()
-    assert len(result["failed"]) == 1
-    assert len(result["ignored"]) == 0
-
-
-def test_template_strings_ignored(self):
-    """Tests ignoring template_strings"""
-    new_pipeline = self._make_pipeline_copy()
-    # Ignore template_strings test
-    nf_core_yml = Path(new_pipeline) / ".nf-core.yml"
-    with open(nf_core_yml, "w") as f:
-        f.write("repository_type: pipeline\nlint:\n  template_strings: False")
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    lint_obj._lint_pipeline()
-    assert len(lint_obj.failed) == 0
-    assert len(lint_obj.ignored) == 1
-
-
-def test_template_strings_ignore_file(self):
-    """Tests ignoring template_strings file"""
-    new_pipeline = self._make_pipeline_copy()
-    # Add template string to a file
-    txt_file = Path(new_pipeline) / "docs" / "test.txt"
-    with open(txt_file, "w") as f:
-        f.write("my {{ template_string }}")
-    subprocess.check_output(["git", "add", "docs"], cwd=new_pipeline)
-    # Ignore template_strings test
-    nf_core_yml = Path(new_pipeline) / ".nf-core.yml"
-    with open(nf_core_yml, "w") as f:
-        f.write("repository_type: pipeline\nlint:\n  template_strings:\n    - docs/test.txt")
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj._load()
-    result = lint_obj.template_strings()
-    assert len(result["failed"]) == 0
-    assert len(result["ignored"]) == 1
diff --git a/tests/pipelines/lint/test_actions_awstest.py b/tests/pipelines/lint/test_actions_awstest.py
new file mode 100644
index 0000000000..51b55cb867
--- /dev/null
+++ b/tests/pipelines/lint/test_actions_awstest.py
@@ -0,0 +1,39 @@
+from pathlib import Path
+
+import yaml
+
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintActionsAws(TestLint):
+    def test_actions_awstest_pass(self):
+        """Lint test: actions_awstest - PASS"""
+        self.lint_obj._load()
+        results = self.lint_obj.actions_awstest()
+        assert results["passed"] == ["'.github/workflows/awstest.yml' is triggered correctly"]
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("failed", [])) == 0
+        assert len(results.get("ignored", [])) == 0
+
+    def test_actions_awstest_fail(self):
+        """Lint test: actions_awsfulltest - FAIL"""
+
+        # Edit .github/workflows/awsfulltest.yml to use -profile test_full
+        new_pipeline = self._make_pipeline_copy()
+        with open(Path(new_pipeline, ".github", "workflows", "awstest.yml")) as fh:
+            awstest_yml = yaml.safe_load(fh)
+        awstest_yml[True]["push"] = ["master"]
+        with open(Path(new_pipeline, ".github", "workflows", "awstest.yml"), "w") as fh:
+            yaml.dump(awstest_yml, fh)
+
+        # Make lint object
+        lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
+        lint_obj._load()
+
+        results = lint_obj.actions_awstest()
+        assert results["failed"] == ["'.github/workflows/awstest.yml' is not triggered correctly"]
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("passed", [])) == 0
+        assert len(results.get("ignored", [])) == 0
diff --git a/tests/pipelines/lint/test_actions_ci.py b/tests/pipelines/lint/test_actions_ci.py
new file mode 100644
index 0000000000..7319ce4b0c
--- /dev/null
+++ b/tests/pipelines/lint/test_actions_ci.py
@@ -0,0 +1,50 @@
+from pathlib import Path
+
+import yaml
+
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintActionsCi(TestLint):
+    def test_actions_ci_pass(self):
+        """Lint test: actions_ci - PASS"""
+        self.lint_obj._load()
+        results = self.lint_obj.actions_ci()
+        assert results["passed"] == [
+            "'.github/workflows/ci.yml' is triggered on expected events",
+            "'.github/workflows/ci.yml' checks minimum NF version",
+        ]
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("failed", [])) == 0
+        assert len(results.get("ignored", [])) == 0
+
+    def test_actions_ci_fail_wrong_nf(self):
+        """Lint test: actions_ci - FAIL - wrong minimum version of Nextflow tested"""
+        self.lint_obj._load()
+        self.lint_obj.minNextflowVersion = "1.2.3"
+        results = self.lint_obj.actions_ci()
+        assert results["failed"] == ["Minimum pipeline NF version '1.2.3' is not tested in '.github/workflows/ci.yml'"]
+
+    def test_actions_ci_fail_wrong_trigger(self):
+        """Lint test: actions_actions_ci - FAIL - workflow triggered incorrectly, NF ver not checked at all"""
+
+        # Edit .github/workflows/actions_ci.yml to mess stuff up!
+        new_pipeline = self._make_pipeline_copy()
+        with open(Path(new_pipeline, ".github", "workflows", "ci.yml")) as fh:
+            ci_yml = yaml.safe_load(fh)
+        ci_yml[True]["push"] = ["dev", "patch"]
+        ci_yml["jobs"]["test"]["strategy"]["matrix"] = {"nxf_versionnn": ["foo", ""]}
+        with open(Path(new_pipeline, ".github", "workflows", "ci.yml"), "w") as fh:
+            yaml.dump(ci_yml, fh)
+
+        # Make lint object
+        lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
+        lint_obj._load()
+
+        results = lint_obj.actions_ci()
+        assert results["failed"] == [
+            "'.github/workflows/ci.yml' is not triggered on expected events",
+            "'.github/workflows/ci.yml' does not check minimum NF version",
+        ]
diff --git a/tests/pipelines/lint/test_actions_schema_validation.py b/tests/pipelines/lint/test_actions_schema_validation.py
new file mode 100644
index 0000000000..34f6b5fcb8
--- /dev/null
+++ b/tests/pipelines/lint/test_actions_schema_validation.py
@@ -0,0 +1,62 @@
+from pathlib import Path
+
+import yaml
+
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintActionsSchemaValidation(TestLint):
+    def setUp(self) -> None:
+        super().setUp()
+        self.new_pipeline = self._make_pipeline_copy()
+        self.awstest_yml_path = Path(self.new_pipeline) / ".github" / "workflows" / "awstest.yml"
+        with open(self.awstest_yml_path) as fh:
+            self.awstest_yml = yaml.safe_load(fh)
+
+    def test_actions_schema_validation_missing_jobs(self):
+        """Missing 'jobs' field should result in failure"""
+
+        self.awstest_yml.pop("jobs")
+        with open(self.awstest_yml_path, "w") as fh:
+            yaml.dump(self.awstest_yml, fh)
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+
+        results = lint_obj.actions_schema_validation()
+
+        assert "Workflow validation failed for awstest.yml: 'jobs' is a required property" in results["failed"][0]
+
+    def test_actions_schema_validation_missing_on(self):
+        """Missing 'on' field should result in failure"""
+
+        self.awstest_yml.pop(True)
+        with open(self.awstest_yml_path, "w") as fh:
+            yaml.dump(self.awstest_yml, fh)
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+
+        results = lint_obj.actions_schema_validation()
+
+        assert results["failed"][0] == "Missing 'on' keyword in awstest.yml"
+        assert "Workflow validation failed for awstest.yml: 'on' is a required property" in results["failed"][1]
+
+    def test_actions_schema_validation_fails_for_additional_property(self):
+        """Missing 'jobs' field should result in failure"""
+
+        self.awstest_yml["not_jobs"] = self.awstest_yml["jobs"]
+        with open(self.awstest_yml_path, "w") as fh:
+            yaml.dump(self.awstest_yml, fh)
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+
+        results = lint_obj.actions_schema_validation()
+
+        assert (
+            "Workflow validation failed for awstest.yml: Additional properties are not allowed ('not_jobs' was unexpected)"
+            in results["failed"][0]
+        )
diff --git a/tests/pipelines/lint/test_configs.py b/tests/pipelines/lint/test_configs.py
new file mode 100644
index 0000000000..7bb6329b5b
--- /dev/null
+++ b/tests/pipelines/lint/test_configs.py
@@ -0,0 +1,91 @@
+from pathlib import Path
+
+import yaml
+
+import nf_core.pipelines.create
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintConfigs(TestLint):
+    def setUp(self) -> None:
+        super().setUp()
+        self.new_pipeline = self._make_pipeline_copy()
+
+    def test_withname_in_modules_config(self):
+        """Tests finding withName in modules.config passes linting."""
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        result = lint_obj.modules_config()
+        assert len(result["failed"]) == 0
+        assert any(
+            ["`FASTQC` found in `conf/modules.config` and Nextflow scripts." in passed for passed in result["passed"]]
+        )
+
+    def test_superfluous_withname_in_modules_config_fails(self):
+        """Tests finding withName in modules.config fails linting."""
+
+        # Add withName to modules.config
+        modules_config = Path(self.new_pipeline) / "conf" / "modules.config"
+        with open(modules_config, "a") as f:
+            f.write("\nwithName: 'BPIPE' {\n cache = false \n}")
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline, hide_progress=False)
+        lint_obj._load()
+        result = lint_obj.modules_config()
+        assert len(result["failed"]) == 1
+        assert result["failed"][0].startswith("`conf/modules.config` contains `withName:BPIPE`")
+
+    def test_ignore_modules_config(self):
+        """Tests ignoring the modules.config passes linting."""
+
+        # ignore modules.config in linting
+        with open(Path(self.new_pipeline) / ".nf-core.yml") as f:
+            content = yaml.safe_load(f)
+            old_content = content.copy()
+            content["lint"] = {"modules_config": False}
+        with open(Path(self.new_pipeline) / ".nf-core.yml", "w") as f:
+            yaml.dump(content, f)
+        Path(self.new_pipeline, "conf", "modules.config").unlink()
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        result = lint_obj.modules_config()
+        assert len(result["ignored"]) == 1
+        assert result["ignored"][0].startswith("`conf/modules.config` not found, but it is ignored.")
+        # cleanup
+        with open(Path(self.new_pipeline) / ".nf-core.yml", "w") as f:
+            yaml.dump(old_content, f)
+
+    def test_superfluous_withname_in_base_config_fails(self):
+        """Tests finding withName in base.config fails linting."""
+
+        # Add withName to base.config
+        base_config = Path(self.new_pipeline) / "conf" / "base.config"
+        with open(base_config, "a") as f:
+            f.write("\nwithName:CUSTOM_DUMPSOFTWAREVERSIONS {\n cache = false \n}")
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        result = lint_obj.base_config()
+        assert len(result["failed"]) == 1
+        assert result["failed"][0].startswith("`conf/base.config` contains `withName:CUSTOM_DUMPSOFTWAREVERSIONS`")
+
+    def test_ignore_base_config(self):
+        """Tests ignoring the base.config passes linting."""
+
+        # ignore base.config in linting
+        with open(Path(self.new_pipeline) / ".nf-core.yml") as f:
+            content = yaml.safe_load(f)
+            old_content = content.copy()
+            content["lint"] = {"base_config": False}
+        with open(Path(self.new_pipeline) / ".nf-core.yml", "w") as f:
+            yaml.dump(content, f)
+        Path(self.new_pipeline, "conf", "base.config").unlink()
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        result = lint_obj.base_config()
+        assert len(result["ignored"]) == 1
+        assert result["ignored"][0].startswith("`conf/base.config` not found, but it is ignored.")
+        # cleanup
+        with open(Path(self.new_pipeline) / ".nf-core.yml", "w") as f:
+            yaml.dump(old_content, f)
diff --git a/tests/pipelines/lint/test_files_exist.py b/tests/pipelines/lint/test_files_exist.py
new file mode 100644
index 0000000000..85ba817536
--- /dev/null
+++ b/tests/pipelines/lint/test_files_exist.py
@@ -0,0 +1,91 @@
+from pathlib import Path
+
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintFilesExist(TestLint):
+    def setUp(self) -> None:
+        super().setUp()
+        self.new_pipeline = self._make_pipeline_copy()
+
+    def test_files_exist_missing_config(self):
+        """Lint test: critical files missing FAIL"""
+
+        Path(self.new_pipeline, "CHANGELOG.md").unlink()
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        lint_obj.nf_config["manifest.name"] = "nf-core/testpipeline"
+
+        results = lint_obj.files_exist()
+        assert "File not found: `CHANGELOG.md`" in results["failed"]
+
+    def test_files_exist_missing_main(self):
+        """Check if missing main issues warning"""
+
+        Path(self.new_pipeline, "main.nf").unlink()
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+
+        results = lint_obj.files_exist()
+        assert "File not found: `main.nf`" in results["warned"]
+
+    def test_files_exist_deprecated_file(self):
+        """Check whether deprecated file issues warning"""
+
+        nf = Path(self.new_pipeline, "parameters.settings.json")
+        nf.touch()
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+
+        results = lint_obj.files_exist()
+        assert results["failed"] == ["File must be removed: `parameters.settings.json`"]
+
+    def test_files_exist_pass(self):
+        """Lint check should pass if all files are there"""
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+
+        results = lint_obj.files_exist()
+        assert results["failed"] == []
+
+    def test_files_exist_pass_conditional(self):
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        lint_obj.nf_config["plugins"] = []
+        lib_dir = Path(self.new_pipeline, "lib")
+        lib_dir.mkdir()
+        (lib_dir / "nfcore_external_java_deps.jar").touch()
+        results = lint_obj.files_exist()
+        assert results["failed"] == []
+        assert results["ignored"] == []
+
+    def test_files_exist_fail_conditional(self):
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        lib_dir = Path(self.new_pipeline, "lib")
+        lib_dir.mkdir()
+        (lib_dir / "nfcore_external_java_deps.jar").touch()
+        results = lint_obj.files_exist()
+        assert results["failed"] == ["File must be removed: `lib/nfcore_external_java_deps.jar`"]
+        assert results["ignored"] == []
+
+    def test_files_exist_pass_conditional_nfschema(self):
+        # replace nf-validation with nf-schema in nextflow.config
+        with open(Path(self.new_pipeline, "nextflow.config")) as f:
+            config = f.read()
+        config = config.replace("nf-validation", "nf-schema")
+        with open(Path(self.new_pipeline, "nextflow.config"), "w") as f:
+            f.write(config)
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        lint_obj.nf_config["manifest.schema"] = "nf-core"
+        results = lint_obj.files_exist()
+        assert results["failed"] == []
+        assert results["ignored"] == []
diff --git a/tests/pipelines/lint/test_files_unchanged.py b/tests/pipelines/lint/test_files_unchanged.py
new file mode 100644
index 0000000000..4282b49958
--- /dev/null
+++ b/tests/pipelines/lint/test_files_unchanged.py
@@ -0,0 +1,28 @@
+from pathlib import Path
+
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintFilesUnchanged(TestLint):
+    def test_files_unchanged_pass(self):
+        self.lint_obj._load()
+        results = self.lint_obj.files_unchanged()
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("failed", [])) == 0
+        assert len(results.get("ignored", [])) == 0
+        assert not results.get("could_fix", True)
+
+    def test_files_unchanged_fail(self):
+        failing_file = Path(".github", "CONTRIBUTING.md")
+        new_pipeline = self._make_pipeline_copy()
+        with open(Path(new_pipeline, failing_file), "a") as fh:
+            fh.write("THIS SHOULD NOT BE HERE")
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
+        lint_obj._load()
+        results = lint_obj.files_unchanged()
+        assert len(results["failed"]) > 0
+        assert str(failing_file) in results["failed"][0]
+        assert results["could_fix"]
diff --git a/tests/pipelines/lint/test_merge_markers.py b/tests/pipelines/lint/test_merge_markers.py
new file mode 100644
index 0000000000..3094d8f8d1
--- /dev/null
+++ b/tests/pipelines/lint/test_merge_markers.py
@@ -0,0 +1,25 @@
+import os
+
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintMergeMarkers(TestLint):
+    def test_merge_markers_found(self):
+        """Missing 'jobs' field should result in failure"""
+        new_pipeline = self._make_pipeline_copy()
+
+        with open(os.path.join(new_pipeline, "main.nf")) as fh:
+            main_nf_content = fh.read()
+        main_nf_content = ">>>>>>>\n" + main_nf_content
+        with open(os.path.join(new_pipeline, "main.nf"), "w") as fh:
+            fh.write(main_nf_content)
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
+        lint_obj._load()
+
+        results = lint_obj.merge_markers()
+        assert len(results["failed"]) > 0
+        assert len(results["passed"]) == 0
+        assert "Merge marker '>>>>>>>' in " in results["failed"][0]
diff --git a/tests/pipelines/lint/test_modules_json.py b/tests/pipelines/lint/test_modules_json.py
new file mode 100644
index 0000000000..0d8333d9a2
--- /dev/null
+++ b/tests/pipelines/lint/test_modules_json.py
@@ -0,0 +1,10 @@
+from ..test_lint import TestLint
+
+
+class TestLintModulesJson(TestLint):
+    def test_modules_json_pass(self):
+        self.lint_obj._load()
+        results = self.lint_obj.modules_json()
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("failed", [])) == 0
+        assert len(results.get("passed", [])) > 0
diff --git a/tests/pipelines/lint/test_multiqc_config.py b/tests/pipelines/lint/test_multiqc_config.py
new file mode 100644
index 0000000000..5da6e567ec
--- /dev/null
+++ b/tests/pipelines/lint/test_multiqc_config.py
@@ -0,0 +1,127 @@
+from pathlib import Path
+
+import yaml
+
+import nf_core.pipelines.bump_version
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintMultiqcConfig(TestLint):
+    def setUp(self) -> None:
+        super().setUp()
+        self.new_pipeline = self._make_pipeline_copy()
+        self.multiqc_config_yml = Path(self.new_pipeline, "assets", "multiqc_config.yml")
+
+    def test_multiqc_config_exists(self):
+        """Test that linting fails if the multiqc_config.yml file is missing"""
+        # Delete the file
+        self.multiqc_config_yml.unlink()
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        result = lint_obj.multiqc_config()
+        assert result["failed"] == ["`assets/multiqc_config.yml` not found."]
+
+    def test_multiqc_config_ignore(self):
+        """Test that linting succeeds if the multiqc_config.yml file is missing but ignored"""
+        # Delete the file
+        self.multiqc_config_yml.unlink()
+        with open(Path(self.new_pipeline, ".nf-core.yml")) as f:
+            content = yaml.safe_load(f)
+            old_content = content.copy()
+            content["lint"] = {"multiqc_config": False}
+        with open(Path(self.new_pipeline, ".nf-core.yml"), "w") as f:
+            yaml.dump(content, f)
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        result = lint_obj.multiqc_config()
+        assert result["ignored"] == ["`assets/multiqc_config.yml` not found, but it is ignored."]
+
+        # cleanup
+        with open(Path(self.new_pipeline, ".nf-core.yml"), "w") as f:
+            yaml.dump(old_content, f)
+
+    def test_multiqc_config_missing_report_section_order(self):
+        """Test that linting fails if the multiqc_config.yml file is missing the report_section_order"""
+        with open(self.multiqc_config_yml) as fh:
+            mqc_yml = yaml.safe_load(fh)
+        mqc_yml_tmp = mqc_yml.copy()
+        mqc_yml.pop("report_section_order")
+        with open(self.multiqc_config_yml, "w") as fh:
+            yaml.safe_dump(mqc_yml, fh)
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        result = lint_obj.multiqc_config()
+        # Reset the file
+        with open(self.multiqc_config_yml, "w") as fh:
+            yaml.safe_dump(mqc_yml_tmp, fh)
+        assert result["failed"] == ["`assets/multiqc_config.yml` does not contain `report_section_order`"]
+
+    def test_multiqc_incorrect_export_plots(self):
+        """Test that linting fails if the multiqc_config.yml file has an incorrect value for export_plots"""
+        with open(self.multiqc_config_yml) as fh:
+            mqc_yml = yaml.safe_load(fh)
+        mqc_yml_tmp = mqc_yml.copy()
+        mqc_yml["export_plots"] = False
+        with open(self.multiqc_config_yml, "w") as fh:
+            yaml.safe_dump(mqc_yml, fh)
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        result = lint_obj.multiqc_config()
+        # Reset the file
+        with open(self.multiqc_config_yml, "w") as fh:
+            yaml.safe_dump(mqc_yml_tmp, fh)
+        assert result["failed"] == ["`assets/multiqc_config.yml` does not contain 'export_plots: true'."]
+
+    def test_multiqc_config_report_comment_fail(self):
+        """Test that linting fails if the multiqc_config.yml file has an incorrect report_comment"""
+        with open(self.multiqc_config_yml) as fh:
+            mqc_yml = yaml.safe_load(fh)
+        mqc_yml_tmp = mqc_yml.copy()
+        mqc_yml["report_comment"] = "This is a test"
+        with open(self.multiqc_config_yml, "w") as fh:
+            yaml.safe_dump(mqc_yml, fh)
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        result = lint_obj.multiqc_config()
+        # Reset the file
+        with open(self.multiqc_config_yml, "w") as fh:
+            yaml.safe_dump(mqc_yml_tmp, fh)
+        assert len(result["failed"]) == 1
+        assert result["failed"][0].startswith(
+            "`assets/multiqc_config.yml` does not contain a matching 'report_comment'."
+        )
+
+    def test_multiqc_config_report_comment_release_fail(self):
+        """Test that linting fails if the multiqc_config.yml file has an incorrect report_comment for a release version"""
+        with open(self.multiqc_config_yml) as fh:
+            mqc_yml = yaml.safe_load(fh)
+        mqc_yml_tmp = mqc_yml.copy()
+        with open(self.multiqc_config_yml, "w") as fh:
+            yaml.safe_dump(mqc_yml, fh)
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        # bump version
+        lint_obj.nf_config["manifest.version"] = "1.0"
+        result = lint_obj.multiqc_config()
+        # Reset the file
+        with open(self.multiqc_config_yml, "w") as fh:
+            yaml.safe_dump(mqc_yml_tmp, fh)
+        assert len(result["failed"]) == 1
+        assert result["failed"][0].startswith(
+            "`assets/multiqc_config.yml` does not contain a matching 'report_comment'."
+        )
+
+    def test_multiqc_config_report_comment_release_succeed(self):
+        """Test that linting fails if the multiqc_config.yml file has a correct report_comment for a release version"""
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        # bump version using the bump_version function
+        nf_core.pipelines.bump_version.bump_pipeline_version(lint_obj, "1.0")
+        # lint again
+        lint_obj._load()
+        result = lint_obj.multiqc_config()
+        assert "`assets/multiqc_config.yml` contains a matching 'report_comment'." in result["passed"]
diff --git a/tests/pipelines/lint/test_nextflow_config.py b/tests/pipelines/lint/test_nextflow_config.py
new file mode 100644
index 0000000000..01173aec34
--- /dev/null
+++ b/tests/pipelines/lint/test_nextflow_config.py
@@ -0,0 +1,200 @@
+import os
+import re
+from pathlib import Path
+
+import nf_core.pipelines.create.create
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintNextflowConfig(TestLint):
+    def setUp(self) -> None:
+        super().setUp()
+        self.new_pipeline = self._make_pipeline_copy()
+
+    def test_nextflow_config_example_pass(self):
+        """Tests that config variable existence test works with good pipeline example"""
+        self.lint_obj.load_pipeline_config()
+        result = self.lint_obj.nextflow_config()
+        assert len(result["failed"]) == 0
+        assert len(result["warned"]) == 0
+
+    def test_default_values_match(self):
+        """Test that the default values in nextflow.config match the default values defined in the nextflow_schema.json."""
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+        result = lint_obj.nextflow_config()
+        assert len(result["failed"]) == 0
+        assert len(result["warned"]) == 0
+        assert "Config default value correct: params.max_cpus" in str(result["passed"])
+        assert "Config default value correct: params.validate_params" in str(result["passed"])
+
+    def test_nextflow_config_bad_name_fail(self):
+        """Tests that config variable existence test fails with bad pipeline name"""
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+
+        lint_obj.nf_config["manifest.name"] = "bad_name"
+        result = lint_obj.nextflow_config()
+        assert len(result["failed"]) > 0
+        assert len(result["warned"]) == 0
+
+    def test_nextflow_config_dev_in_release_mode_failed(self):
+        """Tests that config variable existence test fails with dev version in release mode"""
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+
+        lint_obj.release_mode = True
+        lint_obj.nf_config["manifest.version"] = "dev_is_bad_name"
+        result = lint_obj.nextflow_config()
+        assert len(result["failed"]) > 0
+        assert len(result["warned"]) == 0
+
+    def test_nextflow_config_missing_test_profile_failed(self):
+        """Test failure if config file does not contain `test` profile."""
+        # Change the name of the test profile so there is no such profile
+        nf_conf_file = os.path.join(self.new_pipeline, "nextflow.config")
+        with open(nf_conf_file) as f:
+            content = f.read()
+            fail_content = re.sub(r"\btest\b", "testfail", content)
+        with open(nf_conf_file, "w") as f:
+            f.write(fail_content)
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+        result = lint_obj.nextflow_config()
+        assert len(result["failed"]) > 0
+        assert len(result["warned"]) == 0
+
+    def test_default_values_fail(self):
+        """Test linting fails if the default values in nextflow.config do not match the ones defined in the nextflow_schema.json."""
+        # Change the default value of max_cpus in nextflow.config
+        nf_conf_file = Path(self.new_pipeline) / "nextflow.config"
+        with open(nf_conf_file) as f:
+            content = f.read()
+            fail_content = re.sub(r"\bmax_cpus\s*=\s*16\b", "max_cpus = 0", content)
+        with open(nf_conf_file, "w") as f:
+            f.write(fail_content)
+        # Change the default value of max_memory in nextflow_schema.json
+        nf_schema_file = Path(self.new_pipeline) / "nextflow_schema.json"
+        with open(nf_schema_file) as f:
+            content = f.read()
+            fail_content = re.sub(r'"default": "128.GB"', '"default": "18.GB"', content)
+        with open(nf_schema_file, "w") as f:
+            f.write(fail_content)
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+        result = lint_obj.nextflow_config()
+        assert len(result["failed"]) == 2
+        assert (
+            "Config default value incorrect: `params.max_cpus` is set as `16` in `nextflow_schema.json` but is `0` in `nextflow.config`."
+            in result["failed"]
+        )
+        assert (
+            "Config default value incorrect: `params.max_memory` is set as `18.GB` in `nextflow_schema.json` but is `128.GB` in `nextflow.config`."
+            in result["failed"]
+        )
+
+    def test_catch_params_assignment_in_main_nf(self):
+        """Test linting fails if main.nf contains an assignment to a parameter from nextflow_schema.json."""
+        # Add parameter assignment in main.nf
+        main_nf_file = Path(self.new_pipeline) / "main.nf"
+        with open(main_nf_file, "a") as f:
+            f.write("params.max_time = 42")
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+        result = lint_obj.nextflow_config()
+        assert len(result["failed"]) == 1
+        assert (
+            result["failed"][0]
+            == "Config default value incorrect: `params.max_time` is set as `240.h` in `nextflow_schema.json` but is `null` in `nextflow.config`."
+        )
+
+    def test_allow_params_reference_in_main_nf(self):
+        """Test linting allows for references like `params.aligner == 'bwa'` in main.nf. The test will detect if the bug mentioned in GitHub-issue #2833 reemerges."""
+        # Add parameter reference in main.nf
+        main_nf_file = Path(self.new_pipeline) / "main.nf"
+        with open(main_nf_file, "a") as f:
+            f.write("params.max_time == 42")
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+        result = lint_obj.nextflow_config()
+        assert len(result["failed"]) == 0
+
+    def test_default_values_ignored(self):
+        """Test ignoring linting of default values."""
+        # Add max_cpus to the ignore list
+        nf_core_yml = Path(self.new_pipeline) / ".nf-core.yml"
+        with open(nf_core_yml, "w") as f:
+            f.write(
+                "repository_type: pipeline\nlint:\n  nextflow_config:\n    - config_defaults:\n      - params.max_cpus\n"
+            )
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+        lint_obj._load_lint_config()
+        result = lint_obj.nextflow_config()
+        assert len(result["failed"]) == 0
+        assert len(result["ignored"]) == 1
+        assert "Config default value correct: params.max_cpu" not in str(result["passed"])
+        assert "Config default ignored: params.max_cpus" in str(result["ignored"])
+
+    def test_default_values_float(self):
+        """Test comparing two float values."""
+        # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params`
+        nf_conf_file = Path(self.new_pipeline) / "nextflow.config"
+        with open(nf_conf_file) as f:
+            content = f.read()
+            fail_content = re.sub(
+                r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content
+            )
+        with open(nf_conf_file, "w") as f:
+            f.write(fail_content)
+        # Add a float value `dummy` to the nextflow_schema.json
+        nf_schema_file = Path(self.new_pipeline) / "nextflow_schema.json"
+        with open(nf_schema_file) as f:
+            content = f.read()
+            fail_content = re.sub(
+                r'"validate_params": {',
+                '    "dummy": {"type": "number","default":0.000000001},\n"validate_params": {',
+                content,
+            )
+        with open(nf_schema_file, "w") as f:
+            f.write(fail_content)
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+        result = lint_obj.nextflow_config()
+        assert len(result["failed"]) == 0
+        assert len(result["warned"]) == 0
+        assert "Config default value correct: params.dummy" in str(result["passed"])
+
+    def test_default_values_float_fail(self):
+        """Test comparing two float values."""
+        # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params`
+        nf_conf_file = Path(self.new_pipeline) / "nextflow.config"
+        with open(nf_conf_file) as f:
+            content = f.read()
+            fail_content = re.sub(
+                r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content
+            )
+        with open(nf_conf_file, "w") as f:
+            f.write(fail_content)
+        # Add a float value `dummy` to the nextflow_schema.json
+        nf_schema_file = Path(self.new_pipeline) / "nextflow_schema.json"
+        with open(nf_schema_file) as f:
+            content = f.read()
+            fail_content = re.sub(
+                r'"validate_params": {',
+                '    "dummy": {"type": "float","default":0.000001},\n"validate_params": {',
+                content,
+            )
+        with open(nf_schema_file, "w") as f:
+            f.write(fail_content)
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+        result = lint_obj.nextflow_config()
+
+        assert len(result["failed"]) == 1
+        assert len(result["warned"]) == 0
+        assert "Config default value incorrect: `params.dummy" in str(result["failed"])
diff --git a/tests/pipelines/lint/test_nfcore_yml.py b/tests/pipelines/lint/test_nfcore_yml.py
new file mode 100644
index 0000000000..955c00da81
--- /dev/null
+++ b/tests/pipelines/lint/test_nfcore_yml.py
@@ -0,0 +1,57 @@
+import re
+from pathlib import Path
+
+import nf_core.pipelines.create
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintNfCoreYml(TestLint):
+    def setUp(self) -> None:
+        super().setUp()
+        self.new_pipeline = self._make_pipeline_copy()
+        self.nf_core_yml = Path(self.new_pipeline) / ".nf-core.yml"
+
+    def test_nfcore_yml_pass(self):
+        """Lint test: nfcore_yml - PASS"""
+        self.lint_obj._load()
+        results = self.lint_obj.nfcore_yml()
+
+        assert "Repository type in `.nf-core.yml` is valid" in str(results["passed"])
+        assert "nf-core version in `.nf-core.yml` is set to the latest version" in str(results["passed"])
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("failed", [])) == 0
+        assert len(results.get("ignored", [])) == 0
+
+    def test_nfcore_yml_fail_repo_type(self):
+        """Lint test: nfcore_yml - FAIL - repository type not set"""
+
+        with open(self.nf_core_yml) as fh:
+            content = fh.read()
+            new_content = content.replace("repository_type: pipeline", "repository_type: foo")
+        with open(self.nf_core_yml, "w") as fh:
+            fh.write(new_content)
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        results = lint_obj.nfcore_yml()
+        assert "Repository type in `.nf-core.yml` is not valid." in str(results["failed"])
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("passed", [])) >= 0
+        assert len(results.get("ignored", [])) == 0
+
+    def test_nfcore_yml_fail_nfcore_version(self):
+        """Lint test: nfcore_yml - FAIL - nf-core version not set"""
+
+        with open(self.nf_core_yml) as fh:
+            content = fh.read()
+            new_content = re.sub(r"nf_core_version:.+", "nf_core_version: foo", content)
+        with open(self.nf_core_yml, "w") as fh:
+            fh.write(new_content)
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        results = lint_obj.nfcore_yml()
+        assert "nf-core version in `.nf-core.yml` is not set to the latest version." in str(results["warned"])
+        assert len(results.get("failed", [])) == 0
+        assert len(results.get("passed", [])) >= 0
+        assert len(results.get("ignored", [])) == 0
diff --git a/tests/pipelines/lint/test_template_strings.py b/tests/pipelines/lint/test_template_strings.py
new file mode 100644
index 0000000000..406ba63e0c
--- /dev/null
+++ b/tests/pipelines/lint/test_template_strings.py
@@ -0,0 +1,55 @@
+import subprocess
+from pathlib import Path
+
+import nf_core.pipelines.create
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintTemplateStrings(TestLint):
+    def setUp(self) -> None:
+        super().setUp()
+        self.new_pipeline = self._make_pipeline_copy()
+
+    def test_template_strings(self):
+        """Tests finding a template string in a file fails linting."""
+        # Add template string to a file
+        txt_file = Path(self.new_pipeline) / "docs" / "test.txt"
+        with open(txt_file, "w") as f:
+            f.write("my {{ template_string }}")
+        subprocess.check_output(["git", "add", "docs"], cwd=self.new_pipeline)
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        result = lint_obj.template_strings()
+        assert len(result["failed"]) == 1
+        assert len(result["ignored"]) == 0
+
+    def test_template_strings_ignored(self):
+        """Tests ignoring template_strings"""
+        # Ignore template_strings test
+        nf_core_yml = Path(self.new_pipeline) / ".nf-core.yml"
+        with open(nf_core_yml, "w") as f:
+            f.write("repository_type: pipeline\nlint:\n  template_strings: False")
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        lint_obj._lint_pipeline()
+        assert len(lint_obj.failed) == 0
+        assert len(lint_obj.ignored) == 1
+
+    def test_template_strings_ignore_file(self):
+        """Tests ignoring template_strings file"""
+        # Add template string to a file
+        txt_file = Path(self.new_pipeline) / "docs" / "test.txt"
+        with open(txt_file, "w") as f:
+            f.write("my {{ template_string }}")
+        subprocess.check_output(["git", "add", "docs"], cwd=self.new_pipeline)
+        # Ignore template_strings test
+        nf_core_yml = Path(self.new_pipeline) / ".nf-core.yml"
+        with open(nf_core_yml, "w") as f:
+            f.write("repository_type: pipeline\nlint:\n  template_strings:\n    - docs/test.txt")
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj._load()
+        result = lint_obj.template_strings()
+        assert len(result["failed"]) == 0
+        assert len(result["ignored"]) == 1
diff --git a/tests/pipelines/lint/test_version_consistency.py b/tests/pipelines/lint/test_version_consistency.py
new file mode 100644
index 0000000000..c5a2cc74f1
--- /dev/null
+++ b/tests/pipelines/lint/test_version_consistency.py
@@ -0,0 +1,19 @@
+import nf_core.pipelines.create.create
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintVersionConsistency(TestLint):
+    def test_version_consistency(self):
+        """Tests that config variable existence test fails with bad pipeline name"""
+        new_pipeline = self._make_pipeline_copy()
+        lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
+        lint_obj.load_pipeline_config()
+        lint_obj.nextflow_config()
+
+        result = lint_obj.version_consistency()
+        assert result["passed"] == [
+            "Version tags are numeric and consistent between container, release tag and config."
+        ]
+        assert result["failed"] == ["manifest.version was not numeric: 1.0.0dev!"]
diff --git a/tests/pipelines/lint/version_consistency.py b/tests/pipelines/lint/version_consistency.py
deleted file mode 100644
index 88eadce391..0000000000
--- a/tests/pipelines/lint/version_consistency.py
+++ /dev/null
@@ -1,14 +0,0 @@
-import nf_core.pipelines.create.create
-import nf_core.pipelines.lint
-
-
-def test_version_consistency(self):
-    """Tests that config variable existence test fails with bad pipeline name"""
-    new_pipeline = self._make_pipeline_copy()
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-    lint_obj.load_pipeline_config()
-    lint_obj.nextflow_config()
-
-    result = lint_obj.version_consistency()
-    assert result["passed"] == ["Version tags are numeric and consistent between container, release tag and config."]
-    assert result["failed"] == ["manifest.version was not numeric: 1.0.0dev!"]
diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py
index 54279cd064..b3eac17cb8 100644
--- a/tests/pipelines/test_lint.py
+++ b/tests/pipelines/test_lint.py
@@ -19,204 +19,166 @@ def setUp(self) -> None:
         super().setUp()
         self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir)
 
-    ##########################
-    # CORE lint.py FUNCTIONS #
-    ##########################
-    def test_run_linting_function(self):
-        """Run the master run_linting() function in lint.py
-
-        We don't really check any of this code as it's just a series of function calls
-        and we're testing each of those individually. This is mostly to check for syntax errors."""
-        nf_core.pipelines.lint.run_linting(self.pipeline_dir, False)
-
-    def test_init_pipeline_lint(self):
-        """Simply create a PipelineLint object.
-
-        This checks that all of the lint test imports are working properly,
-        we also check that the git sha was found and that the release flag works properly
-        """
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir, True)
-
-        # Tests that extra test is added for release mode
-        assert "version_consistency" in lint_obj.lint_tests
-        assert lint_obj.git_sha
-        # Tests that parent nf_core.utils.Pipeline class __init__() is working to find git hash
-        assert len(lint_obj.git_sha) > 0
-
-    def test_load_lint_config_not_found(self):
-        """Try to load a linting config file that doesn't exist"""
-        self.lint_obj._load_lint_config()
-        assert self.lint_obj.lint_config == {}
-
-    def test_load_lint_config_ignore_all_tests(self):
-        """Try to load a linting config file that ignores all tests"""
-
-        # Make a copy of the test pipeline and create a lint object
-        new_pipeline = self._make_pipeline_copy()
-        lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-
-        # Make a config file listing all test names
-        config_dict = {"lint": {test_name: False for test_name in lint_obj.lint_tests}}
-        with open(Path(new_pipeline, ".nf-core.yml"), "w") as fh:
-            yaml.dump(config_dict, fh)
-
-        # Load the new lint config file and check
-        lint_obj._load_lint_config()
-        assert sorted(list(lint_obj.lint_config.keys())) == sorted(lint_obj.lint_tests)
-
-        # Try running linting and make sure that all tests are ignored
-        lint_obj._lint_pipeline()
-        assert len(lint_obj.passed) == 0
-        assert len(lint_obj.warned) == 0
-        assert len(lint_obj.failed) == 0
-        assert len(lint_obj.ignored) == len(lint_obj.lint_tests)
-
-    @with_temporary_folder
-    def test_json_output(self, tmp_dir):
-        """
-        Test creation of a JSON file with lint results
-
-        Expected JSON output:
-        {
-            "nf_core_tools_version": "1.10.dev0",
-            "date_run": "2020-06-05 10:56:42",
-            "tests_pass": [
-                [ 1, "This test passed"],
-                [ 2, "This test also passed"]
-            ],
-            "tests_warned": [
-                [ 2, "This test gave a warning"]
-            ],
-            "tests_failed": [],
-            "num_tests_pass": 2,
-            "num_tests_warned": 1,
-            "num_tests_failed": 0,
-            "has_tests_pass": true,
-            "has_tests_warned": true,
-            "has_tests_failed": false
-        }
-        """
-        self.lint_obj.passed.append(("test_one", "This test passed"))
-        self.lint_obj.passed.append(("test_two", "This test also passed"))
-        self.lint_obj.warned.append(("test_three", "This test gave a warning"))
-
-        # Make a temp dir for the JSON output
-        json_fn = Path(tmp_dir, "lint_results.json")
-        self.lint_obj._save_json_results(json_fn)
-
-        # Load created JSON file and check its contents
-        with open(json_fn) as fh:
-            try:
-                saved_json = json.load(fh)
-            except json.JSONDecodeError as e:
-                raise UserWarning(f"Unable to load JSON file '{json_fn}' due to error {e}")
-        assert saved_json["num_tests_pass"] > 0
-        assert saved_json["num_tests_warned"] > 0
-        assert saved_json["num_tests_ignored"] == 0
-        assert saved_json["num_tests_failed"] == 0
-        assert saved_json["has_tests_pass"]
-        assert saved_json["has_tests_warned"]
-        assert not saved_json["has_tests_ignored"]
-        assert not saved_json["has_tests_failed"]
-
-    def test_wrap_quotes(self):
-        md = self.lint_obj._wrap_quotes(["one", "two", "three"])
-        assert md == "`one` or `two` or `three`"
-
-    def test_sphinx_md_files(self):
-        """Check that we have .md files for all lint module code,
-        and that there are no unexpected files (eg. deleted lint tests)"""
-
-        docs_basedir = Path(Path(__file__).parent.parent.parent, "docs", "api", "_src", "pipeline_lint_tests")
-
-        # Get list of existing .md files
-        existing_docs = []
-        existing_docs = [
-            str(Path(docs_basedir, fn))
-            for fn in Path(docs_basedir).iterdir()
-            if fn.match("*.md") and not fn.match("index.md")
-        ]
-
-        # Check .md files against each test name
-        lint_obj = nf_core.pipelines.lint.PipelineLint("", True)
-        for test_name in lint_obj.lint_tests:
-            fn = Path(docs_basedir, f"{test_name}.md")
-            assert fn.exists(), f"Could not find lint docs .md file: {fn}"
-            existing_docs.remove(str(fn))
-
-        # Check that we have no remaining .md files that we didn't expect
-        assert len(existing_docs) == 0, f"Unexpected lint docs .md files found: {', '.join(existing_docs)}"
+
+##########################
+# CORE lint.py FUNCTIONS #
+##########################
+def test_run_linting_function(self):
+    """Run the master run_linting() function in lint.py
+
+    We don't really check any of this code as it's just a series of function calls
+    and we're testing each of those individually. This is mostly to check for syntax errors."""
+    nf_core.pipelines.lint.run_linting(self.pipeline_dir, False)
+
+
+def test_init_pipeline_lint(self):
+    """Simply create a PipelineLint object.
+
+    This checks that all of the lint test imports are working properly,
+    we also check that the git sha was found and that the release flag works properly
+    """
+    lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir, True)
+
+    # Tests that extra test is added for release mode
+    assert "version_consistency" in lint_obj.lint_tests
+    assert lint_obj.git_sha
+    # Tests that parent nf_core.utils.Pipeline class __init__() is working to find git hash
+    assert len(lint_obj.git_sha) > 0
+
+
+def test_load_lint_config_not_found(self):
+    """Try to load a linting config file that doesn't exist"""
+    self.lint_obj._load_lint_config()
+    assert self.lint_obj.lint_config == {}
+
+
+def test_load_lint_config_ignore_all_tests(self):
+    """Try to load a linting config file that ignores all tests"""
+
+    # Make a copy of the test pipeline and create a lint object
+    new_pipeline = self._make_pipeline_copy()
+    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
+
+    # Make a config file listing all test names
+    config_dict = {"lint": {test_name: False for test_name in lint_obj.lint_tests}}
+    with open(Path(new_pipeline, ".nf-core.yml"), "w") as fh:
+        yaml.dump(config_dict, fh)
+
+    # Load the new lint config file and check
+    lint_obj._load_lint_config()
+    assert sorted(list(lint_obj.lint_config.keys())) == sorted(lint_obj.lint_tests)
+
+    # Try running linting and make sure that all tests are ignored
+    lint_obj._lint_pipeline()
+    assert len(lint_obj.passed) == 0
+    assert len(lint_obj.warned) == 0
+    assert len(lint_obj.failed) == 0
+    assert len(lint_obj.ignored) == len(lint_obj.lint_tests)
+
+
+@with_temporary_folder
+def test_json_output(self, tmp_dir):
+    """
+    Test creation of a JSON file with lint results
+
+    Expected JSON output:
+    {
+        "nf_core_tools_version": "1.10.dev0",
+        "date_run": "2020-06-05 10:56:42",
+        "tests_pass": [
+            [ 1, "This test passed"],
+            [ 2, "This test also passed"]
+        ],
+        "tests_warned": [
+            [ 2, "This test gave a warning"]
+        ],
+        "tests_failed": [],
+        "num_tests_pass": 2,
+        "num_tests_warned": 1,
+        "num_tests_failed": 0,
+        "has_tests_pass": true,
+        "has_tests_warned": true,
+        "has_tests_failed": false
+    }
+    """
+    self.lint_obj.passed.append(("test_one", "This test passed"))
+    self.lint_obj.passed.append(("test_two", "This test also passed"))
+    self.lint_obj.warned.append(("test_three", "This test gave a warning"))
+
+    # Make a temp dir for the JSON output
+    json_fn = Path(tmp_dir, "lint_results.json")
+    self.lint_obj._save_json_results(json_fn)
+
+    # Load created JSON file and check its contents
+    with open(json_fn) as fh:
+        try:
+            saved_json = json.load(fh)
+        except json.JSONDecodeError as e:
+            raise UserWarning(f"Unable to load JSON file '{json_fn}' due to error {e}")
+    assert saved_json["num_tests_pass"] > 0
+    assert saved_json["num_tests_warned"] > 0
+    assert saved_json["num_tests_ignored"] == 0
+    assert saved_json["num_tests_failed"] == 0
+    assert saved_json["has_tests_pass"]
+    assert saved_json["has_tests_warned"]
+    assert not saved_json["has_tests_ignored"]
+    assert not saved_json["has_tests_failed"]
+
+
+def test_wrap_quotes(self):
+    md = self.lint_obj._wrap_quotes(["one", "two", "three"])
+    assert md == "`one` or `two` or `three`"
+
+
+def test_sphinx_md_files(self):
+    """Check that we have .md files for all lint module code,
+    and that there are no unexpected files (eg. deleted lint tests)"""
+
+    docs_basedir = Path(Path(__file__).parent.parent.parent, "docs", "api", "_src", "pipeline_lint_tests")
+
+    # Get list of existing .md files
+    existing_docs = []
+    existing_docs = [
+        str(Path(docs_basedir, fn))
+        for fn in Path(docs_basedir).iterdir()
+        if fn.match("*.md") and not fn.match("index.md")
+    ]
+
+    # Check .md files against each test name
+    lint_obj = nf_core.pipelines.lint.PipelineLint("", True)
+    for test_name in lint_obj.lint_tests:
+        fn = Path(docs_basedir, f"{test_name}.md")
+        assert fn.exists(), f"Could not find lint docs .md file: {fn}"
+        existing_docs.remove(str(fn))
+
+    # Check that we have no remaining .md files that we didn't expect
+    assert len(existing_docs) == 0, f"Unexpected lint docs .md files found: {', '.join(existing_docs)}"
 
     #######################
     # SPECIFIC LINT TESTS #
     #######################
 
-    from .lint.actions_awstest import (  # type: ignore[misc]
-        test_actions_awstest_fail,
-        test_actions_awstest_pass,
-    )
-    from .lint.actions_ci import (  # type: ignore[misc]
-        test_actions_ci_fail_wrong_nf,
-        test_actions_ci_fail_wrong_trigger,
-        test_actions_ci_pass,
-    )
-    from .lint.actions_schema_validation import (  # type: ignore[misc]
-        test_actions_schema_validation_fails_for_additional_property,
-        test_actions_schema_validation_missing_jobs,
-        test_actions_schema_validation_missing_on,
-    )
-    from .lint.configs import (  # type: ignore[misc]
-        test_ignore_base_config,
-        test_ignore_modules_config,
-        test_superfluous_withname_in_base_config_fails,
-        test_superfluous_withname_in_modules_config_fails,
-        test_withname_in_modules_config,
-    )
-    from .lint.files_exist import (  # type: ignore[misc]
-        test_files_exist_deprecated_file,
-        test_files_exist_fail_conditional,
-        test_files_exist_missing_config,
-        test_files_exist_missing_main,
-        test_files_exist_pass,
-        test_files_exist_pass_conditional,
-        test_files_exist_pass_conditional_nfschema,
-    )
-    from .lint.files_unchanged import (  # type: ignore[misc]
-        test_files_unchanged_fail,
-        test_files_unchanged_pass,
-    )
-    from .lint.merge_markers import test_merge_markers_found  # type: ignore[misc]
-    from .lint.modules_json import test_modules_json_pass  # type: ignore[misc]
-    from .lint.multiqc_config import (  # type: ignore[misc]
-        test_multiqc_config_exists,
-        test_multiqc_config_ignore,
-        test_multiqc_config_missing_report_section_order,
-        test_multiqc_config_report_comment_fail,
-        test_multiqc_config_report_comment_release_fail,
-        test_multiqc_config_report_comment_release_succeed,
-        test_multiqc_incorrect_export_plots,
-    )
-    from .lint.nextflow_config import (  # type: ignore[misc]
-        test_allow_params_reference_in_main_nf,
-        test_catch_params_assignment_in_main_nf,
-        test_default_values_fail,
-        test_default_values_float,
-        test_default_values_float_fail,
-        test_default_values_ignored,
-        test_default_values_match,
-        test_nextflow_config_bad_name_fail,
-        test_nextflow_config_dev_in_release_mode_failed,
-        test_nextflow_config_example_pass,
-        test_nextflow_config_missing_test_profile_failed,
-    )
-    from .lint.nfcore_yml import (  # type: ignore[misc]
-        test_nfcore_yml_fail_nfcore_version,
-        test_nfcore_yml_fail_repo_type,
-        test_nfcore_yml_pass,
-    )
-    from .lint.template_strings import (  # type: ignore[misc]
-        test_template_strings,
-        test_template_strings_ignore_file,
-        test_template_strings_ignored,
-    )
-    from .lint.version_consistency import test_version_consistency  # type: ignore[misc]
+    # from .lint.nextflow_config import (  # type: ignore[misc]
+    #     test_allow_params_reference_in_main_nf,
+    #     test_catch_params_assignment_in_main_nf,
+    #     test_default_values_fail,
+    #     test_default_values_float,
+    #     test_default_values_float_fail,
+    #     test_default_values_ignored,
+    #     test_default_values_match,
+    #     test_nextflow_config_bad_name_fail,
+    #     test_nextflow_config_dev_in_release_mode_failed,
+    #     test_nextflow_config_example_pass,
+    #     test_nextflow_config_missing_test_profile_failed,
+    # )
+    # from .lint.nfcore_yml import (  # type: ignore[misc]
+    #     test_nfcore_yml_fail_nfcore_version,
+    #     test_nfcore_yml_fail_repo_type,
+    #     test_nfcore_yml_pass,
+    # )
+    # from .lint.template_strings import (  # type: ignore[misc]
+    #     test_template_strings,
+    #     test_template_strings_ignore_file,
+    #     test_template_strings_ignored,
+    # )
+    # from .lint.version_consistency import test_version_consistency  # type: ignore[misc]

From fcc43fd0c337ead404fba843eab51820d0f014a9 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 14:51:51 +0200
Subject: [PATCH 079/414] add more tests to CI

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 4e873385e8..fea96b4526 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -67,7 +67,7 @@ jobs:
       - name: List tests
         id: list_tests
         run: |
-          echo "tests=$(find tests/test_* | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
+          echo "tests=$(find tests/**/test_* | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
     outputs:
       tests: ${{ steps.list_tests.outputs.tests }}
 

From a779d12b7fff23ce9e93b905f49f37221276af43 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 15:15:40 +0200
Subject: [PATCH 080/414] simplify sed command

---
 .github/workflows/pytest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index fea96b4526..18f9b28098 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -67,7 +67,7 @@ jobs:
       - name: List tests
         id: list_tests
         run: |
-          echo "tests=$(find tests/**/test_* | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
+          echo "tests=$(find tests/**/test_* | tac | sed 's/.*\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
     outputs:
       tests: ${{ steps.list_tests.outputs.tests }}
 
@@ -132,7 +132,7 @@ jobs:
 
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$?
+          python3 -m pytest tests/**/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"

From ca0769bd76b207881a8e77d3a18f3902b2307474 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 15:31:01 +0200
Subject: [PATCH 081/414] fix ci tests

---
 .github/workflows/pytest.yml |  11 +-
 tests/pipelines/test_lint.py | 284 +++++++++++++++--------------------
 2 files changed, 133 insertions(+), 162 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 18f9b28098..72bacaeab9 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -67,7 +67,7 @@ jobs:
       - name: List tests
         id: list_tests
         run: |
-          echo "tests=$(find tests/**/test_* | tac | sed 's/.*\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
+          echo "tests=$(find tests/**/test_* | tac | sed 's/tests\///g'  | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
     outputs:
       tests: ${{ steps.list_tests.outputs.tests }}
 
@@ -132,7 +132,7 @@ jobs:
 
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/**/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"
@@ -149,10 +149,15 @@ jobs:
           name: Snapshot Report ${{ matrix.test }}
           path: ./snapshot_report.html
 
+      - name: remove slashes from test name
+        run: |
+          test=$(echo ${{ matrix.test }} | sed 's/\//__/g')
+          echo "test=${test}" >> $GITHUB_ENV
+
       - name: Upload coverage
         uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
-          name: coverage_${{ matrix.test }}
+          name: coverage_${{ env.test }}
           path: .coverage
 
   coverage:
diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py
index b3eac17cb8..ab8bcf6b24 100644
--- a/tests/pipelines/test_lint.py
+++ b/tests/pipelines/test_lint.py
@@ -23,162 +23,128 @@ def setUp(self) -> None:
 ##########################
 # CORE lint.py FUNCTIONS #
 ##########################
-def test_run_linting_function(self):
-    """Run the master run_linting() function in lint.py
-
-    We don't really check any of this code as it's just a series of function calls
-    and we're testing each of those individually. This is mostly to check for syntax errors."""
-    nf_core.pipelines.lint.run_linting(self.pipeline_dir, False)
-
-
-def test_init_pipeline_lint(self):
-    """Simply create a PipelineLint object.
-
-    This checks that all of the lint test imports are working properly,
-    we also check that the git sha was found and that the release flag works properly
-    """
-    lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir, True)
-
-    # Tests that extra test is added for release mode
-    assert "version_consistency" in lint_obj.lint_tests
-    assert lint_obj.git_sha
-    # Tests that parent nf_core.utils.Pipeline class __init__() is working to find git hash
-    assert len(lint_obj.git_sha) > 0
-
-
-def test_load_lint_config_not_found(self):
-    """Try to load a linting config file that doesn't exist"""
-    self.lint_obj._load_lint_config()
-    assert self.lint_obj.lint_config == {}
-
-
-def test_load_lint_config_ignore_all_tests(self):
-    """Try to load a linting config file that ignores all tests"""
-
-    # Make a copy of the test pipeline and create a lint object
-    new_pipeline = self._make_pipeline_copy()
-    lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
-
-    # Make a config file listing all test names
-    config_dict = {"lint": {test_name: False for test_name in lint_obj.lint_tests}}
-    with open(Path(new_pipeline, ".nf-core.yml"), "w") as fh:
-        yaml.dump(config_dict, fh)
-
-    # Load the new lint config file and check
-    lint_obj._load_lint_config()
-    assert sorted(list(lint_obj.lint_config.keys())) == sorted(lint_obj.lint_tests)
-
-    # Try running linting and make sure that all tests are ignored
-    lint_obj._lint_pipeline()
-    assert len(lint_obj.passed) == 0
-    assert len(lint_obj.warned) == 0
-    assert len(lint_obj.failed) == 0
-    assert len(lint_obj.ignored) == len(lint_obj.lint_tests)
-
-
-@with_temporary_folder
-def test_json_output(self, tmp_dir):
-    """
-    Test creation of a JSON file with lint results
-
-    Expected JSON output:
-    {
-        "nf_core_tools_version": "1.10.dev0",
-        "date_run": "2020-06-05 10:56:42",
-        "tests_pass": [
-            [ 1, "This test passed"],
-            [ 2, "This test also passed"]
-        ],
-        "tests_warned": [
-            [ 2, "This test gave a warning"]
-        ],
-        "tests_failed": [],
-        "num_tests_pass": 2,
-        "num_tests_warned": 1,
-        "num_tests_failed": 0,
-        "has_tests_pass": true,
-        "has_tests_warned": true,
-        "has_tests_failed": false
-    }
-    """
-    self.lint_obj.passed.append(("test_one", "This test passed"))
-    self.lint_obj.passed.append(("test_two", "This test also passed"))
-    self.lint_obj.warned.append(("test_three", "This test gave a warning"))
-
-    # Make a temp dir for the JSON output
-    json_fn = Path(tmp_dir, "lint_results.json")
-    self.lint_obj._save_json_results(json_fn)
-
-    # Load created JSON file and check its contents
-    with open(json_fn) as fh:
-        try:
-            saved_json = json.load(fh)
-        except json.JSONDecodeError as e:
-            raise UserWarning(f"Unable to load JSON file '{json_fn}' due to error {e}")
-    assert saved_json["num_tests_pass"] > 0
-    assert saved_json["num_tests_warned"] > 0
-    assert saved_json["num_tests_ignored"] == 0
-    assert saved_json["num_tests_failed"] == 0
-    assert saved_json["has_tests_pass"]
-    assert saved_json["has_tests_warned"]
-    assert not saved_json["has_tests_ignored"]
-    assert not saved_json["has_tests_failed"]
-
-
-def test_wrap_quotes(self):
-    md = self.lint_obj._wrap_quotes(["one", "two", "three"])
-    assert md == "`one` or `two` or `three`"
-
-
-def test_sphinx_md_files(self):
-    """Check that we have .md files for all lint module code,
-    and that there are no unexpected files (eg. deleted lint tests)"""
-
-    docs_basedir = Path(Path(__file__).parent.parent.parent, "docs", "api", "_src", "pipeline_lint_tests")
-
-    # Get list of existing .md files
-    existing_docs = []
-    existing_docs = [
-        str(Path(docs_basedir, fn))
-        for fn in Path(docs_basedir).iterdir()
-        if fn.match("*.md") and not fn.match("index.md")
-    ]
-
-    # Check .md files against each test name
-    lint_obj = nf_core.pipelines.lint.PipelineLint("", True)
-    for test_name in lint_obj.lint_tests:
-        fn = Path(docs_basedir, f"{test_name}.md")
-        assert fn.exists(), f"Could not find lint docs .md file: {fn}"
-        existing_docs.remove(str(fn))
-
-    # Check that we have no remaining .md files that we didn't expect
-    assert len(existing_docs) == 0, f"Unexpected lint docs .md files found: {', '.join(existing_docs)}"
-
-    #######################
-    # SPECIFIC LINT TESTS #
-    #######################
-
-    # from .lint.nextflow_config import (  # type: ignore[misc]
-    #     test_allow_params_reference_in_main_nf,
-    #     test_catch_params_assignment_in_main_nf,
-    #     test_default_values_fail,
-    #     test_default_values_float,
-    #     test_default_values_float_fail,
-    #     test_default_values_ignored,
-    #     test_default_values_match,
-    #     test_nextflow_config_bad_name_fail,
-    #     test_nextflow_config_dev_in_release_mode_failed,
-    #     test_nextflow_config_example_pass,
-    #     test_nextflow_config_missing_test_profile_failed,
-    # )
-    # from .lint.nfcore_yml import (  # type: ignore[misc]
-    #     test_nfcore_yml_fail_nfcore_version,
-    #     test_nfcore_yml_fail_repo_type,
-    #     test_nfcore_yml_pass,
-    # )
-    # from .lint.template_strings import (  # type: ignore[misc]
-    #     test_template_strings,
-    #     test_template_strings_ignore_file,
-    #     test_template_strings_ignored,
-    # )
-    # from .lint.version_consistency import test_version_consistency  # type: ignore[misc]
+class TestPipelinesLint(TestLint):
+    def test_run_linting_function(self):
+        """Run the master run_linting() function in lint.py
+
+        We don't really check any of this code as it's just a series of function calls
+        and we're testing each of those individually. This is mostly to check for syntax errors."""
+        nf_core.pipelines.lint.run_linting(self.pipeline_dir, False)
+
+    def test_init_pipeline_lint(self):
+        """Simply create a PipelineLint object.
+
+        This checks that all of the lint test imports are working properly,
+        we also check that the git sha was found and that the release flag works properly
+        """
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir, True)
+
+        # Tests that extra test is added for release mode
+        assert "version_consistency" in lint_obj.lint_tests
+        assert lint_obj.git_sha
+        # Tests that parent nf_core.utils.Pipeline class __init__() is working to find git hash
+        assert len(lint_obj.git_sha) > 0
+
+    def test_load_lint_config_not_found(self):
+        """Try to load a linting config file that doesn't exist"""
+        self.lint_obj._load_lint_config()
+        assert self.lint_obj.lint_config == {}
+
+    def test_load_lint_config_ignore_all_tests(self):
+        """Try to load a linting config file that ignores all tests"""
+
+        # Make a copy of the test pipeline and create a lint object
+        new_pipeline = self._make_pipeline_copy()
+        lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
+
+        # Make a config file listing all test names
+        config_dict = {"lint": {test_name: False for test_name in lint_obj.lint_tests}}
+        with open(Path(new_pipeline, ".nf-core.yml"), "w") as fh:
+            yaml.dump(config_dict, fh)
+
+        # Load the new lint config file and check
+        lint_obj._load_lint_config()
+        assert sorted(list(lint_obj.lint_config.keys())) == sorted(lint_obj.lint_tests)
+
+        # Try running linting and make sure that all tests are ignored
+        lint_obj._lint_pipeline()
+        assert len(lint_obj.passed) == 0
+        assert len(lint_obj.warned) == 0
+        assert len(lint_obj.failed) == 0
+        assert len(lint_obj.ignored) == len(lint_obj.lint_tests)
+
+    @with_temporary_folder
+    def test_json_output(self, tmp_dir):
+        """
+        Test creation of a JSON file with lint results
+
+        Expected JSON output:
+        {
+            "nf_core_tools_version": "1.10.dev0",
+            "date_run": "2020-06-05 10:56:42",
+            "tests_pass": [
+                [ 1, "This test passed"],
+                [ 2, "This test also passed"]
+            ],
+            "tests_warned": [
+                [ 2, "This test gave a warning"]
+            ],
+            "tests_failed": [],
+            "num_tests_pass": 2,
+            "num_tests_warned": 1,
+            "num_tests_failed": 0,
+            "has_tests_pass": true,
+            "has_tests_warned": true,
+            "has_tests_failed": false
+        }
+        """
+        self.lint_obj.passed.append(("test_one", "This test passed"))
+        self.lint_obj.passed.append(("test_two", "This test also passed"))
+        self.lint_obj.warned.append(("test_three", "This test gave a warning"))
+
+        # Make a temp dir for the JSON output
+        json_fn = Path(tmp_dir, "lint_results.json")
+        self.lint_obj._save_json_results(json_fn)
+
+        # Load created JSON file and check its contents
+        with open(json_fn) as fh:
+            try:
+                saved_json = json.load(fh)
+            except json.JSONDecodeError as e:
+                raise UserWarning(f"Unable to load JSON file '{json_fn}' due to error {e}")
+        assert saved_json["num_tests_pass"] > 0
+        assert saved_json["num_tests_warned"] > 0
+        assert saved_json["num_tests_ignored"] == 0
+        assert saved_json["num_tests_failed"] == 0
+        assert saved_json["has_tests_pass"]
+        assert saved_json["has_tests_warned"]
+        assert not saved_json["has_tests_ignored"]
+        assert not saved_json["has_tests_failed"]
+
+    def test_wrap_quotes(self):
+        md = self.lint_obj._wrap_quotes(["one", "two", "three"])
+        assert md == "`one` or `two` or `three`"
+
+    def test_sphinx_md_files(self):
+        """Check that we have .md files for all lint module code,
+        and that there are no unexpected files (eg. deleted lint tests)"""
+
+        docs_basedir = Path(Path(__file__).parent.parent.parent, "docs", "api", "_src", "pipeline_lint_tests")
+
+        # Get list of existing .md files
+        existing_docs = []
+        existing_docs = [
+            str(Path(docs_basedir, fn))
+            for fn in Path(docs_basedir).iterdir()
+            if fn.match("*.md") and not fn.match("index.md")
+        ]
+
+        # Check .md files against each test name
+        lint_obj = nf_core.pipelines.lint.PipelineLint("", True)
+        for test_name in lint_obj.lint_tests:
+            fn = Path(docs_basedir, f"{test_name}.md")
+            assert fn.exists(), f"Could not find lint docs .md file: {fn}"
+            existing_docs.remove(str(fn))
+
+        # Check that we have no remaining .md files that we didn't expect
+        assert len(existing_docs) == 0, f"Unexpected lint docs .md files found: {', '.join(existing_docs)}"

From 768cfc31fff05bf4136d987f7dc811599766b7f9 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 15:36:13 +0200
Subject: [PATCH 082/414] find ALL test files in CI

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 72bacaeab9..dc88031886 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -67,7 +67,7 @@ jobs:
       - name: List tests
         id: list_tests
         run: |
-          echo "tests=$(find tests/**/test_* | tac | sed 's/tests\///g'  | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
+          echo "tests=$(find tests -type f -name "test_*.py" | tac | sed 's/tests\///g'  | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
     outputs:
       tests: ${{ steps.list_tests.outputs.tests }}
 

From 3aee9cbfd0950a7f78cfcd273ce7a61bbc3d4ed9 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 15:49:21 +0200
Subject: [PATCH 083/414] add pytest-asyncio

---
 requirements-dev.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements-dev.txt b/requirements-dev.txt
index 2c7bb0c8cf..82087edcba 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -14,6 +14,7 @@ types-Markdown
 types-PyYAML
 types-requests
 types-setuptools
+pytest-asyncio
 pytest-textual-snapshot==0.4.0
 pytest-workflow>=2.0.0
 pytest>=8.0.0

From 09b0623a9682b58b1be9b5fe12bba117805681b4 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 17 Jul 2024 16:10:41 +0200
Subject: [PATCH 084/414] convert subworkflow tests to new structure

---
 nf_core/modules/bump_versions.py   |   7 +-
 nf_core/modules/modules_json.py    |   3 +-
 tests/subworkflows/create.py       | 110 --------
 tests/subworkflows/info.py         |  64 -----
 tests/subworkflows/install.py      | 154 -----------
 tests/subworkflows/lint.py         | 403 -----------------------------
 tests/subworkflows/list.py         |  49 ----
 tests/subworkflows/remove.py       | 100 -------
 tests/subworkflows/test_create.py  | 109 ++++++++
 tests/subworkflows/test_info.py    |  63 +++++
 tests/subworkflows/test_install.py | 157 +++++++++++
 tests/subworkflows/test_lint.py    | 391 ++++++++++++++++++++++++++++
 tests/subworkflows/test_list.py    |  48 ++++
 tests/subworkflows/test_remove.py  | 101 ++++++++
 tests/subworkflows/test_update.py  | 370 ++++++++++++++++++++++++++
 tests/subworkflows/update.py       | 376 ---------------------------
 tests/test_subworkflows.py         | 105 +++-----
 17 files changed, 1278 insertions(+), 1332 deletions(-)
 delete mode 100644 tests/subworkflows/create.py
 delete mode 100644 tests/subworkflows/info.py
 delete mode 100644 tests/subworkflows/install.py
 delete mode 100644 tests/subworkflows/lint.py
 delete mode 100644 tests/subworkflows/list.py
 delete mode 100644 tests/subworkflows/remove.py
 create mode 100644 tests/subworkflows/test_create.py
 create mode 100644 tests/subworkflows/test_info.py
 create mode 100644 tests/subworkflows/test_install.py
 create mode 100644 tests/subworkflows/test_lint.py
 create mode 100644 tests/subworkflows/test_list.py
 create mode 100644 tests/subworkflows/test_remove.py
 create mode 100644 tests/subworkflows/test_update.py
 delete mode 100644 tests/subworkflows/update.py

diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
index 6556dcf0f4..fae3793079 100644
--- a/nf_core/modules/bump_versions.py
+++ b/nf_core/modules/bump_versions.py
@@ -176,7 +176,12 @@ def bump_module_version(self, module: NFCoreComponent) -> bool:
             try:
                 response = nf_core.utils.anaconda_package(bp)
             except (LookupError, ValueError):
-                self.failed.append((f"Conda version not specified correctly: {module.main_nf}", module.component_name))
+                self.failed.append(
+                    (
+                        f"Conda version not specified correctly: {module.main_nf.relative_to(self.dir)}",
+                        module.component_name,
+                    )
+                )
                 return False
 
             # Check that required version is available at all
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 0d6779a8d4..2c2f1a32c9 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -6,6 +6,7 @@
 import shutil
 import tempfile
 from pathlib import Path
+from typing import Union
 
 import git
 import questionary
@@ -31,7 +32,7 @@ class ModulesJson:
     An object for handling a 'modules.json' file in a pipeline
     """
 
-    def __init__(self, pipeline_dir: str):
+    def __init__(self, pipeline_dir: Union[str, Path]):
         """
         Initialise the object.
 
diff --git a/tests/subworkflows/create.py b/tests/subworkflows/create.py
deleted file mode 100644
index 002b889671..0000000000
--- a/tests/subworkflows/create.py
+++ /dev/null
@@ -1,110 +0,0 @@
-import os
-import shutil
-from pathlib import Path
-from unittest import mock
-
-import pytest
-import yaml
-from git.repo import Repo
-
-import nf_core.subworkflows
-from tests.utils import GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH, GITLAB_URL
-
-
-def test_subworkflows_create_succeed(self):
-    """Succeed at creating a subworkflow from the template inside a pipeline"""
-    subworkflow_create = nf_core.subworkflows.SubworkflowCreate(
-        self.pipeline_dir, "test_subworkflow_local", "@author", True
-    )
-    subworkflow_create.create()
-    assert os.path.exists(os.path.join(self.pipeline_dir, "subworkflows", "local", "test_subworkflow_local.nf"))
-
-
-def test_subworkflows_create_fail_exists(self):
-    """Fail at creating the same subworkflow twice"""
-    subworkflow_create = nf_core.subworkflows.SubworkflowCreate(
-        self.pipeline_dir, "test_subworkflow2", "@author", False
-    )
-    subworkflow_create.create()
-    with pytest.raises(UserWarning) as excinfo:
-        subworkflow_create.create()
-    assert "Subworkflow file exists already" in str(excinfo.value)
-
-
-def test_subworkflows_create_nfcore_modules(self):
-    """Create a subworkflow in nf-core/modules clone"""
-    subworkflow_create = nf_core.subworkflows.SubworkflowCreate(
-        self.nfcore_modules, "test_subworkflow", "@author", force=True
-    )
-    subworkflow_create.create()
-    assert os.path.exists(os.path.join(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "main.nf"))
-    assert os.path.exists(
-        os.path.join(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test")
-    )
-
-
-@mock.patch("rich.prompt.Confirm.ask")
-def test_subworkflows_migrate(self, mock_rich_ask):
-    """Create a subworkflow with the --migrate-pytest option to convert pytest to nf-test"""
-    pytest_dir = Path(self.nfcore_modules, "tests", "subworkflows", "nf-core", "bam_stats_samtools")
-    subworkflow_dir = Path(self.nfcore_modules, "subworkflows", "nf-core", "bam_stats_samtools")
-
-    # Clone modules repo with pytests
-    shutil.rmtree(self.nfcore_modules)
-    Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
-    with open(subworkflow_dir / "main.nf") as fh:
-        old_main_nf = fh.read()
-    with open(subworkflow_dir / "meta.yml") as fh:
-        old_meta_yml = fh.read()
-
-    # Create a subworkflow with --migrate-pytest
-    mock_rich_ask.return_value = True
-    subworkflow_create = nf_core.subworkflows.SubworkflowCreate(
-        self.nfcore_modules, "bam_stats_samtools", migrate_pytest=True
-    )
-    subworkflow_create.create()
-
-    with open(subworkflow_dir / "main.nf") as fh:
-        new_main_nf = fh.read()
-    with open(subworkflow_dir / "meta.yml") as fh:
-        new_meta_yml = fh.read()
-    nextflow_config = subworkflow_dir / "tests" / "nextflow.config"
-
-    # Check that old files have been copied to the new module
-    assert old_main_nf == new_main_nf
-    assert old_meta_yml == new_meta_yml
-    assert nextflow_config.is_file()
-
-    # Check that pytest folder is deleted
-    assert not pytest_dir.is_dir()
-
-    # Check that pytest_modules.yml is updated
-    with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
-        modules_yml = yaml.safe_load(fh)
-    assert "subworkflows/bam_stats_samtools" not in modules_yml.keys()
-
-
-@mock.patch("rich.prompt.Confirm.ask")
-def test_subworkflows_migrate_no_delete(self, mock_rich_ask):
-    """Create a subworkflow with the --migrate-pytest option to convert pytest to nf-test.
-    Test that pytest directory is not deleted."""
-    pytest_dir = Path(self.nfcore_modules, "tests", "subworkflows", "nf-core", "bam_stats_samtools")
-
-    # Clone modules repo with pytests
-    shutil.rmtree(self.nfcore_modules)
-    Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
-
-    # Create a module with --migrate-pytest
-    mock_rich_ask.return_value = False
-    module_create = nf_core.subworkflows.SubworkflowCreate(
-        self.nfcore_modules, "bam_stats_samtools", migrate_pytest=True
-    )
-    module_create.create()
-
-    # Check that pytest folder is not deleted
-    assert pytest_dir.is_dir()
-
-    # Check that pytest_modules.yml is updated
-    with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
-        modules_yml = yaml.safe_load(fh)
-    assert "subworkflows/bam_stats_samtools" not in modules_yml.keys()
diff --git a/tests/subworkflows/info.py b/tests/subworkflows/info.py
deleted file mode 100644
index 688120ac02..0000000000
--- a/tests/subworkflows/info.py
+++ /dev/null
@@ -1,64 +0,0 @@
-from rich.console import Console
-
-import nf_core.subworkflows
-
-from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL
-
-
-def test_subworkflows_info_remote(self):
-    """Test getting info about a remote subworkflow"""
-    mods_info = nf_core.subworkflows.SubworkflowInfo(self.pipeline_dir, "bam_sort_stats_samtools")
-    mods_info_output = mods_info.get_component_info()
-    console = Console(record=True)
-    console.print(mods_info_output)
-    output = console.export_text()
-
-    assert "Subworkflow: bam_sort_stats_samtools" in output
-    assert "Inputs" in output
-    assert "Outputs" in output
-
-
-def test_subworkflows_info_remote_gitlab(self):
-    """Test getting info about a subworkflow in the remote gitlab repo"""
-    mods_info = nf_core.subworkflows.SubworkflowInfo(
-        self.pipeline_dir, "bam_sort_stats_samtools", remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
-    )
-    mods_info_output = mods_info.get_component_info()
-    console = Console(record=True)
-    console.print(mods_info_output)
-    output = console.export_text()
-
-    assert "Subworkflow: bam_sort_stats_samtools" in output
-    assert "Inputs" in output
-    assert "Outputs" in output
-    assert "--git-remote" in output
-
-
-def test_subworkflows_info_local(self):
-    """Test getting info about a locally installed subworkflow"""
-    self.subworkflow_install.install("bam_sort_stats_samtools")
-    mods_info = nf_core.subworkflows.SubworkflowInfo(self.pipeline_dir, "bam_sort_stats_samtools")
-    mods_info.local = True
-    mods_info_output = mods_info.get_component_info()
-    console = Console(record=True)
-    console.print(mods_info_output)
-    output = console.export_text()
-
-    assert "Subworkflow: bam_sort_stats_samtools" in output
-    assert "Inputs" in output
-    assert "Outputs" in output
-
-
-def test_subworkflows_info_in_modules_repo(self):
-    """Test getting info about a locally subworkflow in the modules repo"""
-    self.subworkflow_install.install("bam_sort_stats_samtools")
-    mods_info = nf_core.subworkflows.SubworkflowInfo(self.nfcore_modules, "bam_sort_stats_samtools")
-    mods_info.local = True
-    mods_info_output = mods_info.get_component_info()
-    console = Console(record=True)
-    console.print(mods_info_output)
-    output = console.export_text()
-
-    assert "Subworkflow: bam_sort_stats_samtools" in output
-    assert "Inputs" in output
-    assert "Outputs" in output
diff --git a/tests/subworkflows/install.py b/tests/subworkflows/install.py
deleted file mode 100644
index dfe71686fb..0000000000
--- a/tests/subworkflows/install.py
+++ /dev/null
@@ -1,154 +0,0 @@
-import os
-
-import pytest
-
-from nf_core.modules.modules_json import ModulesJson
-from nf_core.subworkflows.install import SubworkflowInstall
-
-from ..utils import (
-    GITLAB_BRANCH_TEST_BRANCH,
-    GITLAB_REPO,
-    GITLAB_SUBWORKFLOWS_BRANCH,
-    GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH,
-    GITLAB_URL,
-    with_temporary_folder,
-)
-
-
-def test_subworkflow_install_nopipeline(self):
-    """Test installing a subworkflow - no pipeline given"""
-    self.subworkflow_install.dir = None
-    assert self.subworkflow_install.install("foo") is False
-
-
-@with_temporary_folder
-def test_subworkflows_install_emptypipeline(self, tmpdir):
-    """Test installing a subworkflow - empty dir given"""
-    os.mkdir(os.path.join(tmpdir, "nf-core-pipe"))
-    self.subworkflow_install.dir = os.path.join(tmpdir, "nf-core-pipe")
-    with pytest.raises(UserWarning) as excinfo:
-        self.subworkflow_install.install("foo")
-    assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
-
-
-def test_subworkflows_install_nosubworkflow(self):
-    """Test installing a subworkflow - unrecognised subworkflow given"""
-    assert self.subworkflow_install.install("foo") is False
-
-
-def test_subworkflows_install_bam_sort_stats_samtools(self):
-    """Test installing a subworkflow - bam_sort_stats_samtools"""
-    assert self.subworkflow_install.install("bam_sort_stats_samtools") is not False
-    subworkflow_path = os.path.join(self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_sort_stats_samtools")
-    sub_subworkflow_path = os.path.join(self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_stats_samtools")
-    samtools_index_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
-    samtools_sort_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "sort")
-    samtools_stats_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats")
-    samtools_idxstats_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "idxstats")
-    samtools_flagstat_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "flagstat")
-    assert os.path.exists(subworkflow_path)
-    assert os.path.exists(sub_subworkflow_path)
-    assert os.path.exists(samtools_index_path)
-    assert os.path.exists(samtools_sort_path)
-    assert os.path.exists(samtools_stats_path)
-    assert os.path.exists(samtools_idxstats_path)
-    assert os.path.exists(samtools_flagstat_path)
-
-
-def test_subworkflows_install_bam_sort_stats_samtools_twice(self):
-    """Test installing a subworkflow - bam_sort_stats_samtools already there"""
-    self.subworkflow_install.install("bam_sort_stats_samtools")
-    assert self.subworkflow_install.install("bam_sort_stats_samtools") is False
-
-
-def test_subworkflows_install_from_gitlab(self):
-    """Test installing a subworkflow from GitLab"""
-    assert self.subworkflow_install_gitlab.install("bam_stats_samtools") is True
-    # Verify that the branch entry was added correctly
-    modules_json = ModulesJson(self.pipeline_dir)
-    assert (
-        modules_json.get_component_branch(self.component_type, "bam_stats_samtools", GITLAB_URL, GITLAB_REPO)
-        == GITLAB_SUBWORKFLOWS_BRANCH
-    )
-
-
-def test_subworkflows_install_different_branch_fail(self):
-    """Test installing a subworkflow from a different branch"""
-    install_obj = SubworkflowInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH)
-    # The bam_stats_samtools subworkflow does not exists in the branch-test branch
-    assert install_obj.install("bam_stats_samtools") is False
-
-
-def test_subworkflows_install_tracking(self):
-    """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json"""
-    self.subworkflow_install.install("bam_sort_stats_samtools")
-
-    # Verify that the installed_by entry was added correctly
-    modules_json = ModulesJson(self.pipeline_dir)
-    mod_json = modules_json.get_modules_json()
-    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][
-        "bam_sort_stats_samtools"
-    ]["installed_by"] == ["subworkflows"]
-    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"]["bam_stats_samtools"][
-        "installed_by"
-    ] == ["bam_sort_stats_samtools"]
-    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["samtools/stats"][
-        "installed_by"
-    ] == ["bam_stats_samtools"]
-    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["samtools/sort"][
-        "installed_by"
-    ] == ["bam_sort_stats_samtools"]
-
-    # Clean directory
-    self.subworkflow_remove.remove("bam_sort_stats_samtools")
-
-
-def test_subworkflows_install_tracking_added_already_installed(self):
-    """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json"""
-    self.subworkflow_install.install("bam_sort_stats_samtools")
-    self.subworkflow_install.install("bam_stats_samtools")
-
-    # Verify that the installed_by entry was added correctly
-    modules_json = ModulesJson(self.pipeline_dir)
-    mod_json = modules_json.get_modules_json()
-    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][
-        "bam_sort_stats_samtools"
-    ]["installed_by"] == ["subworkflows"]
-    assert sorted(
-        mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"]["bam_stats_samtools"][
-            "installed_by"
-        ]
-    ) == sorted(["bam_sort_stats_samtools", "subworkflows"])
-
-    # Clean directory
-    self.subworkflow_remove.remove("bam_sort_stats_samtools")
-    self.subworkflow_remove.remove("bam_stats_samtools")
-
-
-def test_subworkflows_install_tracking_added_super_subworkflow(self):
-    """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json"""
-    self.subworkflow_install.install("bam_stats_samtools")
-    self.subworkflow_install.install("bam_sort_stats_samtools")
-
-    # Verify that the installed_by entry was added correctly
-    modules_json = ModulesJson(self.pipeline_dir)
-    mod_json = modules_json.get_modules_json()
-    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][
-        "bam_sort_stats_samtools"
-    ]["installed_by"] == ["subworkflows"]
-    assert sorted(
-        mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"]["bam_stats_samtools"][
-            "installed_by"
-        ]
-    ) == sorted(["subworkflows", "bam_sort_stats_samtools"])
-
-
-def test_subworkflows_install_alternate_remote(self):
-    """Test installing a module from a different remote with the same organization path"""
-    install_obj = SubworkflowInstall(
-        self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH
-    )
-    # Install a subworkflow from GitLab which is also installed from GitHub with the same org_path
-    with pytest.raises(Exception) as excinfo:
-        install_obj.install("fastqc")
-        assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
diff --git a/tests/subworkflows/lint.py b/tests/subworkflows/lint.py
deleted file mode 100644
index 540f421ad2..0000000000
--- a/tests/subworkflows/lint.py
+++ /dev/null
@@ -1,403 +0,0 @@
-import json
-import shutil
-from pathlib import Path
-
-import pytest
-
-import nf_core.subworkflows
-
-from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL
-
-
-def test_subworkflows_lint(self):
-    """Test linting the fastq_align_bowtie2 subworkflow"""
-    self.subworkflow_install.install("fastq_align_bowtie2")
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
-    subworkflow_lint.lint(print_results=False, subworkflow="fastq_align_bowtie2")
-    assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) >= 0
-
-
-def test_subworkflows_lint_empty(self):
-    """Test linting a pipeline with no subworkflows installed"""
-    self.subworkflow_remove.remove("utils_nextflow_pipeline", force=True)
-    self.subworkflow_remove.remove("utils_nfcore_pipeline", force=True)
-    self.subworkflow_remove.remove("utils_nfvalidation_plugin", force=True)
-    with pytest.raises(LookupError):
-        nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
-
-
-def test_subworkflows_lint_new_subworkflow(self):
-    """lint a new subworkflow"""
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
-    subworkflow_lint.lint(print_results=True, all_subworkflows=True)
-    assert len(subworkflow_lint.failed) == 0
-
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) >= 0
-
-
-def test_subworkflows_lint_no_gitlab(self):
-    """Test linting a pipeline with no subworkflows installed"""
-    with pytest.raises(LookupError):
-        nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
-
-
-def test_subworkflows_lint_gitlab_subworkflows(self):
-    """Lint subworkflows from a different remote"""
-    self.subworkflow_install_gitlab.install("bam_stats_samtools")
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(
-        dir=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
-    )
-    subworkflow_lint.lint(print_results=False, all_subworkflows=True)
-    assert len(subworkflow_lint.failed) == 0
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) >= 0
-
-
-def test_subworkflows_lint_multiple_remotes(self):
-    """Lint subworkflows from a different remote"""
-    self.subworkflow_install_gitlab.install("bam_stats_samtools")
-    self.subworkflow_install.install("fastq_align_bowtie2")
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(
-        dir=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
-    )
-    subworkflow_lint.lint(print_results=False, all_subworkflows=True)
-    assert len(subworkflow_lint.failed) == 0
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) >= 0
-
-
-def test_subworkflows_lint_snapshot_file(self):
-    """Test linting a subworkflow with a snapshot file"""
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
-    subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
-    assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) >= 0
-
-
-def test_subworkflows_lint_snapshot_file_missing_fail(self):
-    """Test linting a subworkflow with a snapshot file missing, which should fail"""
-    Path(
-        self.nfcore_modules,
-        "subworkflows",
-        "nf-core",
-        "test_subworkflow",
-        "tests",
-        "main.nf.test.snap",
-    ).unlink()
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
-    subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
-    Path(
-        self.nfcore_modules,
-        "subworkflows",
-        "nf-core",
-        "test_subworkflow",
-        "tests",
-        "main.nf.test.snap",
-    ).touch()
-    assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) >= 0
-
-
-def test_subworkflows_lint_snapshot_file_not_needed(self):
-    """Test linting a subworkflow which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file"""
-    with open(
-        Path(
-            self.nfcore_modules,
-            "subworkflows",
-            "nf-core",
-            "test_subworkflow",
-            "tests",
-            "main.nf.test",
-        )
-    ) as fh:
-        content = fh.read()
-        new_content = content.replace("snapshot(", "snap (")
-    with open(
-        Path(
-            self.nfcore_modules,
-            "subworkflows",
-            "nf-core",
-            "test_subworkflow",
-            "tests",
-            "main.nf.test",
-        ),
-        "w",
-    ) as fh:
-        fh.write(new_content)
-
-    Path(
-        self.nfcore_modules,
-        "subworkflows",
-        "nf-core",
-        "test_subworkflow",
-        "tests",
-        "main.nf.test.snap",
-    ).unlink()
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
-    subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
-    Path(
-        self.nfcore_modules,
-        "subworkflows",
-        "nf-core",
-        "test_subworkflow",
-        "tests",
-        "main.nf.test.snap",
-    ).touch()
-    assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) >= 0
-
-
-def test_subworkflows_lint_less_than_two_modules_warning(self):
-    """Test linting a subworkflow with less than two modules"""
-    self.subworkflow_install.install("bam_stats_samtools")
-    # Remove two modules
-    with open(
-        Path(
-            self.pipeline_dir,
-            "subworkflows",
-            "nf-core",
-            "bam_stats_samtools",
-            "main.nf",
-        )
-    ) as fh:
-        content = fh.read()
-        new_content = content.replace(
-            "include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main'",
-            "",
-        )
-        new_content = new_content.replace(
-            "include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main'",
-            "",
-        )
-    with open(
-        Path(
-            self.pipeline_dir,
-            "subworkflows",
-            "nf-core",
-            "bam_stats_samtools",
-            "main.nf",
-        ),
-        "w",
-    ) as fh:
-        fh.write(new_content)
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
-    subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools")
-    assert len(subworkflow_lint.failed) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) > 0
-    assert subworkflow_lint.warned[0].lint_test == "main_nf_include"
-    # cleanup
-    self.subworkflow_remove.remove("bam_stats_samtools", force=True)
-
-
-def test_subworkflows_lint_include_multiple_alias(self):
-    """Test linting a subworkflow with multiple include methods"""
-    self.subworkflow_install.install("bam_stats_samtools")
-    with open(
-        Path(
-            self.pipeline_dir,
-            "subworkflows",
-            "nf-core",
-            "bam_stats_samtools",
-            "main.nf",
-        )
-    ) as fh:
-        content = fh.read()
-        new_content = content.replace("SAMTOOLS_STATS", "SAMTOOLS_STATS_1")
-        new_content = new_content.replace(
-            "include { SAMTOOLS_STATS_1 ",
-            "include { SAMTOOLS_STATS as SAMTOOLS_STATS_1; SAMTOOLS_STATS as SAMTOOLS_STATS_2 ",
-        )
-    with open(
-        Path(
-            self.pipeline_dir,
-            "subworkflows",
-            "nf-core",
-            "bam_stats_samtools",
-            "main.nf",
-        ),
-        "w",
-    ) as fh:
-        fh.write(new_content)
-
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
-    subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools")
-    assert len(subworkflow_lint.failed) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) == 2
-    assert any(
-        [
-            x.message == "Included component 'SAMTOOLS_STATS_1' versions are added in main.nf"
-            for x in subworkflow_lint.passed
-        ]
-    )
-    assert any([x.message == "Included component 'SAMTOOLS_STATS_1' used in main.nf" for x in subworkflow_lint.passed])
-    assert any(
-        [x.message == "Included component 'SAMTOOLS_STATS_2' not used in main.nf" for x in subworkflow_lint.warned]
-    )
-
-    # cleanup
-    self.subworkflow_remove.remove("bam_stats_samtools", force=True)
-
-
-def test_subworkflows_lint_capitalization_fail(self):
-    """Test linting a subworkflow with a capitalization fail"""
-    self.subworkflow_install.install("bam_stats_samtools")
-    # change workflow name to lowercase
-    with open(
-        Path(
-            self.pipeline_dir,
-            "subworkflows",
-            "nf-core",
-            "bam_stats_samtools",
-            "main.nf",
-        )
-    ) as fh:
-        content = fh.read()
-        new_content = content.replace("workflow BAM_STATS_SAMTOOLS {", "workflow bam_stats_samtools {")
-    with open(
-        Path(
-            self.pipeline_dir,
-            "subworkflows",
-            "nf-core",
-            "bam_stats_samtools",
-            "main.nf",
-        ),
-        "w",
-    ) as fh:
-        fh.write(new_content)
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
-    subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools")
-    assert len(subworkflow_lint.failed) >= 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) >= 0
-    assert any([x.lint_test == "workflow_capitals" for x in subworkflow_lint.failed])
-
-    # cleanup
-    self.subworkflow_remove.remove("bam_stats_samtools", force=True)
-
-
-def test_subworkflows_absent_version(self):
-    """Test linting a nf-test module if the versions is absent in the snapshot file `"""
-    snap_file = Path(
-        self.nfcore_modules,
-        "subworkflows",
-        "nf-core",
-        "test_subworkflow",
-        "tests",
-        "main.nf.test.snap",
-    )
-    with open(snap_file) as fh:
-        content = fh.read()
-        new_content = content.replace("versions", "foo")
-    with open(snap_file, "w") as fh:
-        fh.write(new_content)
-
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
-    subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
-    assert len(subworkflow_lint.failed) == 0
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) >= 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
-    assert any([x.lint_test == "test_snap_versions" for x in subworkflow_lint.warned])
-
-    # cleanup
-    with open(snap_file, "w") as fh:
-        fh.write(content)
-
-
-def test_subworkflows_missing_test_dir(self):
-    """Test linting a nf-test subworkflow if the tests directory is missing"""
-    test_dir = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests")
-    test_dir_copy = shutil.copytree(test_dir, test_dir.parent / "tests_copy")
-    shutil.rmtree(test_dir)
-
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
-    subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
-    assert len(subworkflow_lint.failed) == 0
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) >= 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
-    assert any([x.lint_test == "test_dir_versions" for x in subworkflow_lint.warned])
-
-    # cleanup
-    shutil.copytree(test_dir_copy, test_dir)
-
-
-def test_subworkflows_missing_main_nf(self):
-    """Test linting a nf-test subworkflow if the main.nf file is missing"""
-    main_nf = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "main.nf")
-    main_nf_copy = shutil.copy(main_nf, main_nf.parent / "main_nf_copy")
-    main_nf.unlink()
-
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
-    subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
-    assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) >= 0
-    assert subworkflow_lint.failed[0].lint_test == "main_nf_exists"
-
-    # cleanup
-    shutil.copy(main_nf_copy, main_nf)
-
-
-def test_subworkflows_empty_file_in_snapshot(self):
-    """Test linting a nf-test subworkflow with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)"""
-    snap_file = Path(
-        self.nfcore_modules,
-        "subworkflows",
-        "nf-core",
-        "test_subworkflow",
-        "tests",
-        "main.nf.test.snap",
-    )
-    snap = json.load(snap_file.open())
-    content = snap_file.read_text()
-    snap["my test"]["content"][0]["0"] = "test:md5,d41d8cd98f00b204e9800998ecf8427e"
-
-    with open(snap_file, "w") as fh:
-        json.dump(snap, fh)
-
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
-    subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
-    assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) >= 0
-    assert subworkflow_lint.failed[0].lint_test == "test_snap_md5sum"
-
-    # reset the file
-    with open(snap_file, "w") as fh:
-        fh.write(content)
-
-
-def test_subworkflows_empty_file_in_stub_snapshot(self):
-    """Test linting a nf-test subworkflow with an empty file sha sum in the stub test snapshot, which should make it not fail"""
-    snap_file = Path(
-        self.nfcore_modules,
-        "subworkflows",
-        "nf-core",
-        "test_subworkflow",
-        "tests",
-        "main.nf.test.snap",
-    )
-    snap = json.load(snap_file.open())
-    content = snap_file.read_text()
-    snap["my_test_stub"] = {"content": [{"0": "test:md5,d41d8cd98f00b204e9800998ecf8427e", "versions": {}}]}
-
-    with open(snap_file, "w") as fh:
-        json.dump(snap, fh)
-
-    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
-    subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
-    assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
-    assert len(subworkflow_lint.passed) > 0
-    assert len(subworkflow_lint.warned) >= 0
-    assert any(x.lint_test == "test_snap_md5sum" for x in subworkflow_lint.passed)
-
-    # reset the file
-    with open(snap_file, "w") as fh:
-        fh.write(content)
diff --git a/tests/subworkflows/list.py b/tests/subworkflows/list.py
deleted file mode 100644
index c65999d42c..0000000000
--- a/tests/subworkflows/list.py
+++ /dev/null
@@ -1,49 +0,0 @@
-from rich.console import Console
-
-import nf_core.subworkflows
-
-from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL
-
-
-def test_subworkflows_list_remote(self):
-    """Test listing available subworkflows"""
-    subworkflows_list = nf_core.subworkflows.SubworkflowList(None, remote=True)
-    listed_subworkflows = subworkflows_list.list_components()
-    console = Console(record=True)
-    console.print(listed_subworkflows)
-    output = console.export_text()
-    assert "bam_stats" in output
-
-
-def test_subworkflows_list_remote_gitlab(self):
-    """Test listing the subworkflows in the remote gitlab repo"""
-    subworkflows_list = nf_core.subworkflows.SubworkflowList(
-        None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
-    )
-    listed_subworkflows = subworkflows_list.list_components()
-    console = Console(record=True)
-    console.print(listed_subworkflows)
-    output = console.export_text()
-    assert "bam_stats" in output
-
-
-def test_subworkflows_install_and_list_subworkflows(self):
-    """Test listing locally installed subworkflows"""
-    self.subworkflow_install.install("bam_sort_stats_samtools")
-    subworkflows_list = nf_core.subworkflows.SubworkflowList(self.pipeline_dir, remote=False)
-    listed_subworkflows = subworkflows_list.list_components()
-    console = Console(record=True)
-    console.print(listed_subworkflows)
-    output = console.export_text()
-    assert "bam_stats" in output
-
-
-def test_subworkflows_install_gitlab_and_list_subworkflows(self):
-    """Test listing locally installed subworkflows"""
-    self.subworkflow_install_gitlab.install("bam_sort_stats_samtools")
-    subworkflows_list = nf_core.subworkflows.SubworkflowList(self.pipeline_dir, remote=False)
-    listed_subworkflows = subworkflows_list.list_components()
-    console = Console(record=True)
-    console.print(listed_subworkflows)
-    output = console.export_text()
-    assert "bam_stats" in output
diff --git a/tests/subworkflows/remove.py b/tests/subworkflows/remove.py
deleted file mode 100644
index c6a3b98454..0000000000
--- a/tests/subworkflows/remove.py
+++ /dev/null
@@ -1,100 +0,0 @@
-from pathlib import Path
-
-from nf_core.modules.modules_json import ModulesJson
-
-
-def test_subworkflows_remove_uninstalled_subworkflow(self):
-    """Test removing subworkflow without installing it"""
-    assert self.subworkflow_remove.remove("bam_sort_stats_samtools") is False
-
-
-def test_subworkflows_remove_subworkflow(self):
-    """Test removing subworkflow and all it's dependencies after installing it"""
-    self.subworkflow_install.install("bam_sort_stats_samtools")
-
-    subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
-    bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
-    bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
-    samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
-    ModulesJson(self.pipeline_dir)
-    mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json()
-    assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
-    mod_json_after = ModulesJson(self.pipeline_dir).get_modules_json()
-    assert Path.exists(bam_sort_stats_samtools_path) is False
-    assert Path.exists(bam_stats_samtools_path) is False
-    assert Path.exists(samtools_index_path) is False
-    assert mod_json_before != mod_json_after
-    # assert subworkflows key is removed from modules.json
-    assert (
-        "bam_sort_stats_samtools"
-        not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"].keys()
-    )
-    assert "samtools/index" not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"].keys()
-
-
-def test_subworkflows_remove_subworkflow_keep_installed_module(self):
-    """Test removing subworkflow and all it's dependencies after installing it, except for a separately installed module"""
-    self.subworkflow_install.install("bam_sort_stats_samtools")
-    self.mods_install.install("samtools/index")
-
-    subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
-    bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
-    bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
-    samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
-
-    mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json()
-    assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
-    mod_json_after = ModulesJson(self.pipeline_dir).get_modules_json()
-
-    assert Path.exists(bam_sort_stats_samtools_path) is False
-    assert Path.exists(bam_stats_samtools_path) is False
-    assert Path.exists(samtools_index_path) is True
-    assert mod_json_before != mod_json_after
-    # assert subworkflows key is removed from modules.json
-    assert (
-        "bam_sort_stats_samtools"
-        not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"].keys()
-    )
-    assert (
-        "samtools/index"
-        in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"].keys()
-    )
-
-
-def test_subworkflows_remove_one_of_two_subworkflow(self):
-    """Test removing subworkflow and all it's dependencies after installing it"""
-    self.subworkflow_install.install("bam_sort_stats_samtools")
-    self.subworkflow_install.install("bam_stats_samtools")
-    subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
-    bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
-    bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
-    samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
-    samtools_stats_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats")
-
-    assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
-
-    assert Path.exists(subworkflow_path) is True
-    assert Path.exists(bam_sort_stats_samtools_path) is False
-    assert Path.exists(bam_stats_samtools_path) is True
-    assert Path.exists(samtools_index_path) is False
-    assert Path.exists(samtools_stats_path) is True
-    self.subworkflow_remove.remove("bam_stats_samtools")
-
-
-def test_subworkflows_remove_included_subworkflow(self):
-    """Test removing subworkflow which is installed by another subworkflow and all it's dependencies."""
-    self.subworkflow_install.install("bam_sort_stats_samtools")
-    subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
-    bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
-    bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
-    samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
-    samtools_stats_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats")
-
-    assert self.subworkflow_remove.remove("bam_stats_samtools") is False
-
-    assert Path.exists(subworkflow_path) is True
-    assert Path.exists(bam_sort_stats_samtools_path) is True
-    assert Path.exists(bam_stats_samtools_path) is True
-    assert Path.exists(samtools_index_path) is True
-    assert Path.exists(samtools_stats_path) is True
-    self.subworkflow_remove.remove("bam_sort_stats_samtools")
diff --git a/tests/subworkflows/test_create.py b/tests/subworkflows/test_create.py
new file mode 100644
index 0000000000..48cb482260
--- /dev/null
+++ b/tests/subworkflows/test_create.py
@@ -0,0 +1,109 @@
+import shutil
+from pathlib import Path
+from unittest import mock
+
+import pytest
+import yaml
+from git.repo import Repo
+
+import nf_core.subworkflows
+from tests.utils import GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH, GITLAB_URL
+
+from ..test_subworkflows import TestSubworkflows
+
+
+class TestSubworkflowsCreate(TestSubworkflows):
+    def test_subworkflows_create_succeed(self):
+        """Succeed at creating a subworkflow from the template inside a pipeline"""
+        subworkflow_create = nf_core.subworkflows.SubworkflowCreate(
+            self.pipeline_dir, "test_subworkflow_local", "@author", True
+        )
+        subworkflow_create.create()
+        assert Path(self.pipeline_dir, "subworkflows", "local", "test_subworkflow_local.nf").exists()
+
+    def test_subworkflows_create_fail_exists(self):
+        """Fail at creating the same subworkflow twice"""
+        subworkflow_create = nf_core.subworkflows.SubworkflowCreate(
+            self.pipeline_dir, "test_subworkflow2", "@author", False
+        )
+        subworkflow_create.create()
+        with pytest.raises(UserWarning) as excinfo:
+            subworkflow_create.create()
+        assert "Subworkflow file exists already" in str(excinfo.value)
+
+    def test_subworkflows_create_nfcore_modules(self):
+        """Create a subworkflow in nf-core/modules clone"""
+        subworkflow_create = nf_core.subworkflows.SubworkflowCreate(
+            self.nfcore_modules, "test_subworkflow", "@author", force=True
+        )
+        subworkflow_create.create()
+        assert Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "main.nf").exists()
+
+        assert Path(
+            self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test"
+        ).exists()
+
+    @mock.patch("rich.prompt.Confirm.ask")
+    def test_subworkflows_migrate(self, mock_rich_ask):
+        """Create a subworkflow with the --migrate-pytest option to convert pytest to nf-test"""
+        pytest_dir = Path(self.nfcore_modules, "tests", "subworkflows", "nf-core", "bam_stats_samtools")
+        subworkflow_dir = Path(self.nfcore_modules, "subworkflows", "nf-core", "bam_stats_samtools")
+
+        # Clone modules repo with pytests
+        shutil.rmtree(self.nfcore_modules)
+        Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
+        with open(subworkflow_dir / "main.nf") as fh:
+            old_main_nf = fh.read()
+        with open(subworkflow_dir / "meta.yml") as fh:
+            old_meta_yml = fh.read()
+
+        # Create a subworkflow with --migrate-pytest
+        mock_rich_ask.return_value = True
+        subworkflow_create = nf_core.subworkflows.SubworkflowCreate(
+            self.nfcore_modules, "bam_stats_samtools", migrate_pytest=True
+        )
+        subworkflow_create.create()
+
+        with open(subworkflow_dir / "main.nf") as fh:
+            new_main_nf = fh.read()
+        with open(subworkflow_dir / "meta.yml") as fh:
+            new_meta_yml = fh.read()
+        nextflow_config = subworkflow_dir / "tests" / "nextflow.config"
+
+        # Check that old files have been copied to the new module
+        assert old_main_nf == new_main_nf
+        assert old_meta_yml == new_meta_yml
+        assert nextflow_config.is_file()
+
+        # Check that pytest folder is deleted
+        assert not pytest_dir.is_dir()
+
+        # Check that pytest_modules.yml is updated
+        with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
+            modules_yml = yaml.safe_load(fh)
+        assert "subworkflows/bam_stats_samtools" not in modules_yml.keys()
+
+    @mock.patch("rich.prompt.Confirm.ask")
+    def test_subworkflows_migrate_no_delete(self, mock_rich_ask):
+        """Create a subworkflow with the --migrate-pytest option to convert pytest to nf-test.
+        Test that pytest directory is not deleted."""
+        pytest_dir = Path(self.nfcore_modules, "tests", "subworkflows", "nf-core", "bam_stats_samtools")
+
+        # Clone modules repo with pytests
+        shutil.rmtree(self.nfcore_modules)
+        Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
+
+        # Create a module with --migrate-pytest
+        mock_rich_ask.return_value = False
+        module_create = nf_core.subworkflows.SubworkflowCreate(
+            self.nfcore_modules, "bam_stats_samtools", migrate_pytest=True
+        )
+        module_create.create()
+
+        # Check that pytest folder is not deleted
+        assert pytest_dir.is_dir()
+
+        # Check that pytest_modules.yml is updated
+        with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
+            modules_yml = yaml.safe_load(fh)
+        assert "subworkflows/bam_stats_samtools" not in modules_yml.keys()
diff --git a/tests/subworkflows/test_info.py b/tests/subworkflows/test_info.py
new file mode 100644
index 0000000000..cf0f492710
--- /dev/null
+++ b/tests/subworkflows/test_info.py
@@ -0,0 +1,63 @@
+from rich.console import Console
+
+import nf_core.subworkflows
+
+from ..test_subworkflows import TestSubworkflows
+from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL
+
+
+class TestSubworkflowsInfo(TestSubworkflows):
+    def test_subworkflows_info_remote(self):
+        """Test getting info about a remote subworkflow"""
+        mods_info = nf_core.subworkflows.SubworkflowInfo(self.pipeline_dir, "bam_sort_stats_samtools")
+        mods_info_output = mods_info.get_component_info()
+        console = Console(record=True)
+        console.print(mods_info_output)
+        output = console.export_text()
+
+        assert "Subworkflow: bam_sort_stats_samtools" in output
+        assert "Inputs" in output
+        assert "Outputs" in output
+
+    def test_subworkflows_info_remote_gitlab(self):
+        """Test getting info about a subworkflow in the remote gitlab repo"""
+        mods_info = nf_core.subworkflows.SubworkflowInfo(
+            self.pipeline_dir, "bam_sort_stats_samtools", remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
+        )
+        mods_info_output = mods_info.get_component_info()
+        console = Console(record=True)
+        console.print(mods_info_output)
+        output = console.export_text()
+
+        assert "Subworkflow: bam_sort_stats_samtools" in output
+        assert "Inputs" in output
+        assert "Outputs" in output
+        assert "--git-remote" in output
+
+    def test_subworkflows_info_local(self):
+        """Test getting info about a locally installed subworkflow"""
+        self.subworkflow_install.install("bam_sort_stats_samtools")
+        mods_info = nf_core.subworkflows.SubworkflowInfo(self.pipeline_dir, "bam_sort_stats_samtools")
+        mods_info.local = True
+        mods_info_output = mods_info.get_component_info()
+        console = Console(record=True)
+        console.print(mods_info_output)
+        output = console.export_text()
+
+        assert "Subworkflow: bam_sort_stats_samtools" in output
+        assert "Inputs" in output
+        assert "Outputs" in output
+
+    def test_subworkflows_info_in_modules_repo(self):
+        """Test getting info about a locally subworkflow in the modules repo"""
+        self.subworkflow_install.install("bam_sort_stats_samtools")
+        mods_info = nf_core.subworkflows.SubworkflowInfo(self.nfcore_modules, "bam_sort_stats_samtools")
+        mods_info.local = True
+        mods_info_output = mods_info.get_component_info()
+        console = Console(record=True)
+        console.print(mods_info_output)
+        output = console.export_text()
+
+        assert "Subworkflow: bam_sort_stats_samtools" in output
+        assert "Inputs" in output
+        assert "Outputs" in output
diff --git a/tests/subworkflows/test_install.py b/tests/subworkflows/test_install.py
new file mode 100644
index 0000000000..e0b2fc1ab6
--- /dev/null
+++ b/tests/subworkflows/test_install.py
@@ -0,0 +1,157 @@
+import os
+from pathlib import Path
+
+import pytest
+
+from nf_core.modules.modules_json import ModulesJson
+from nf_core.subworkflows.install import SubworkflowInstall
+
+from ..test_subworkflows import TestSubworkflows
+from ..utils import (
+    GITLAB_BRANCH_TEST_BRANCH,
+    GITLAB_REPO,
+    GITLAB_SUBWORKFLOWS_BRANCH,
+    GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH,
+    GITLAB_URL,
+    with_temporary_folder,
+)
+
+
+class TestSubworkflowsInstall(TestSubworkflows):
+    def test_subworkflow_install_nopipeline(self):
+        """Test installing a subworkflow - no pipeline given"""
+        assert self.subworkflow_install.dir is not None
+        self.subworkflow_install.dir = ""
+        assert self.subworkflow_install.install("foo") is False
+
+    @with_temporary_folder
+    def test_subworkflows_install_emptypipeline(self, tmpdir):
+        """Test installing a subworkflow - empty dir given"""
+
+        Path(tmpdir, "nf-core-pipe").mkdir(exist_ok=True)
+        self.subworkflow_install.dir = os.path.join(tmpdir, "nf-core-pipe")
+        with pytest.raises(UserWarning) as excinfo:
+            self.subworkflow_install.install("foo")
+        assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
+
+    def test_subworkflows_install_nosubworkflow(self):
+        """Test installing a subworkflow - unrecognised subworkflow given"""
+        assert self.subworkflow_install.install("foo") is False
+
+    def test_subworkflows_install_bam_sort_stats_samtools(self):
+        """Test installing a subworkflow - bam_sort_stats_samtools"""
+        assert self.subworkflow_install.install("bam_sort_stats_samtools") is not False
+        subworkflow_path = os.path.join(
+            self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_sort_stats_samtools"
+        )
+        sub_subworkflow_path = os.path.join(
+            self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_stats_samtools"
+        )
+        samtools_index_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
+        samtools_sort_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "sort")
+        samtools_stats_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats")
+        samtools_idxstats_path = os.path.join(
+            self.subworkflow_install.dir, "modules", "nf-core", "samtools", "idxstats"
+        )
+        samtools_flagstat_path = os.path.join(
+            self.subworkflow_install.dir, "modules", "nf-core", "samtools", "flagstat"
+        )
+        assert os.path.exists(subworkflow_path)
+        assert os.path.exists(sub_subworkflow_path)
+        assert os.path.exists(samtools_index_path)
+        assert os.path.exists(samtools_sort_path)
+        assert os.path.exists(samtools_stats_path)
+        assert os.path.exists(samtools_idxstats_path)
+        assert os.path.exists(samtools_flagstat_path)
+
+    def test_subworkflows_install_bam_sort_stats_samtools_twice(self):
+        """Test installing a subworkflow - bam_sort_stats_samtools already there"""
+        self.subworkflow_install.install("bam_sort_stats_samtools")
+        assert self.subworkflow_install.install("bam_sort_stats_samtools") is False
+
+    def test_subworkflows_install_from_gitlab(self):
+        """Test installing a subworkflow from GitLab"""
+        assert self.subworkflow_install_gitlab.install("bam_stats_samtools") is True
+        # Verify that the branch entry was added correctly
+        modules_json = ModulesJson(self.pipeline_dir)
+        assert (
+            modules_json.get_component_branch(self.component_type, "bam_stats_samtools", GITLAB_URL, GITLAB_REPO)
+            == GITLAB_SUBWORKFLOWS_BRANCH
+        )
+
+    def test_subworkflows_install_different_branch_fail(self):
+        """Test installing a subworkflow from a different branch"""
+        install_obj = SubworkflowInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH)
+        # The bam_stats_samtools subworkflow does not exists in the branch-test branch
+        assert install_obj.install("bam_stats_samtools") is False
+
+    def test_subworkflows_install_tracking(self):
+        """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json"""
+        self.subworkflow_install.install("bam_sort_stats_samtools")
+
+        # Verify that the installed_by entry was added correctly
+        modules_json = ModulesJson(self.pipeline_dir)
+        mod_json = modules_json.get_modules_json()
+        assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][
+            "bam_sort_stats_samtools"
+        ]["installed_by"] == ["subworkflows"]
+        assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][
+            "bam_stats_samtools"
+        ]["installed_by"] == ["bam_sort_stats_samtools"]
+        assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["samtools/stats"][
+            "installed_by"
+        ] == ["bam_stats_samtools"]
+        assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["samtools/sort"][
+            "installed_by"
+        ] == ["bam_sort_stats_samtools"]
+
+        # Clean directory
+        self.subworkflow_remove.remove("bam_sort_stats_samtools")
+
+    def test_subworkflows_install_tracking_added_already_installed(self):
+        """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json"""
+        self.subworkflow_install.install("bam_sort_stats_samtools")
+        self.subworkflow_install.install("bam_stats_samtools")
+
+        # Verify that the installed_by entry was added correctly
+        modules_json = ModulesJson(self.pipeline_dir)
+        mod_json = modules_json.get_modules_json()
+        assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][
+            "bam_sort_stats_samtools"
+        ]["installed_by"] == ["subworkflows"]
+        assert sorted(
+            mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][
+                "bam_stats_samtools"
+            ]["installed_by"]
+        ) == sorted(["bam_sort_stats_samtools", "subworkflows"])
+
+        # Clean directory
+        self.subworkflow_remove.remove("bam_sort_stats_samtools")
+        self.subworkflow_remove.remove("bam_stats_samtools")
+
+    def test_subworkflows_install_tracking_added_super_subworkflow(self):
+        """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json"""
+        self.subworkflow_install.install("bam_stats_samtools")
+        self.subworkflow_install.install("bam_sort_stats_samtools")
+
+        # Verify that the installed_by entry was added correctly
+        modules_json = ModulesJson(self.pipeline_dir)
+        mod_json = modules_json.get_modules_json()
+        assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][
+            "bam_sort_stats_samtools"
+        ]["installed_by"] == ["subworkflows"]
+        assert sorted(
+            mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][
+                "bam_stats_samtools"
+            ]["installed_by"]
+        ) == sorted(["subworkflows", "bam_sort_stats_samtools"])
+
+    def test_subworkflows_install_alternate_remote(self):
+        """Test installing a module from a different remote with the same organization path"""
+        install_obj = SubworkflowInstall(
+            self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH
+        )
+        # Install a subworkflow from GitLab which is also installed from GitHub with the same org_path
+        with pytest.raises(Exception) as excinfo:
+            install_obj.install("fastqc")
+            assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py
new file mode 100644
index 0000000000..f8c9bedbf3
--- /dev/null
+++ b/tests/subworkflows/test_lint.py
@@ -0,0 +1,391 @@
+import json
+import shutil
+from pathlib import Path
+
+import pytest
+
+import nf_core.subworkflows
+
+from ..test_subworkflows import TestSubworkflows
+from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL
+
+
+class TestSubworkflowsLint(TestSubworkflows):
+    def test_subworkflows_lint(self):
+        """Test linting the fastq_align_bowtie2 subworkflow"""
+        self.subworkflow_install.install("fastq_align_bowtie2")
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
+        subworkflow_lint.lint(print_results=False, subworkflow="fastq_align_bowtie2")
+        assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0
+
+    def test_subworkflows_lint_empty(self):
+        """Test linting a pipeline with no subworkflows installed"""
+        self.subworkflow_remove.remove("utils_nextflow_pipeline", force=True)
+        self.subworkflow_remove.remove("utils_nfcore_pipeline", force=True)
+        self.subworkflow_remove.remove("utils_nfvalidation_plugin", force=True)
+        with pytest.raises(LookupError):
+            nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
+
+    def test_subworkflows_lint_new_subworkflow(self):
+        """lint a new subworkflow"""
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint.lint(print_results=True, all_subworkflows=True)
+        assert len(subworkflow_lint.failed) == 0
+
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0
+
+    def test_subworkflows_lint_no_gitlab(self):
+        """Test linting a pipeline with no subworkflows installed"""
+        with pytest.raises(LookupError):
+            nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+
+    def test_subworkflows_lint_gitlab_subworkflows(self):
+        """Lint subworkflows from a different remote"""
+        self.subworkflow_install_gitlab.install("bam_stats_samtools")
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(
+            dir=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
+        )
+        subworkflow_lint.lint(print_results=False, all_subworkflows=True)
+        assert len(subworkflow_lint.failed) == 0
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0
+
+    def test_subworkflows_lint_multiple_remotes(self):
+        """Lint subworkflows from a different remote"""
+        self.subworkflow_install_gitlab.install("bam_stats_samtools")
+        self.subworkflow_install.install("fastq_align_bowtie2")
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(
+            dir=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
+        )
+        subworkflow_lint.lint(print_results=False, all_subworkflows=True)
+        assert len(subworkflow_lint.failed) == 0
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0
+
+    def test_subworkflows_lint_snapshot_file(self):
+        """Test linting a subworkflow with a snapshot file"""
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+        assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0
+
+    def test_subworkflows_lint_snapshot_file_missing_fail(self):
+        """Test linting a subworkflow with a snapshot file missing, which should fail"""
+        Path(
+            self.nfcore_modules,
+            "subworkflows",
+            "nf-core",
+            "test_subworkflow",
+            "tests",
+            "main.nf.test.snap",
+        ).unlink()
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+        Path(
+            self.nfcore_modules,
+            "subworkflows",
+            "nf-core",
+            "test_subworkflow",
+            "tests",
+            "main.nf.test.snap",
+        ).touch()
+        assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0
+
+    def test_subworkflows_lint_snapshot_file_not_needed(self):
+        """Test linting a subworkflow which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file"""
+        with open(
+            Path(
+                self.nfcore_modules,
+                "subworkflows",
+                "nf-core",
+                "test_subworkflow",
+                "tests",
+                "main.nf.test",
+            )
+        ) as fh:
+            content = fh.read()
+            new_content = content.replace("snapshot(", "snap (")
+        with open(
+            Path(
+                self.nfcore_modules,
+                "subworkflows",
+                "nf-core",
+                "test_subworkflow",
+                "tests",
+                "main.nf.test",
+            ),
+            "w",
+        ) as fh:
+            fh.write(new_content)
+
+        Path(
+            self.nfcore_modules,
+            "subworkflows",
+            "nf-core",
+            "test_subworkflow",
+            "tests",
+            "main.nf.test.snap",
+        ).unlink()
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+        Path(
+            self.nfcore_modules,
+            "subworkflows",
+            "nf-core",
+            "test_subworkflow",
+            "tests",
+            "main.nf.test.snap",
+        ).touch()
+        assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0
+
+    def test_subworkflows_lint_less_than_two_modules_warning(self):
+        """Test linting a subworkflow with less than two modules"""
+        self.subworkflow_install.install("bam_stats_samtools")
+        # Remove two modules
+        with open(
+            Path(
+                self.pipeline_dir,
+                "subworkflows",
+                "nf-core",
+                "bam_stats_samtools",
+                "main.nf",
+            )
+        ) as fh:
+            content = fh.read()
+            new_content = content.replace(
+                "include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main'",
+                "",
+            )
+            new_content = new_content.replace(
+                "include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main'",
+                "",
+            )
+        with open(
+            Path(
+                self.pipeline_dir,
+                "subworkflows",
+                "nf-core",
+                "bam_stats_samtools",
+                "main.nf",
+            ),
+            "w",
+        ) as fh:
+            fh.write(new_content)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
+        subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools")
+        assert len(subworkflow_lint.failed) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) > 0
+        assert subworkflow_lint.warned[0].lint_test == "main_nf_include"
+        # cleanup
+        self.subworkflow_remove.remove("bam_stats_samtools", force=True)
+
+    def test_subworkflows_lint_include_multiple_alias(self):
+        """Test linting a subworkflow with multiple include methods"""
+        self.subworkflow_install.install("bam_stats_samtools")
+        with open(
+            Path(
+                self.pipeline_dir,
+                "subworkflows",
+                "nf-core",
+                "bam_stats_samtools",
+                "main.nf",
+            )
+        ) as fh:
+            content = fh.read()
+            new_content = content.replace("SAMTOOLS_STATS", "SAMTOOLS_STATS_1")
+            new_content = new_content.replace(
+                "include { SAMTOOLS_STATS_1 ",
+                "include { SAMTOOLS_STATS as SAMTOOLS_STATS_1; SAMTOOLS_STATS as SAMTOOLS_STATS_2 ",
+            )
+        with open(
+            Path(
+                self.pipeline_dir,
+                "subworkflows",
+                "nf-core",
+                "bam_stats_samtools",
+                "main.nf",
+            ),
+            "w",
+        ) as fh:
+            fh.write(new_content)
+
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
+        subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools")
+        assert len(subworkflow_lint.failed) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) == 2
+        assert any(
+            [
+                x.message == "Included component 'SAMTOOLS_STATS_1' versions are added in main.nf"
+                for x in subworkflow_lint.passed
+            ]
+        )
+        assert any(
+            [x.message == "Included component 'SAMTOOLS_STATS_1' used in main.nf" for x in subworkflow_lint.passed]
+        )
+        assert any(
+            [x.message == "Included component 'SAMTOOLS_STATS_2' not used in main.nf" for x in subworkflow_lint.warned]
+        )
+
+        # cleanup
+        self.subworkflow_remove.remove("bam_stats_samtools", force=True)
+
+    def test_subworkflows_lint_capitalization_fail(self):
+        """Test linting a subworkflow with a capitalization fail"""
+        self.subworkflow_install.install("bam_stats_samtools")
+        # change workflow name to lowercase
+        with open(
+            Path(
+                self.pipeline_dir,
+                "subworkflows",
+                "nf-core",
+                "bam_stats_samtools",
+                "main.nf",
+            )
+        ) as fh:
+            content = fh.read()
+            new_content = content.replace("workflow BAM_STATS_SAMTOOLS {", "workflow bam_stats_samtools {")
+        with open(
+            Path(
+                self.pipeline_dir,
+                "subworkflows",
+                "nf-core",
+                "bam_stats_samtools",
+                "main.nf",
+            ),
+            "w",
+        ) as fh:
+            fh.write(new_content)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
+        subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools")
+        assert len(subworkflow_lint.failed) >= 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0
+        assert any([x.lint_test == "workflow_capitals" for x in subworkflow_lint.failed])
+
+        # cleanup
+        self.subworkflow_remove.remove("bam_stats_samtools", force=True)
+
+    def test_subworkflows_absent_version(self):
+        """Test linting a nf-test module if the versions is absent in the snapshot file `"""
+        snap_file = Path(
+            self.nfcore_modules,
+            "subworkflows",
+            "nf-core",
+            "test_subworkflow",
+            "tests",
+            "main.nf.test.snap",
+        )
+        with open(snap_file) as fh:
+            content = fh.read()
+            new_content = content.replace("versions", "foo")
+        with open(snap_file, "w") as fh:
+            fh.write(new_content)
+
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+        assert len(subworkflow_lint.failed) == 0
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
+        assert any([x.lint_test == "test_snap_versions" for x in subworkflow_lint.warned])
+
+        # cleanup
+        with open(snap_file, "w") as fh:
+            fh.write(content)
+
+    def test_subworkflows_missing_test_dir(self):
+        """Test linting a nf-test subworkflow if the tests directory is missing"""
+        test_dir = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests")
+        test_dir_copy = shutil.copytree(test_dir, test_dir.parent / "tests_copy")
+        shutil.rmtree(test_dir)
+
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+        assert len(subworkflow_lint.failed) == 0
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
+        assert any([x.lint_test == "test_dir_versions" for x in subworkflow_lint.warned])
+
+        # cleanup
+        shutil.copytree(test_dir_copy, test_dir)
+
+    def test_subworkflows_missing_main_nf(self):
+        """Test linting a nf-test subworkflow if the main.nf file is missing"""
+        main_nf = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "main.nf")
+        main_nf_copy = shutil.copy(main_nf, main_nf.parent / "main_nf_copy")
+        main_nf.unlink()
+
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+        assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0
+        assert subworkflow_lint.failed[0].lint_test == "main_nf_exists"
+
+        # cleanup
+        shutil.copy(main_nf_copy, main_nf)
+
+    def test_subworkflows_empty_file_in_snapshot(self):
+        """Test linting a nf-test subworkflow with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)"""
+        snap_file = Path(
+            self.nfcore_modules,
+            "subworkflows",
+            "nf-core",
+            "test_subworkflow",
+            "tests",
+            "main.nf.test.snap",
+        )
+        snap = json.load(snap_file.open())
+        content = snap_file.read_text()
+        snap["my test"]["content"][0]["0"] = "test:md5,d41d8cd98f00b204e9800998ecf8427e"
+
+        with open(snap_file, "w") as fh:
+            json.dump(snap, fh)
+
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+        assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0
+        assert subworkflow_lint.failed[0].lint_test == "test_snap_md5sum"
+
+        # reset the file
+        with open(snap_file, "w") as fh:
+            fh.write(content)
+
+    def test_subworkflows_empty_file_in_stub_snapshot(self):
+        """Test linting a nf-test subworkflow with an empty file sha sum in the stub test snapshot, which should make it not fail"""
+        snap_file = Path(
+            self.nfcore_modules,
+            "subworkflows",
+            "nf-core",
+            "test_subworkflow",
+            "tests",
+            "main.nf.test.snap",
+        )
+        snap = json.load(snap_file.open())
+        content = snap_file.read_text()
+        snap["my_test_stub"] = {"content": [{"0": "test:md5,d41d8cd98f00b204e9800998ecf8427e", "versions": {}}]}
+
+        with open(snap_file, "w") as fh:
+            json.dump(snap, fh)
+
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+        assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0
+        assert any(x.lint_test == "test_snap_md5sum" for x in subworkflow_lint.passed)
+
+        # reset the file
+        with open(snap_file, "w") as fh:
+            fh.write(content)
diff --git a/tests/subworkflows/test_list.py b/tests/subworkflows/test_list.py
new file mode 100644
index 0000000000..5e4e6feb0a
--- /dev/null
+++ b/tests/subworkflows/test_list.py
@@ -0,0 +1,48 @@
+from rich.console import Console
+
+import nf_core.subworkflows
+
+from ..test_subworkflows import TestSubworkflows
+from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL
+
+
+class TestSubworkflowsList(TestSubworkflows):
+    def test_subworkflows_list_remote(self):
+        """Test listing available subworkflows"""
+        subworkflows_list = nf_core.subworkflows.SubworkflowList(None, remote=True)
+        listed_subworkflows = subworkflows_list.list_components()
+        console = Console(record=True)
+        console.print(listed_subworkflows)
+        output = console.export_text()
+        assert "bam_stats" in output
+
+    def test_subworkflows_list_remote_gitlab(self):
+        """Test listing the subworkflows in the remote gitlab repo"""
+        subworkflows_list = nf_core.subworkflows.SubworkflowList(
+            None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
+        )
+        listed_subworkflows = subworkflows_list.list_components()
+        console = Console(record=True)
+        console.print(listed_subworkflows)
+        output = console.export_text()
+        assert "bam_stats" in output
+
+    def test_subworkflows_install_and_list_subworkflows(self):
+        """Test listing locally installed subworkflows"""
+        self.subworkflow_install.install("bam_sort_stats_samtools")
+        subworkflows_list = nf_core.subworkflows.SubworkflowList(self.pipeline_dir, remote=False)
+        listed_subworkflows = subworkflows_list.list_components()
+        console = Console(record=True)
+        console.print(listed_subworkflows)
+        output = console.export_text()
+        assert "bam_stats" in output
+
+    def test_subworkflows_install_gitlab_and_list_subworkflows(self):
+        """Test listing locally installed subworkflows"""
+        self.subworkflow_install_gitlab.install("bam_sort_stats_samtools")
+        subworkflows_list = nf_core.subworkflows.SubworkflowList(self.pipeline_dir, remote=False)
+        listed_subworkflows = subworkflows_list.list_components()
+        console = Console(record=True)
+        console.print(listed_subworkflows)
+        output = console.export_text()
+        assert "bam_stats" in output
diff --git a/tests/subworkflows/test_remove.py b/tests/subworkflows/test_remove.py
new file mode 100644
index 0000000000..61c016b232
--- /dev/null
+++ b/tests/subworkflows/test_remove.py
@@ -0,0 +1,101 @@
+from pathlib import Path
+
+from nf_core.modules.modules_json import ModulesJson
+
+from ..test_subworkflows import TestSubworkflows
+
+
+class TestSubworkflowsRemove(TestSubworkflows):
+    def test_subworkflows_remove_uninstalled_subworkflow(self):
+        """Test removing subworkflow without installing it"""
+        assert self.subworkflow_remove.remove("bam_sort_stats_samtools") is False
+
+    def test_subworkflows_remove_subworkflow(self):
+        """Test removing subworkflow and all it's dependencies after installing it"""
+        self.subworkflow_install.install("bam_sort_stats_samtools")
+
+        subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
+        bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
+        bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
+        samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
+        ModulesJson(self.pipeline_dir)
+        mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json()
+        assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
+        mod_json_after = ModulesJson(self.pipeline_dir).get_modules_json()
+        assert Path.exists(bam_sort_stats_samtools_path) is False
+        assert Path.exists(bam_stats_samtools_path) is False
+        assert Path.exists(samtools_index_path) is False
+        assert mod_json_before != mod_json_after
+        # assert subworkflows key is removed from modules.json
+        assert (
+            "bam_sort_stats_samtools"
+            not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"].keys()
+        )
+        assert (
+            "samtools/index" not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"].keys()
+        )
+
+    def test_subworkflows_remove_subworkflow_keep_installed_module(self):
+        """Test removing subworkflow and all it's dependencies after installing it, except for a separately installed module"""
+        self.subworkflow_install.install("bam_sort_stats_samtools")
+        self.mods_install.install("samtools/index")
+
+        subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
+        bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
+        bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
+        samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
+
+        mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json()
+        assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
+        mod_json_after = ModulesJson(self.pipeline_dir).get_modules_json()
+
+        assert Path.exists(bam_sort_stats_samtools_path) is False
+        assert Path.exists(bam_stats_samtools_path) is False
+        assert Path.exists(samtools_index_path) is True
+        assert mod_json_before != mod_json_after
+        # assert subworkflows key is removed from modules.json
+        assert (
+            "bam_sort_stats_samtools"
+            not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"].keys()
+        )
+        assert (
+            "samtools/index"
+            in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"].keys()
+        )
+
+    def test_subworkflows_remove_one_of_two_subworkflow(self):
+        """Test removing subworkflow and all it's dependencies after installing it"""
+        self.subworkflow_install.install("bam_sort_stats_samtools")
+        self.subworkflow_install.install("bam_stats_samtools")
+        subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
+        bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
+        bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
+        samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
+        samtools_stats_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats")
+
+        assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
+
+        assert Path.exists(subworkflow_path) is True
+        assert Path.exists(bam_sort_stats_samtools_path) is False
+        assert Path.exists(bam_stats_samtools_path) is True
+        assert Path.exists(samtools_index_path) is False
+        assert Path.exists(samtools_stats_path) is True
+        self.subworkflow_remove.remove("bam_stats_samtools")
+
+    def test_subworkflows_remove_included_subworkflow(self):
+        """Test removing subworkflow which is installed by another subworkflow and all it's dependencies."""
+        self.subworkflow_install.install("bam_sort_stats_samtools")
+        subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
+        bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
+        bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
+        samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
+        samtools_stats_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats")
+
+        assert self.subworkflow_remove.remove("bam_stats_samtools") is False
+
+        assert Path.exists(subworkflow_path) is True
+        assert Path.exists(bam_sort_stats_samtools_path) is True
+        assert Path.exists(bam_stats_samtools_path) is True
+        assert Path.exists(samtools_index_path) is True
+        assert Path.exists(samtools_stats_path) is True
+        self.subworkflow_remove.remove("bam_sort_stats_samtools")
diff --git a/tests/subworkflows/test_update.py b/tests/subworkflows/test_update.py
new file mode 100644
index 0000000000..d3b2433572
--- /dev/null
+++ b/tests/subworkflows/test_update.py
@@ -0,0 +1,370 @@
+import logging
+import shutil
+import tempfile
+from pathlib import Path
+from unittest import mock
+
+import questionary
+import yaml
+
+import nf_core.utils
+from nf_core.modules.modules_json import ModulesJson
+from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
+from nf_core.modules.update import ModuleUpdate
+from nf_core.subworkflows.update import SubworkflowUpdate
+
+from ..test_subworkflows import TestSubworkflows
+from ..utils import OLD_SUBWORKFLOWS_SHA, cmp_component
+
+
+class TestSubworkflowsUpdate(TestSubworkflows):
+    def test_install_and_update(self):
+        """Installs a subworkflow in the pipeline and updates it (no change)"""
+        self.subworkflow_install.install("bam_stats_samtools")
+        update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False)
+
+        # Copy the sw files and check that they are unaffected by the update
+        tmpdir = Path(tempfile.TemporaryDirectory().name)
+        sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "bam_stats_samtools")
+        shutil.copytree(sw_path, tmpdir)
+
+        assert update_obj.update("bam_stats_samtools") is True
+        assert cmp_component(tmpdir, sw_path) is True
+
+    def test_install_at_hash_and_update(self):
+        """Installs an old version of a subworkflow in the pipeline and updates it"""
+        assert self.subworkflow_install_old.install("fastq_align_bowtie2")
+        update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False, update_deps=True)
+        old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+
+        # Copy the sw files and check that they are affected by the update
+        tmpdir = Path(tempfile.TemporaryDirectory().name)
+
+        sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
+        shutil.copytree(sw_path, tmpdir)
+
+        assert update_obj.update("fastq_align_bowtie2") is True
+        assert cmp_component(tmpdir, sw_path) is False
+
+        # Check that the modules.json is correctly updated
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        # Get the up-to-date git_sha for the sw from the ModulesRepo object
+        assert (
+            old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
+                "git_sha"
+            ]
+            != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
+                "git_sha"
+            ]
+        )
+
+    # Mock questionary answer: update components
+    @mock.patch.object(questionary.Question, "unsafe_ask", return_value=True)
+    def test_install_at_hash_and_update_limit_output(self, mock_prompt):
+        """Installs an old version of a subworkflow in the pipeline and updates it with limit_output=True"""
+        self.caplog.set_level(logging.INFO)
+        assert self.subworkflow_install_old.install("fastq_align_bowtie2")
+
+        update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=True, update_deps=True, limit_output=True)
+
+        assert update_obj.update("fastq_align_bowtie2")
+
+        # Check changes not shown for non-.nf files
+        assert "Changes in 'fastq_align_bowtie2/meta.yml' but not shown" in self.caplog.text
+        assert "Changes in 'bam_sort_stats_samtools/meta.yml' but not shown" in self.caplog.text
+        assert "Changes in 'bam_stats_samtools/meta.yml' but not shown" in self.caplog.text
+        assert "Changes in 'samtools/flagstat/meta.yml' but not shown" in self.caplog.text
+        # Check changes only shown for main.nf files
+        assert "Changes in 'fastq_align_bowtie2/main.nf'" in self.caplog.text
+        for line in self.caplog.text.split("\n"):
+            if line.startswith("---"):
+                assert line.endswith("main.nf")
+
+    def test_install_at_hash_and_update_and_save_diff_to_file(self):
+        """Installs an old version of a sw in the pipeline and updates it. Save differences to a file."""
+        assert self.subworkflow_install_old.install("fastq_align_bowtie2")
+        patch_path = Path(self.pipeline_dir, "fastq_align_bowtie2.patch")
+        update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True)
+
+        # Copy the sw files and check that they are affected by the update
+        tmpdir = Path(tempfile.TemporaryDirectory().name)
+
+        sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
+        shutil.copytree(sw_path, tmpdir)
+
+        assert update_obj.update("fastq_align_bowtie2") is True
+        assert cmp_component(tmpdir, sw_path) is True
+
+        with open(patch_path) as fh:
+            line = fh.readline()
+            assert line.startswith(
+                "Changes in module 'nf-core/fastq_align_bowtie2' between (f3c078809a2513f1c95de14f6633fe1f03572fdb) and"
+            )
+
+    def test_install_at_hash_and_update_and_save_diff_limit_output(self):
+        """Installs an old version of a sw in the pipeline and updates it. Save differences to a file."""
+        # Install old version of fastq_align_bowtie2
+        self.subworkflow_install_old.install("fastq_align_bowtie2")
+        patch_path = Path(self.pipeline_dir, "fastq_align_bowtie2.patch")
+        # Update saving the differences to a patch file and with `limit_output`
+        update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True, limit_output=True)
+        assert update_obj.update("fastq_align_bowtie2")
+
+        # Check that the patch file was created
+        assert patch_path.exists(), f"Patch file was not created at {patch_path}"
+
+        # Read the contents of the patch file
+        with open(patch_path) as fh:
+            content = fh.read()
+            # Check changes not shown for non-.nf files
+            assert "Changes in 'fastq_align_bowtie2/meta.yml' but not shown" in content
+            assert "Changes in 'bam_sort_stats_samtools/meta.yml' but not shown" in content
+            assert "Changes in 'bam_stats_samtools/meta.yml' but not shown" in content
+            assert "Changes in 'samtools/flagstat/meta.yml' but not shown" in content
+            # Check changes only shown for main.nf files
+            assert "Changes in 'fastq_align_bowtie2/main.nf'" in content
+            for line in content:
+                if line.startswith("---"):
+                    assert line.endswith("main.nf")
+
+    def test_update_all(self):
+        """Updates all subworkflows present in the pipeline"""
+        # Install subworkflows fastq_align_bowtie2, bam_sort_stats_samtools, bam_stats_samtools
+        self.subworkflow_install.install("fastq_align_bowtie2")
+        # Update all subworkflows
+        update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False)
+        assert update_obj.update() is True
+
+        # We must reload the modules.json to get the updated version
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+        mod_json = mod_json_obj.get_modules_json()
+        # Loop through all subworkflows and check that they are updated (according to the modules.json file)
+        for sw in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]:
+            correct_git_sha = list(update_obj.modules_repo.get_component_git_log(sw, "subworkflows", depth=1))[0][
+                "git_sha"
+            ]
+            current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw][
+                "git_sha"
+            ]
+            assert correct_git_sha == current_git_sha
+
+    def test_update_with_config_fixed_version(self):
+        """Try updating when there are entries in the .nf-core.yml"""
+        # Install subworkflow at the latest version
+        assert self.subworkflow_install.install("fastq_align_bowtie2")
+
+        # Fix the subworkflow version in the .nf-core.yml to an old version
+        update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": OLD_SUBWORKFLOWS_SHA}}}
+        config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
+        tools_config["update"] = update_config
+        with open(Path(self.pipeline_dir, config_fn), "w") as f:
+            yaml.dump(tools_config, f)
+
+        # Update all subworkflows in the pipeline
+        update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False)
+        assert update_obj.update() is True
+
+        # Check that the git sha for fastq_align_bowtie2 is correctly downgraded
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        assert "fastq_align_bowtie2" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]
+        assert (
+            "git_sha"
+            in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"]
+        )
+        assert (
+            mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
+                "git_sha"
+            ]
+            == OLD_SUBWORKFLOWS_SHA
+        )
+
+    def test_update_with_config_dont_update(self):
+        """Try updating when sw is to be ignored"""
+        # Install an old version of fastq_align_bowtie2
+        self.subworkflow_install_old.install("fastq_align_bowtie2")
+
+        # Set the fastq_align_bowtie2 field to no update in the .nf-core.yml
+        update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": False}}}
+        config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
+        tools_config["update"] = update_config
+        with open(Path(self.pipeline_dir, config_fn), "w") as f:
+            yaml.dump(tools_config, f)
+
+        # Update all modules in the pipeline
+        update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False)
+        assert update_obj.update() is True
+
+        # Check that the git sha for fastq_align_bowtie2 is correctly downgraded
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        assert "fastq_align_bowtie2" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]
+        assert (
+            "git_sha"
+            in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"]
+        )
+        assert (
+            mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
+                "git_sha"
+            ]
+            == OLD_SUBWORKFLOWS_SHA
+        )
+
+    def test_update_with_config_fix_all(self):
+        """Fix the version of all nf-core subworkflows"""
+        # Install subworkflow at the latest version
+        assert self.subworkflow_install.install("fastq_align_bowtie2")
+
+        # Fix the version of all nf-core subworkflows in the .nf-core.yml to an old version
+        update_config = {NF_CORE_MODULES_REMOTE: OLD_SUBWORKFLOWS_SHA}
+        config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
+        tools_config["update"] = update_config
+        with open(Path(self.pipeline_dir, config_fn), "w") as f:
+            yaml.dump(tools_config, f)
+
+        # Update fastq_align_bowtie2
+        update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=False, update_deps=True, show_diff=False)
+        assert update_obj.update("fastq_align_bowtie2") is True
+
+        # Check that the git sha for fastq_align_bowtie2 is correctly downgraded
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        assert (
+            "git_sha"
+            in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"]
+        )
+        assert (
+            mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
+                "git_sha"
+            ]
+            == OLD_SUBWORKFLOWS_SHA
+        )
+
+    def test_update_with_config_no_updates(self):
+        """Don't update any nf-core subworkflows"""
+        # Install an old version of fastq_align_bowtie2
+        self.subworkflow_install_old.install("fastq_align_bowtie2")
+        old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+
+        # Set all repository updates to False
+        update_config = {NF_CORE_MODULES_REMOTE: False}
+        config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
+        tools_config["update"] = update_config
+        with open(Path(self.pipeline_dir, config_fn), "w") as f:
+            yaml.dump(tools_config, f)
+
+        # Update all subworkflows in the pipeline
+        update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False)
+        assert update_obj.update() is True
+
+        # Check that the git sha for fastq_align_bowtie2 is correctly downgraded and none of the subworkflows has changed
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        for sw in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]:
+            assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]
+            assert (
+                mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"]
+                == old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"]
+            )
+
+    def test_update_all_linked_components_from_subworkflow(self):
+        """Update a subworkflow and all modules and subworkflows used on it"""
+        # Install an old version of fastq_align_bowtie2
+        self.subworkflow_install_old.install("fastq_align_bowtie2")
+        old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+
+        # Copy the sw files and check that they are affected by the update
+        tmpdir = Path(tempfile.TemporaryDirectory().name)
+        subworkflows_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME)
+        modules_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME)
+        shutil.copytree(subworkflows_path, Path(tmpdir, "subworkflows"))
+        shutil.copytree(modules_path, Path(tmpdir, "modules"))
+
+        # Update fastq_align_bowtie2 and all modules and subworkflows used by that
+        update_obj = SubworkflowUpdate(self.pipeline_dir, update_deps=True, show_diff=False)
+        assert update_obj.update("fastq_align_bowtie2") is True
+
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        # Loop through all modules and subworkflows used in fastq_align_bowtie2
+        # check that they are updated (according to the modules.json file)
+        for sw in ["fastq_align_bowtie2", "bam_sort_stats_samtools", "bam_stats_samtools"]:
+            assert (
+                old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"]
+                != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"]
+            )
+        for mod in [
+            "bowtie2/align",
+            "samtools/index",
+            "samtools/sort",
+            "samtools/flagstat",
+            "samtools/idxstats",
+            "samtools/stats",
+        ]:
+            assert (
+                old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
+                != mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
+            )
+        # Check that the subworkflow files are updated
+        assert (
+            cmp_component(
+                Path(tmpdir, "subworkflows", "fastq_align_bowtie2"), Path(subworkflows_path, "fastq_align_bowtie2")
+            )
+            is False
+        )
+
+    def test_update_all_subworkflows_from_module(self):
+        """Update a module and all subworkflows that use this module"""
+        # Install an old version of fastq_align_bowtie2 and thus all modules used by it (bowtie2/align)
+        self.subworkflow_install_old.install("fastq_align_bowtie2")
+        old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+
+        # Copy the sw files and check that they are affected by the update
+        tmpdir = Path(tempfile.TemporaryDirectory().name)
+        sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
+        shutil.copytree(sw_path, Path(tmpdir, "fastq_align_bowtie2"))
+
+        # Update bowtie2/align and all subworkflows using it
+        update_obj = ModuleUpdate(self.pipeline_dir, update_deps=True, show_diff=False)
+        assert update_obj.update("bowtie2/align") is True
+
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        # Check that bowtie2/align and fastq_align_bowtie2 are updated
+        assert (
+            old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
+                "git_sha"
+            ]
+            != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
+                "git_sha"
+            ]
+        )
+        assert cmp_component(Path(tmpdir, "fastq_align_bowtie2"), sw_path) is False
+        assert (
+            old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]["bowtie2/align"]["git_sha"]
+            != mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]["bowtie2/align"]["git_sha"]
+        )
+
+    def test_update_change_of_included_modules(self):
+        """Update a subworkflow which has a module change in the new version."""
+        # Install an old version of vcf_annotate_ensemblvep with tabix/bgziptabix and without tabix/tabix
+        self.subworkflow_install_module_change.install("vcf_annotate_ensemblvep")
+        old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+
+        # Check that tabix/bgziptabix is there
+        assert "tabix/bgziptabix" in old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
+        assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/bgziptabix").is_dir()
+        # Check that tabix/tabix is not there
+        assert "tabix/tabix" not in old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
+        assert not Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/tabix").is_dir()
+
+        # Update vcf_annotate_ensemblvep without tabix/bgziptabix and with tabix/tabix
+        update_obj = SubworkflowUpdate(self.pipeline_dir, update_deps=True, show_diff=False)
+        assert update_obj.update("vcf_annotate_ensemblvep") is True
+
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+
+        # Check that tabix/bgziptabix is not there
+        assert "tabix/bgziptabix" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
+        assert not Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/bgziptabix").is_dir()
+        # Check that tabix/tabix is there
+        assert "tabix/tabix" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
+        assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/tabix").is_dir()
+        # Check that ensemblevep is not there but instead we have ensemblevep/vep (due to a file re-naming)
+        assert "ensemblvep" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
+        assert "ensemblvep/vep" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
+        assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "ensemblvep/vep").is_dir()
diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py
deleted file mode 100644
index 42ed716b1c..0000000000
--- a/tests/subworkflows/update.py
+++ /dev/null
@@ -1,376 +0,0 @@
-import logging
-import shutil
-import tempfile
-from pathlib import Path
-from unittest import mock
-
-import questionary
-import yaml
-
-import nf_core.utils
-from nf_core.modules.modules_json import ModulesJson
-from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
-from nf_core.modules.update import ModuleUpdate
-from nf_core.subworkflows.update import SubworkflowUpdate
-
-from ..utils import OLD_SUBWORKFLOWS_SHA, cmp_component
-
-
-def test_install_and_update(self):
-    """Installs a subworkflow in the pipeline and updates it (no change)"""
-    self.subworkflow_install.install("bam_stats_samtools")
-    update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False)
-
-    # Copy the sw files and check that they are unaffected by the update
-    tmpdir = Path(tempfile.TemporaryDirectory().name)
-    sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "bam_stats_samtools")
-    shutil.copytree(sw_path, tmpdir)
-
-    assert update_obj.update("bam_stats_samtools") is True
-    assert cmp_component(tmpdir, sw_path) is True
-
-
-def test_install_at_hash_and_update(self):
-    """Installs an old version of a subworkflow in the pipeline and updates it"""
-    assert self.subworkflow_install_old.install("fastq_align_bowtie2")
-    update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False, update_deps=True)
-    old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-
-    # Copy the sw files and check that they are affected by the update
-    tmpdir = Path(tempfile.TemporaryDirectory().name)
-
-    sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
-    shutil.copytree(sw_path, tmpdir)
-
-    assert update_obj.update("fastq_align_bowtie2") is True
-    assert cmp_component(tmpdir, sw_path) is False
-
-    # Check that the modules.json is correctly updated
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    # Get the up-to-date git_sha for the sw from the ModulesRepo object
-    assert (
-        old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
-            "git_sha"
-        ]
-        != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
-            "git_sha"
-        ]
-    )
-
-
-# Mock questionary answer: update components
-@mock.patch.object(questionary.Question, "unsafe_ask", return_value=True)
-def test_install_at_hash_and_update_limit_output(self, mock_prompt):
-    """Installs an old version of a subworkflow in the pipeline and updates it with limit_output=True"""
-    self.caplog.set_level(logging.INFO)
-    assert self.subworkflow_install_old.install("fastq_align_bowtie2")
-
-    update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=True, update_deps=True, limit_output=True)
-
-    assert update_obj.update("fastq_align_bowtie2")
-
-    # Check changes not shown for non-.nf files
-    assert "Changes in 'fastq_align_bowtie2/meta.yml' but not shown" in self.caplog.text
-    assert "Changes in 'bam_sort_stats_samtools/meta.yml' but not shown" in self.caplog.text
-    assert "Changes in 'bam_stats_samtools/meta.yml' but not shown" in self.caplog.text
-    assert "Changes in 'samtools/flagstat/meta.yml' but not shown" in self.caplog.text
-    # Check changes only shown for main.nf files
-    assert "Changes in 'fastq_align_bowtie2/main.nf'" in self.caplog.text
-    for line in self.caplog.text.split("\n"):
-        if line.startswith("---"):
-            assert line.endswith("main.nf")
-
-
-def test_install_at_hash_and_update_and_save_diff_to_file(self):
-    """Installs an old version of a sw in the pipeline and updates it. Save differences to a file."""
-    assert self.subworkflow_install_old.install("fastq_align_bowtie2")
-    patch_path = Path(self.pipeline_dir, "fastq_align_bowtie2.patch")
-    update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True)
-
-    # Copy the sw files and check that they are affected by the update
-    tmpdir = Path(tempfile.TemporaryDirectory().name)
-
-    sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
-    shutil.copytree(sw_path, tmpdir)
-
-    assert update_obj.update("fastq_align_bowtie2") is True
-    assert cmp_component(tmpdir, sw_path) is True
-
-    with open(patch_path) as fh:
-        line = fh.readline()
-        assert line.startswith(
-            "Changes in module 'nf-core/fastq_align_bowtie2' between (f3c078809a2513f1c95de14f6633fe1f03572fdb) and"
-        )
-
-
-def test_install_at_hash_and_update_and_save_diff_limit_output(self):
-    """Installs an old version of a sw in the pipeline and updates it. Save differences to a file."""
-    # Install old version of fastq_align_bowtie2
-    self.subworkflow_install_old.install("fastq_align_bowtie2")
-    patch_path = Path(self.pipeline_dir, "fastq_align_bowtie2.patch")
-    # Update saving the differences to a patch file and with `limit_output`
-    update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True, limit_output=True)
-    assert update_obj.update("fastq_align_bowtie2")
-
-    # Check that the patch file was created
-    assert patch_path.exists(), f"Patch file was not created at {patch_path}"
-
-    # Read the contents of the patch file
-    with open(patch_path) as fh:
-        content = fh.read()
-        # Check changes not shown for non-.nf files
-        assert "Changes in 'fastq_align_bowtie2/meta.yml' but not shown" in content
-        assert "Changes in 'bam_sort_stats_samtools/meta.yml' but not shown" in content
-        assert "Changes in 'bam_stats_samtools/meta.yml' but not shown" in content
-        assert "Changes in 'samtools/flagstat/meta.yml' but not shown" in content
-        # Check changes only shown for main.nf files
-        assert "Changes in 'fastq_align_bowtie2/main.nf'" in content
-        for line in content:
-            if line.startswith("---"):
-                assert line.endswith("main.nf")
-
-
-def test_update_all(self):
-    """Updates all subworkflows present in the pipeline"""
-    # Install subworkflows fastq_align_bowtie2, bam_sort_stats_samtools, bam_stats_samtools
-    self.subworkflow_install.install("fastq_align_bowtie2")
-    # Update all subworkflows
-    update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False)
-    assert update_obj.update() is True
-
-    # We must reload the modules.json to get the updated version
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    mod_json = mod_json_obj.get_modules_json()
-    # Loop through all subworkflows and check that they are updated (according to the modules.json file)
-    for sw in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]:
-        correct_git_sha = list(update_obj.modules_repo.get_component_git_log(sw, "subworkflows", depth=1))[0]["git_sha"]
-        current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"]
-        assert correct_git_sha == current_git_sha
-
-
-def test_update_with_config_fixed_version(self):
-    """Try updating when there are entries in the .nf-core.yml"""
-    # Install subworkflow at the latest version
-    assert self.subworkflow_install.install("fastq_align_bowtie2")
-
-    # Fix the subworkflow version in the .nf-core.yml to an old version
-    update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": OLD_SUBWORKFLOWS_SHA}}}
-    config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-    tools_config["update"] = update_config
-    with open(Path(self.pipeline_dir, config_fn), "w") as f:
-        yaml.dump(tools_config, f)
-
-    # Update all subworkflows in the pipeline
-    update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False)
-    assert update_obj.update() is True
-
-    # Check that the git sha for fastq_align_bowtie2 is correctly downgraded
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    assert "fastq_align_bowtie2" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]
-    assert (
-        "git_sha"
-        in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"]
-    )
-    assert (
-        mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
-            "git_sha"
-        ]
-        == OLD_SUBWORKFLOWS_SHA
-    )
-
-
-def test_update_with_config_dont_update(self):
-    """Try updating when sw is to be ignored"""
-    # Install an old version of fastq_align_bowtie2
-    self.subworkflow_install_old.install("fastq_align_bowtie2")
-
-    # Set the fastq_align_bowtie2 field to no update in the .nf-core.yml
-    update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": False}}}
-    config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-    tools_config["update"] = update_config
-    with open(Path(self.pipeline_dir, config_fn), "w") as f:
-        yaml.dump(tools_config, f)
-
-    # Update all modules in the pipeline
-    update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False)
-    assert update_obj.update() is True
-
-    # Check that the git sha for fastq_align_bowtie2 is correctly downgraded
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    assert "fastq_align_bowtie2" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]
-    assert (
-        "git_sha"
-        in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"]
-    )
-    assert (
-        mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
-            "git_sha"
-        ]
-        == OLD_SUBWORKFLOWS_SHA
-    )
-
-
-def test_update_with_config_fix_all(self):
-    """Fix the version of all nf-core subworkflows"""
-    # Install subworkflow at the latest version
-    assert self.subworkflow_install.install("fastq_align_bowtie2")
-
-    # Fix the version of all nf-core subworkflows in the .nf-core.yml to an old version
-    update_config = {NF_CORE_MODULES_REMOTE: OLD_SUBWORKFLOWS_SHA}
-    config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-    tools_config["update"] = update_config
-    with open(Path(self.pipeline_dir, config_fn), "w") as f:
-        yaml.dump(tools_config, f)
-
-    # Update fastq_align_bowtie2
-    update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=False, update_deps=True, show_diff=False)
-    assert update_obj.update("fastq_align_bowtie2") is True
-
-    # Check that the git sha for fastq_align_bowtie2 is correctly downgraded
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    assert (
-        "git_sha"
-        in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"]
-    )
-    assert (
-        mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
-            "git_sha"
-        ]
-        == OLD_SUBWORKFLOWS_SHA
-    )
-
-
-def test_update_with_config_no_updates(self):
-    """Don't update any nf-core subworkflows"""
-    # Install an old version of fastq_align_bowtie2
-    self.subworkflow_install_old.install("fastq_align_bowtie2")
-    old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-
-    # Set all repository updates to False
-    update_config = {NF_CORE_MODULES_REMOTE: False}
-    config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-    tools_config["update"] = update_config
-    with open(Path(self.pipeline_dir, config_fn), "w") as f:
-        yaml.dump(tools_config, f)
-
-    # Update all subworkflows in the pipeline
-    update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False)
-    assert update_obj.update() is True
-
-    # Check that the git sha for fastq_align_bowtie2 is correctly downgraded and none of the subworkflows has changed
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    for sw in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]:
-        assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]
-        assert (
-            mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"]
-            == old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"]
-        )
-
-
-def test_update_all_linked_components_from_subworkflow(self):
-    """Update a subworkflow and all modules and subworkflows used on it"""
-    # Install an old version of fastq_align_bowtie2
-    self.subworkflow_install_old.install("fastq_align_bowtie2")
-    old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-
-    # Copy the sw files and check that they are affected by the update
-    tmpdir = Path(tempfile.TemporaryDirectory().name)
-    subworkflows_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME)
-    modules_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME)
-    shutil.copytree(subworkflows_path, Path(tmpdir, "subworkflows"))
-    shutil.copytree(modules_path, Path(tmpdir, "modules"))
-
-    # Update fastq_align_bowtie2 and all modules and subworkflows used by that
-    update_obj = SubworkflowUpdate(self.pipeline_dir, update_deps=True, show_diff=False)
-    assert update_obj.update("fastq_align_bowtie2") is True
-
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    # Loop through all modules and subworkflows used in fastq_align_bowtie2
-    # check that they are updated (according to the modules.json file)
-    for sw in ["fastq_align_bowtie2", "bam_sort_stats_samtools", "bam_stats_samtools"]:
-        assert (
-            old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"]
-            != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"]
-        )
-    for mod in [
-        "bowtie2/align",
-        "samtools/index",
-        "samtools/sort",
-        "samtools/flagstat",
-        "samtools/idxstats",
-        "samtools/stats",
-    ]:
-        assert (
-            old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
-            != mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
-        )
-    # Check that the subworkflow files are updated
-    assert (
-        cmp_component(
-            Path(tmpdir, "subworkflows", "fastq_align_bowtie2"), Path(subworkflows_path, "fastq_align_bowtie2")
-        )
-        is False
-    )
-
-
-def test_update_all_subworkflows_from_module(self):
-    """Update a module and all subworkflows that use this module"""
-    # Install an old version of fastq_align_bowtie2 and thus all modules used by it (bowtie2/align)
-    self.subworkflow_install_old.install("fastq_align_bowtie2")
-    old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-
-    # Copy the sw files and check that they are affected by the update
-    tmpdir = Path(tempfile.TemporaryDirectory().name)
-    sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2")
-    shutil.copytree(sw_path, Path(tmpdir, "fastq_align_bowtie2"))
-
-    # Update bowtie2/align and all subworkflows using it
-    update_obj = ModuleUpdate(self.pipeline_dir, update_deps=True, show_diff=False)
-    assert update_obj.update("bowtie2/align") is True
-
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    # Check that bowtie2/align and fastq_align_bowtie2 are updated
-    assert (
-        old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
-            "git_sha"
-        ]
-        != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
-            "git_sha"
-        ]
-    )
-    assert cmp_component(Path(tmpdir, "fastq_align_bowtie2"), sw_path) is False
-    assert (
-        old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]["bowtie2/align"]["git_sha"]
-        != mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]["bowtie2/align"]["git_sha"]
-    )
-
-
-def test_update_change_of_included_modules(self):
-    """Update a subworkflow which has a module change in the new version."""
-    # Install an old version of vcf_annotate_ensemblvep with tabix/bgziptabix and without tabix/tabix
-    self.subworkflow_install_module_change.install("vcf_annotate_ensemblvep")
-    old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-
-    # Check that tabix/bgziptabix is there
-    assert "tabix/bgziptabix" in old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
-    assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/bgziptabix").is_dir()
-    # Check that tabix/tabix is not there
-    assert "tabix/tabix" not in old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
-    assert not Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/tabix").is_dir()
-
-    # Update vcf_annotate_ensemblvep without tabix/bgziptabix and with tabix/tabix
-    update_obj = SubworkflowUpdate(self.pipeline_dir, update_deps=True, show_diff=False)
-    assert update_obj.update("vcf_annotate_ensemblvep") is True
-
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-
-    # Check that tabix/bgziptabix is not there
-    assert "tabix/bgziptabix" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
-    assert not Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/bgziptabix").is_dir()
-    # Check that tabix/tabix is there
-    assert "tabix/tabix" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
-    assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/tabix").is_dir()
-    # Check that ensemblevep is not there but instead we have ensemblevep/vep (due to a file re-naming)
-    assert "ensemblvep" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
-    assert "ensemblvep/vep" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
-    assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "ensemblvep/vep").is_dir()
diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py
index 17bc678cad..af581fc9ab 100644
--- a/tests/test_subworkflows.py
+++ b/tests/test_subworkflows.py
@@ -119,77 +119,34 @@ def tearDown(self):
     def _use_caplog(self, caplog):
         self.caplog = caplog
 
-    ################################################
-    # Test of the individual subworkflow commands. #
-    ################################################
-
-    from .subworkflows.create import (  # type: ignore[misc]
-        test_subworkflows_create_fail_exists,
-        test_subworkflows_create_nfcore_modules,
-        test_subworkflows_create_succeed,
-        test_subworkflows_migrate,
-        test_subworkflows_migrate_no_delete,
-    )
-    from .subworkflows.info import (  # type: ignore[misc]
-        test_subworkflows_info_in_modules_repo,
-        test_subworkflows_info_local,
-        test_subworkflows_info_remote,
-        test_subworkflows_info_remote_gitlab,
-    )
-    from .subworkflows.install import (  # type: ignore[misc]
-        test_subworkflow_install_nopipeline,
-        test_subworkflows_install_alternate_remote,
-        test_subworkflows_install_bam_sort_stats_samtools,
-        test_subworkflows_install_bam_sort_stats_samtools_twice,
-        test_subworkflows_install_different_branch_fail,
-        test_subworkflows_install_emptypipeline,
-        test_subworkflows_install_from_gitlab,
-        test_subworkflows_install_nosubworkflow,
-        test_subworkflows_install_tracking,
-        test_subworkflows_install_tracking_added_already_installed,
-        test_subworkflows_install_tracking_added_super_subworkflow,
-    )
-    from .subworkflows.lint import (  # type: ignore[misc]
-        test_subworkflows_absent_version,
-        test_subworkflows_empty_file_in_snapshot,
-        test_subworkflows_empty_file_in_stub_snapshot,
-        test_subworkflows_lint,
-        test_subworkflows_lint_capitalization_fail,
-        test_subworkflows_lint_empty,
-        test_subworkflows_lint_gitlab_subworkflows,
-        test_subworkflows_lint_include_multiple_alias,
-        test_subworkflows_lint_less_than_two_modules_warning,
-        test_subworkflows_lint_multiple_remotes,
-        test_subworkflows_lint_new_subworkflow,
-        test_subworkflows_lint_no_gitlab,
-        test_subworkflows_lint_snapshot_file,
-        test_subworkflows_lint_snapshot_file_missing_fail,
-        test_subworkflows_lint_snapshot_file_not_needed,
-    )
-    from .subworkflows.list import (  # type: ignore[misc]
-        test_subworkflows_install_and_list_subworkflows,
-        test_subworkflows_install_gitlab_and_list_subworkflows,
-        test_subworkflows_list_remote,
-        test_subworkflows_list_remote_gitlab,
-    )
-    from .subworkflows.remove import (  # type: ignore[misc]
-        test_subworkflows_remove_included_subworkflow,
-        test_subworkflows_remove_one_of_two_subworkflow,
-        test_subworkflows_remove_subworkflow,
-        test_subworkflows_remove_subworkflow_keep_installed_module,
-    )
-    from .subworkflows.update import (  # type: ignore[misc]
-        test_install_and_update,
-        test_install_at_hash_and_update,
-        test_install_at_hash_and_update_and_save_diff_limit_output,
-        test_install_at_hash_and_update_and_save_diff_to_file,
-        test_install_at_hash_and_update_limit_output,
-        test_update_all,
-        test_update_all_linked_components_from_subworkflow,
-        test_update_all_subworkflows_from_module,
-        test_update_change_of_included_modules,
-        test_update_with_config_dont_update,
-        test_update_with_config_fix_all,
-        test_update_with_config_fixed_version,
-        test_update_with_config_no_updates,
-    )
+    # ################################################
+    # # Test of the individual subworkflow commands. #
+    # ################################################
+
+    # from .subworkflows.list import (  # type: ignore[misc]
+    #     test_subworkflows_install_and_list_subworkflows,
+    #     test_subworkflows_install_gitlab_and_list_subworkflows,
+    #     test_subworkflows_list_remote,
+    #     test_subworkflows_list_remote_gitlab,
+    # )
+    # from .subworkflows.remove import (  # type: ignore[misc]
+    #     test_subworkflows_remove_included_subworkflow,
+    #     test_subworkflows_remove_one_of_two_subworkflow,
+    #     test_subworkflows_remove_subworkflow,
+    #     test_subworkflows_remove_subworkflow_keep_installed_module,
+    # )
+    # from .subworkflows.update import (  # type: ignore[misc]
+    #     test_install_and_update,
+    #     test_install_at_hash_and_update,
+    #     test_install_at_hash_and_update_and_save_diff_limit_output,
+    #     test_install_at_hash_and_update_and_save_diff_to_file,
+    #     test_install_at_hash_and_update_limit_output,
+    #     test_update_all,
+    #     test_update_all_linked_components_from_subworkflow,
+    #     test_update_all_subworkflows_from_module,
+    #     test_update_change_of_included_modules,
+    #     test_update_with_config_dont_update,
+    #     test_update_with_config_fix_all,
+    #     test_update_with_config_fixed_version,
+    #     test_update_with_config_no_updates,
+    # )

From c00623dda555b708dca2fc7e90d62a5aaa65d6c4 Mon Sep 17 00:00:00 2001
From: laurencekuhl <laurence.kuhlburger@gmail.com>
Date: Wed, 17 Jul 2024 16:20:43 +0200
Subject: [PATCH 085/414] Remove release announcement for non nf-core pipelines

---
 nf_core/pipelines/create/create.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index bdbbca646f..f9ba2ff7f6 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -92,6 +92,7 @@ def __init__(
                 "CODE_OF_CONDUCT.md",
                 ".github/workflows/awsfulltest.yml",
                 ".github/workflows/awstest.yml",
+                ".github/workflows/release-announcements.yml"
             ],
         }
         # Get list of files we're skipping with the supplied skip keys

From c71dac8e6e2217324a417b9b58c60716102b1ae5 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Tue, 16 Jul 2024 09:54:59 +0000
Subject: [PATCH 086/414] Update python:3.12-slim Docker digest to f11725a

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 7178b65267..8943b70627 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:d5f16749562233aa4bd26538771d76bf0dfd0a0ea7ea8771985e267451397ae4
+FROM python:3.12-slim@sha256:f11725aba18c19664a408902103365eaf8013823ffc56270f921d1dc78a198cb
 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for nf-core/tools"
 

From 33a4b67479000a458774b68c107a6c5794bcfec5 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 17 Jul 2024 13:50:05 +0000
Subject: [PATCH 087/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 823e000beb..fba54a9539 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -50,6 +50,7 @@
 - update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054))
 - Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058))
 - handle new jsonschema error type ([#3061](https://github.com/nf-core/tools/pull/3061))
+- Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From 4e7be452d4fb16f8949a6bde0de70271bb5977a8 Mon Sep 17 00:00:00 2001
From: laurencekuhl <laurence.kuhlburger@gmail.com>
Date: Wed, 17 Jul 2024 16:28:01 +0200
Subject: [PATCH 088/414] Ran pre commit

---
 nf_core/pipelines/create/create.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index f9ba2ff7f6..27ca8ac847 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -92,7 +92,7 @@ def __init__(
                 "CODE_OF_CONDUCT.md",
                 ".github/workflows/awsfulltest.yml",
                 ".github/workflows/awstest.yml",
-                ".github/workflows/release-announcements.yml"
+                ".github/workflows/release-announcements.yml",
             ],
         }
         # Get list of files we're skipping with the supplied skip keys

From 77f9dd73d1e4a755406e70af4ad5bdc462eaa1ba Mon Sep 17 00:00:00 2001
From: laurencekuhl <laurence.kuhlburger@gmail.com>
Date: Wed, 17 Jul 2024 16:32:30 +0200
Subject: [PATCH 089/414] update changelog

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fba54a9539..8cda88788b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,8 @@
 - Run awsfulltest on PRs to `master` with two PR approvals ([#3042](https://github.com/nf-core/tools/pull/3042))
 - Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046))
 - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055))
+- Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055))
+- Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072))
 
 ### Linting
 

From 789a7841af08b9f621043e8701a79c39a8c9877e Mon Sep 17 00:00:00 2001
From: laurencekuhl <laurence.kuhlburger@gmail.com>
Date: Wed, 17 Jul 2024 17:01:15 +0200
Subject: [PATCH 090/414] Fix number of arguments for pipelines_create

---
 nf_core/__main__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index f33c63e87c..192c7cd139 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -2181,14 +2181,14 @@ def command_lint(
     help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)",
 )
 @click.pass_context
-def command_create(ctx, name, description, author, version, force, outdir, template_yaml, plain, organisation):
+def command_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation):
     """
     Use `nf-core pipelines create` instead.
     """
     log.warning(
         "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead."
     )
-    pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, plain, organisation)
+    pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation)
 
 
 # Main script is being run - launch the CLI

From 2f66b482c0945099d8bdca78dbffb96810482525 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 17 Jul 2024 15:05:41 +0000
Subject: [PATCH 091/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fba54a9539..b3f1688e72 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -51,6 +51,7 @@
 - Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058))
 - handle new jsonschema error type ([#3061](https://github.com/nf-core/tools/pull/3061))
 - Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071))
+- Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From f7be79d6d599918af49513fb41bd5943df9b7e60 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 18 Jul 2024 10:12:10 +0200
Subject: [PATCH 092/414] migrate modules tests to new structure

---
 nf_core/components/components_command.py |   4 +-
 nf_core/modules/bump_versions.py         |   3 +-
 tests/modules/bump_versions.py           |  50 --
 tests/modules/create.py                  | 165 -----
 tests/modules/info.py                    |  63 --
 tests/modules/install.py                 |  95 ---
 tests/modules/lint.py                    | 892 -----------------------
 tests/modules/list.py                    | 134 ----
 tests/modules/modules_json.py            | 253 -------
 tests/modules/patch.py                   | 360 ---------
 tests/modules/remove.py                  |  22 -
 tests/modules/test_bump_versions.py      |  50 ++
 tests/modules/test_create.py             | 164 +++++
 tests/modules/test_info.py               |  62 ++
 tests/modules/test_install.py            |  90 +++
 tests/modules/test_lint.py               | 865 ++++++++++++++++++++++
 tests/modules/test_list.py               | 126 ++++
 tests/modules/test_modules_json.py       | 245 +++++++
 tests/modules/test_patch.py              | 365 ++++++++++
 tests/modules/test_remove.py             |  26 +
 tests/modules/test_update.py             | 435 +++++++++++
 tests/modules/update.py                  | 444 -----------
 tests/test_modules.py                    | 128 ----
 23 files changed, 2432 insertions(+), 2609 deletions(-)
 delete mode 100644 tests/modules/bump_versions.py
 delete mode 100644 tests/modules/create.py
 delete mode 100644 tests/modules/info.py
 delete mode 100644 tests/modules/install.py
 delete mode 100644 tests/modules/lint.py
 delete mode 100644 tests/modules/list.py
 delete mode 100644 tests/modules/modules_json.py
 delete mode 100644 tests/modules/patch.py
 delete mode 100644 tests/modules/remove.py
 create mode 100644 tests/modules/test_bump_versions.py
 create mode 100644 tests/modules/test_create.py
 create mode 100644 tests/modules/test_info.py
 create mode 100644 tests/modules/test_install.py
 create mode 100644 tests/modules/test_lint.py
 create mode 100644 tests/modules/test_list.py
 create mode 100644 tests/modules/test_modules_json.py
 create mode 100644 tests/modules/test_patch.py
 create mode 100644 tests/modules/test_remove.py
 create mode 100644 tests/modules/test_update.py
 delete mode 100644 tests/modules/update.py

diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 4df67639e2..aa1dccc0d4 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -22,7 +22,7 @@ class ComponentCommand:
     def __init__(
         self,
         component_type: str,
-        dir: str,
+        dir: Union[str, Path],
         remote_url: Optional[str] = None,
         branch: Optional[str] = None,
         no_pull: bool = False,
@@ -33,7 +33,7 @@ def __init__(
         Initialise the ComponentClass object
         """
         self.component_type = component_type
-        self.dir = dir
+        self.dir = Path(dir) if dir else None
         self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)
         self.hide_progress = hide_progress
         self.no_prompts = no_prompts
diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
index fae3793079..1b94d5910c 100644
--- a/nf_core/modules/bump_versions.py
+++ b/nf_core/modules/bump_versions.py
@@ -6,6 +6,7 @@
 import logging
 import os
 import re
+from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple, Union
 
 import questionary
@@ -30,7 +31,7 @@
 class ModuleVersionBumper(ComponentCommand):  # type: ignore[misc]
     def __init__(
         self,
-        pipeline_dir: str,
+        pipeline_dir: Union[str, Path],
         remote_url: Optional[str] = None,
         branch: Optional[str] = None,
         no_pull: bool = False,
diff --git a/tests/modules/bump_versions.py b/tests/modules/bump_versions.py
deleted file mode 100644
index ce8c6dbe11..0000000000
--- a/tests/modules/bump_versions.py
+++ /dev/null
@@ -1,50 +0,0 @@
-import os
-import re
-
-import pytest
-
-import nf_core.modules
-from nf_core.modules.modules_utils import ModuleExceptionError
-
-
-def test_modules_bump_versions_single_module(self):
-    """Test updating a single module"""
-    # Change the bpipe/test version to an older version
-    env_yml_path = os.path.join(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")
-    with open(env_yml_path) as fh:
-        content = fh.read()
-    new_content = re.sub(r"bioconda::star=\d.\d.\d\D?", r"bioconda::star=2.6.1d", content)
-    with open(env_yml_path, "w") as fh:
-        fh.write(new_content)
-    version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
-    version_bumper.bump_versions(module="bpipe/test")
-    assert len(version_bumper.failed) == 0
-
-
-def test_modules_bump_versions_all_modules(self):
-    """Test updating all modules"""
-    version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
-    version_bumper.bump_versions(all_modules=True)
-    assert len(version_bumper.failed) == 0
-
-
-def test_modules_bump_versions_fail(self):
-    """Fail updating a module with wrong name"""
-    version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
-    with pytest.raises(ModuleExceptionError) as excinfo:
-        version_bumper.bump_versions(module="no/module")
-    assert "Could not find the specified module:" in str(excinfo.value)
-
-
-def test_modules_bump_versions_fail_unknown_version(self):
-    """Fail because of an unknown version"""
-    # Change the bpipe/test version to an older version
-    env_yml_path = os.path.join(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")
-    with open(env_yml_path) as fh:
-        content = fh.read()
-    new_content = re.sub(r"bioconda::bpipe=\d.\d.\d\D?", r"bioconda::bpipe=xxx", content)
-    with open(env_yml_path, "w") as fh:
-        fh.write(new_content)
-    version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
-    version_bumper.bump_versions(module="bpipe/test")
-    assert "Conda package had unknown version" in version_bumper.failed[0][0]
diff --git a/tests/modules/create.py b/tests/modules/create.py
deleted file mode 100644
index cf39621f07..0000000000
--- a/tests/modules/create.py
+++ /dev/null
@@ -1,165 +0,0 @@
-import os
-import shutil
-from pathlib import Path
-from unittest import mock
-
-import pytest
-import requests_cache
-import responses
-import yaml
-from git.repo import Repo
-
-import nf_core.modules
-from tests.utils import (
-    GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH,
-    GITLAB_URL,
-    mock_anaconda_api_calls,
-    mock_biocontainers_api_calls,
-)
-
-
-def test_modules_create_succeed(self):
-    """Succeed at creating the TrimGalore! module"""
-    with responses.RequestsMock() as rsps:
-        mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7")
-        mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7")
-        module_create = nf_core.modules.ModuleCreate(
-            self.pipeline_dir, "trimgalore", "@author", "process_single", True, True, conda_name="trim-galore"
-        )
-        with requests_cache.disabled():
-            module_create.create()
-    assert os.path.exists(os.path.join(self.pipeline_dir, "modules", "local", "trimgalore.nf"))
-
-
-def test_modules_create_fail_exists(self):
-    """Fail at creating the same module twice"""
-    with responses.RequestsMock() as rsps:
-        mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7")
-        mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7")
-        module_create = nf_core.modules.ModuleCreate(
-            self.pipeline_dir, "trimgalore", "@author", "process_single", False, False, conda_name="trim-galore"
-        )
-        with requests_cache.disabled():
-            module_create.create()
-        with pytest.raises(UserWarning) as excinfo:
-            with requests_cache.disabled():
-                module_create.create()
-    assert "Module file exists already" in str(excinfo.value)
-
-
-def test_modules_create_nfcore_modules(self):
-    """Create a module in nf-core/modules clone"""
-    with responses.RequestsMock() as rsps:
-        mock_anaconda_api_calls(rsps, "fastqc", "0.11.9")
-        mock_biocontainers_api_calls(rsps, "fastqc", "0.11.9")
-        module_create = nf_core.modules.ModuleCreate(
-            self.nfcore_modules, "fastqc", "@author", "process_low", False, False
-        )
-        with requests_cache.disabled():
-            module_create.create()
-    assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "fastqc", "main.nf"))
-    assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "fastqc", "tests", "main.nf.test"))
-
-
-def test_modules_create_nfcore_modules_subtool(self):
-    """Create a tool/subtool module in a nf-core/modules clone"""
-    with responses.RequestsMock() as rsps:
-        mock_anaconda_api_calls(rsps, "star", "2.8.10a")
-        mock_biocontainers_api_calls(rsps, "star", "2.8.10a")
-        module_create = nf_core.modules.ModuleCreate(
-            self.nfcore_modules, "star/index", "@author", "process_medium", False, False
-        )
-        with requests_cache.disabled():
-            module_create.create()
-    assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "star", "index", "main.nf"))
-    assert os.path.exists(
-        os.path.join(self.nfcore_modules, "modules", "nf-core", "star", "index", "tests", "main.nf.test")
-    )
-
-
-@mock.patch("rich.prompt.Confirm.ask")
-def test_modules_migrate(self, mock_rich_ask):
-    """Create a module with the --migrate-pytest option to convert pytest to nf-test"""
-    pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort")
-    module_dir = Path(self.nfcore_modules, "modules", "nf-core", "samtools", "sort")
-
-    # Clone modules repo with pytests
-    shutil.rmtree(self.nfcore_modules)
-    Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
-    with open(module_dir / "main.nf") as fh:
-        old_main_nf = fh.read()
-    with open(module_dir / "meta.yml") as fh:
-        old_meta_yml = fh.read()
-
-    # Create a module with --migrate-pytest
-    mock_rich_ask.return_value = True
-    module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
-    module_create.create()
-
-    with open(module_dir / "main.nf") as fh:
-        new_main_nf = fh.read()
-    with open(module_dir / "meta.yml") as fh:
-        new_meta_yml = fh.read()
-    nextflow_config = module_dir / "tests" / "nextflow.config"
-
-    # Check that old files have been copied to the new module
-    assert old_main_nf == new_main_nf
-    assert old_meta_yml == new_meta_yml
-    assert nextflow_config.is_file()
-
-    # Check that pytest folder is deleted
-    assert not pytest_dir.is_dir()
-
-    # Check that pytest_modules.yml is updated
-    with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
-        modules_yml = yaml.safe_load(fh)
-    assert "samtools/sort" not in modules_yml.keys()
-
-
-@mock.patch("rich.prompt.Confirm.ask")
-def test_modules_migrate_no_delete(self, mock_rich_ask):
-    """Create a module with the --migrate-pytest option to convert pytest to nf-test.
-    Test that pytest directory is not deleted."""
-    pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort")
-
-    # Clone modules repo with pytests
-    shutil.rmtree(self.nfcore_modules)
-    Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
-
-    # Create a module with --migrate-pytest
-    mock_rich_ask.return_value = False
-    module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
-    module_create.create()
-
-    # Check that pytest folder is not deleted
-    assert pytest_dir.is_dir()
-
-    # Check that pytest_modules.yml is updated
-    with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
-        modules_yml = yaml.safe_load(fh)
-    assert "samtools/sort" not in modules_yml.keys()
-
-
-@mock.patch("rich.prompt.Confirm.ask")
-def test_modules_migrate_symlink(self, mock_rich_ask):
-    """Create a module with the --migrate-pytest option to convert pytest with symlinks to nf-test.
-    Test that the symlink is deleted and the file is copied."""
-
-    pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort")
-    module_dir = Path(self.nfcore_modules, "modules", "nf-core", "samtools", "sort")
-
-    # Clone modules repo with pytests
-    shutil.rmtree(self.nfcore_modules)
-    Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
-
-    # Create a symlinked file in the pytest directory
-    symlink_file = pytest_dir / "symlink_file.txt"
-    symlink_file.symlink_to(module_dir / "main.nf")
-
-    # Create a module with --migrate-pytest
-    mock_rich_ask.return_value = True
-    module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
-    module_create.create()
-
-    # Check that symlink is deleted
-    assert not symlink_file.is_symlink()
diff --git a/tests/modules/info.py b/tests/modules/info.py
deleted file mode 100644
index 2dbd48b240..0000000000
--- a/tests/modules/info.py
+++ /dev/null
@@ -1,63 +0,0 @@
-from rich.console import Console
-
-import nf_core.modules
-
-from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL
-
-
-def test_modules_info_remote(self):
-    """Test getting info about a remote module"""
-    mods_info = nf_core.modules.ModuleInfo(self.pipeline_dir, "fastqc")
-    mods_info_output = mods_info.get_component_info()
-    console = Console(record=True)
-    console.print(mods_info_output)
-    output = console.export_text()
-
-    assert "Module: fastqc" in output
-    assert "Inputs" in output
-    assert "Outputs" in output
-
-
-def test_modules_info_remote_gitlab(self):
-    """Test getting info about a module in the remote gitlab repo"""
-    mods_info = nf_core.modules.ModuleInfo(
-        self.pipeline_dir, "fastqc", remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH
-    )
-    mods_info_output = mods_info.get_component_info()
-    console = Console(record=True)
-    console.print(mods_info_output)
-    output = console.export_text()
-
-    assert "Module: fastqc" in output
-    assert "Inputs" in output
-    assert "Outputs" in output
-    assert "--git-remote" in output
-
-
-def test_modules_info_local(self):
-    """Test getting info about a locally installed module"""
-    self.mods_install.install("trimgalore")
-    mods_info = nf_core.modules.ModuleInfo(self.pipeline_dir, "trimgalore")
-    mods_info_output = mods_info.get_component_info()
-    console = Console(record=True)
-    console.print(mods_info_output)
-    output = console.export_text()
-
-    assert "Module: trimgalore" in output
-    assert "Inputs" in output
-    assert "Outputs" in output
-    assert "Location" in output
-
-
-def test_modules_info_in_modules_repo(self):
-    """Test getting info about a module in the modules repo"""
-    mods_info = nf_core.modules.ModuleInfo(self.nfcore_modules, "fastqc")
-    mods_info.local = True
-    mods_info_output = mods_info.get_component_info()
-    console = Console(record=True)
-    console.print(mods_info_output)
-    output = console.export_text()
-
-    assert "Module: fastqc" in output
-    assert "Inputs" in output
-    assert "Outputs" in output
diff --git a/tests/modules/install.py b/tests/modules/install.py
deleted file mode 100644
index deca31204e..0000000000
--- a/tests/modules/install.py
+++ /dev/null
@@ -1,95 +0,0 @@
-import os
-
-import pytest
-
-from nf_core.modules.install import ModuleInstall
-from nf_core.modules.modules_json import ModulesJson
-
-from ..utils import (
-    GITLAB_BRANCH_ORG_PATH_BRANCH,
-    GITLAB_BRANCH_TEST_BRANCH,
-    GITLAB_REPO,
-    GITLAB_URL,
-    with_temporary_folder,
-)
-
-
-def test_modules_install_nopipeline(self):
-    """Test installing a module - no pipeline given"""
-    self.mods_install.dir = None
-    assert self.mods_install.install("foo") is False
-
-
-@with_temporary_folder
-def test_modules_install_emptypipeline(self, tmpdir):
-    """Test installing a module - empty dir given"""
-    os.mkdir(os.path.join(tmpdir, "nf-core-pipe"))
-    self.mods_install.dir = os.path.join(tmpdir, "nf-core-pipe")
-    with pytest.raises(UserWarning) as excinfo:
-        self.mods_install.install("foo")
-    assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
-
-
-def test_modules_install_nomodule(self):
-    """Test installing a module - unrecognised module given"""
-    assert self.mods_install.install("foo") is False
-
-
-def test_modules_install_trimgalore(self):
-    """Test installing a module - TrimGalore!"""
-    assert self.mods_install.install("trimgalore") is not False
-    module_path = os.path.join(self.mods_install.dir, "modules", "nf-core", "trimgalore")
-    assert os.path.exists(module_path)
-
-
-def test_modules_install_trimgalore_twice(self):
-    """Test installing a module - TrimGalore! already there"""
-    self.mods_install.install("trimgalore")
-    assert self.mods_install.install("trimgalore") is True
-
-
-def test_modules_install_from_gitlab(self):
-    """Test installing a module from GitLab"""
-    assert self.mods_install_gitlab.install("fastqc") is True
-
-
-def test_modules_install_different_branch_fail(self):
-    """Test installing a module from a different branch"""
-    install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH)
-    # The FastQC module does not exists in the branch-test branch
-    assert install_obj.install("fastqc") is False
-
-
-def test_modules_install_different_branch_succeed(self):
-    """Test installing a module from a different branch"""
-    install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH)
-    # The fastp module does exists in the branch-test branch
-    assert install_obj.install("fastp") is True
-
-    # Verify that the branch entry was added correctly
-    modules_json = ModulesJson(self.pipeline_dir)
-    assert (
-        modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO)
-        == GITLAB_BRANCH_TEST_BRANCH
-    )
-
-
-def test_modules_install_tracking(self):
-    """Test installing a module and finding 'modules' in the installed_by section of modules.json"""
-    self.mods_install.install("trimgalore")
-
-    # Verify that the installed_by entry was added correctly
-    modules_json = ModulesJson(self.pipeline_dir)
-    mod_json = modules_json.get_modules_json()
-    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["trimgalore"][
-        "installed_by"
-    ] == ["modules"]
-
-
-def test_modules_install_alternate_remote(self):
-    """Test installing a module from a different remote with the same organization path"""
-    install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_ORG_PATH_BRANCH)
-    # Install fastqc from GitLab which is also installed from GitHub with the same org_path
-    with pytest.raises(Exception) as excinfo:
-        install_obj.install("fastqc")
-        assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
diff --git a/tests/modules/lint.py b/tests/modules/lint.py
deleted file mode 100644
index e1a4e27ff8..0000000000
--- a/tests/modules/lint.py
+++ /dev/null
@@ -1,892 +0,0 @@
-import json
-from pathlib import Path
-
-import pytest
-import yaml
-from git.repo import Repo
-
-import nf_core.modules
-from nf_core.modules.lint import main_nf
-from nf_core.utils import set_wd
-
-from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL
-from .patch import BISMARK_ALIGN, CORRECT_SHA, PATCH_BRANCH, REPO_NAME, modify_main_nf
-
-
-def setup_patch(pipeline_dir: str, modify_module: bool):
-    install_obj = nf_core.modules.ModuleInstall(
-        pipeline_dir,
-        prompt=False,
-        force=False,
-        remote_url=GITLAB_URL,
-        branch=PATCH_BRANCH,
-        sha=CORRECT_SHA,
-    )
-
-    # Install the module
-    install_obj.install(BISMARK_ALIGN)
-
-    if modify_module:
-        # Modify the module
-        module_path = Path(pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
-        modify_main_nf(module_path / "main.nf")
-
-
-def test_modules_lint_trimgalore(self):
-    """Test linting the TrimGalore! module"""
-    self.mods_install.install("trimgalore")
-    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
-    module_lint.lint(print_results=False, module="trimgalore")
-    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-
-
-def test_modules_lint_empty(self):
-    """Test linting a pipeline with no modules installed"""
-    self.mods_remove.remove("fastqc", force=True)
-    self.mods_remove.remove("multiqc", force=True)
-    with pytest.raises(LookupError):
-        nf_core.modules.ModuleLint(dir=self.pipeline_dir)
-
-
-def test_modules_lint_new_modules(self):
-    """lint a new module"""
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, all_modules=True)
-    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-
-
-def test_modules_lint_no_gitlab(self):
-    """Test linting a pipeline with no modules installed"""
-    self.mods_remove.remove("fastqc", force=True)
-    self.mods_remove.remove("multiqc", force=True)
-    with pytest.raises(LookupError):
-        nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
-
-
-def test_modules_lint_gitlab_modules(self):
-    """Lint modules from a different remote"""
-    self.mods_install_gitlab.install("fastqc")
-    self.mods_install_gitlab.install("multiqc")
-    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
-    module_lint.lint(print_results=False, all_modules=True)
-    assert len(module_lint.failed) == 2
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-
-
-def test_modules_lint_multiple_remotes(self):
-    """Lint modules from a different remote"""
-    self.mods_install_gitlab.install("multiqc")
-    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
-    module_lint.lint(print_results=False, all_modules=True)
-    assert len(module_lint.failed) == 1
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-
-
-def test_modules_lint_registry(self):
-    """Test linting the samtools module and alternative registry"""
-    self.mods_install.install("samtools")
-    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, registry="public.ecr.aws")
-    module_lint.lint(print_results=False, module="samtools")
-    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
-    module_lint.lint(print_results=False, module="samtools")
-    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-
-
-def test_modules_lint_patched_modules(self):
-    """
-    Test creating a patch file and applying it to a new version of the the files
-    """
-    setup_patch(self.pipeline_dir, True)
-
-    # Create a patch file
-    patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
-    patch_obj.patch(BISMARK_ALIGN)
-
-    # change temporarily working directory to the pipeline directory
-    # to avoid error from try_apply_patch() during linting
-    with set_wd(self.pipeline_dir):
-        module_lint = nf_core.modules.ModuleLint(
-            dir=self.pipeline_dir,
-            remote_url=GITLAB_URL,
-            branch=PATCH_BRANCH,
-            hide_progress=True,
-        )
-        module_lint.lint(
-            print_results=False,
-            all_modules=True,
-        )
-
-    assert len(module_lint.failed) == 1
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-
-
-# A skeleton object with the passed/warned/failed list attrs
-# Use this in place of a ModuleLint object to test behaviour of
-# linting methods which don't need the full setup
-class MockModuleLint:
-    def __init__(self):
-        self.passed = []
-        self.warned = []
-        self.failed = []
-
-        self.main_nf = "main_nf"
-
-
-PROCESS_LABEL_GOOD = (
-    """
-    label 'process_high'
-    cpus 12
-    """,
-    1,
-    0,
-    0,
-)
-PROCESS_LABEL_NON_ALPHANUMERIC = (
-    """
-    label 'a:label:with:colons'
-    cpus 12
-    """,
-    0,
-    2,
-    0,
-)
-PROCESS_LABEL_GOOD_CONFLICTING = (
-    """
-    label 'process_high'
-    label 'process_low'
-    cpus 12
-    """,
-    0,
-    1,
-    0,
-)
-PROCESS_LABEL_GOOD_DUPLICATES = (
-    """
-    label 'process_high'
-    label 'process_high'
-    cpus 12
-    """,
-    0,
-    2,
-    0,
-)
-PROCESS_LABEL_GOOD_AND_NONSTANDARD = (
-    """
-    label 'process_high'
-    label 'process_extra_label'
-    cpus 12
-    """,
-    1,
-    1,
-    0,
-)
-PROCESS_LABEL_NONSTANDARD = (
-    """
-    label 'process_extra_label'
-    cpus 12
-    """,
-    0,
-    2,
-    0,
-)
-PROCESS_LABEL_NONSTANDARD_DUPLICATES = (
-    """
-    label process_extra_label
-    label process_extra_label
-    cpus 12
-    """,
-    0,
-    3,
-    0,
-)
-PROCESS_LABEL_NONE_FOUND = (
-    """
-    cpus 12
-    """,
-    0,
-    1,
-    0,
-)
-
-PROCESS_LABEL_TEST_CASES = [
-    PROCESS_LABEL_GOOD,
-    PROCESS_LABEL_NON_ALPHANUMERIC,
-    PROCESS_LABEL_GOOD_CONFLICTING,
-    PROCESS_LABEL_GOOD_DUPLICATES,
-    PROCESS_LABEL_GOOD_AND_NONSTANDARD,
-    PROCESS_LABEL_NONSTANDARD,
-    PROCESS_LABEL_NONSTANDARD_DUPLICATES,
-    PROCESS_LABEL_NONE_FOUND,
-]
-
-
-def test_modules_lint_check_process_labels(self):
-    for test_case in PROCESS_LABEL_TEST_CASES:
-        process, passed, warned, failed = test_case
-        mocked_ModuleLint = MockModuleLint()
-        main_nf.check_process_labels(mocked_ModuleLint, process.splitlines())
-        assert len(mocked_ModuleLint.passed) == passed
-        assert len(mocked_ModuleLint.warned) == warned
-        assert len(mocked_ModuleLint.failed) == failed
-
-
-# Test cases for linting the container definitions
-
-CONTAINER_SINGLE_GOOD = (
-    "Single-line container definition should pass",
-    """
-    container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package
-    """,
-    2,  # passed
-    0,  # warned
-    0,  # failed
-)
-
-CONTAINER_TWO_LINKS_GOOD = (
-    "Multi-line container definition should pass",
-    """
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
-    """,
-    6,
-    0,
-    0,
-)
-
-CONTAINER_WITH_SPACE_BAD = (
-    "Space in container URL should fail",
-    """
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ':
-        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
-    """,
-    5,
-    0,
-    1,
-)
-
-CONTAINER_MULTIPLE_DBLQUOTES_BAD = (
-    "Incorrect quoting of container string should fail",
-    """
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ':
-        "biocontainers/gatk4:4.4.0.0--py36hdfd78af_0" }"
-    """,
-    4,
-    0,
-    1,
-)
-
-CONTAINER_TEST_CASES = [
-    CONTAINER_SINGLE_GOOD,
-    CONTAINER_TWO_LINKS_GOOD,
-    CONTAINER_WITH_SPACE_BAD,
-    CONTAINER_MULTIPLE_DBLQUOTES_BAD,
-]
-
-
-def test_modules_lint_check_url(self):
-    for test_case in CONTAINER_TEST_CASES:
-        test, process, passed, warned, failed = test_case
-        mocked_ModuleLint = MockModuleLint()
-        for line in process.splitlines():
-            if line.strip():
-                main_nf.check_container_link_line(mocked_ModuleLint, line, registry="quay.io")
-
-        assert (
-            len(mocked_ModuleLint.passed) == passed
-        ), f"{test}: Expected {passed} PASS, got {len(mocked_ModuleLint.passed)}."
-        assert (
-            len(mocked_ModuleLint.warned) == warned
-        ), f"{test}: Expected {warned} WARN, got {len(mocked_ModuleLint.warned)}."
-        assert (
-            len(mocked_ModuleLint.failed) == failed
-        ), f"{test}: Expected {failed} FAIL, got {len(mocked_ModuleLint.failed)}."
-
-
-def test_modules_lint_snapshot_file(self):
-    """Test linting a module with a snapshot file"""
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-
-
-def test_modules_lint_snapshot_file_missing_fail(self):
-    """Test linting a module with a snapshot file missing, which should fail"""
-    Path(
-        self.nfcore_modules,
-        "modules",
-        "nf-core",
-        "bpipe",
-        "test",
-        "tests",
-        "main.nf.test.snap",
-    ).unlink()
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    Path(
-        self.nfcore_modules,
-        "modules",
-        "nf-core",
-        "bpipe",
-        "test",
-        "tests",
-        "main.nf.test.snap",
-    ).touch()
-    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-    assert module_lint.failed[0].lint_test == "test_snapshot_exists"
-
-
-def test_modules_lint_snapshot_file_not_needed(self):
-    """Test linting a module which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file"""
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "tests",
-            "main.nf.test",
-        )
-    ) as fh:
-        content = fh.read()
-        new_content = content.replace("snapshot(", "snap (")
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "tests",
-            "main.nf.test",
-        ),
-        "w",
-    ) as fh:
-        fh.write(new_content)
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-
-
-def test_modules_environment_yml_file_doesnt_exists(self):
-    """Test linting a module with an environment.yml file"""
-    Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml").rename(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "environment.yml.bak",
-        )
-    )
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    Path(
-        self.nfcore_modules,
-        "modules",
-        "nf-core",
-        "bpipe",
-        "test",
-        "environment.yml.bak",
-    ).rename(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "environment.yml",
-        )
-    )
-    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-    assert module_lint.failed[0].lint_test == "environment_yml_exists"
-
-
-def test_modules_environment_yml_file_sorted_correctly(self):
-    """Test linting a module with a correctly sorted environment.yml file"""
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-
-
-def test_modules_environment_yml_file_sorted_incorrectly(self):
-    """Test linting a module with an incorrectly sorted environment.yml file"""
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "environment.yml",
-        )
-    ) as fh:
-        yaml_content = yaml.safe_load(fh)
-    # Add a new dependency to the environment.yml file and reverse the order
-    yaml_content["dependencies"].append("z")
-    yaml_content["dependencies"].reverse()
-    yaml_content = yaml.dump(yaml_content)
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "environment.yml",
-        ),
-        "w",
-    ) as fh:
-        fh.write(yaml_content)
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    # we fix the sorting on the fly, so this should pass
-    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-
-
-def test_modules_environment_yml_file_not_array(self):
-    """Test linting a module with an incorrectly formatted environment.yml file"""
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "environment.yml",
-        )
-    ) as fh:
-        yaml_content = yaml.safe_load(fh)
-    yaml_content["dependencies"] = "z"
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "environment.yml",
-        ),
-        "w",
-    ) as fh:
-        fh.write(yaml.dump(yaml_content))
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-    assert module_lint.failed[0].lint_test == "environment_yml_valid"
-
-
-def test_modules_environment_yml_file_name_mismatch(self):
-    """Test linting a module with a different name in the environment.yml file"""
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "environment.yml",
-        )
-    ) as fh:
-        yaml_content = yaml.safe_load(fh)
-    yaml_content["name"] = "bpipe-test"
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "environment.yml",
-        ),
-        "w",
-    ) as fh:
-        fh.write(yaml.dump(yaml_content))
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    # reset changes
-    yaml_content["name"] = "bpipe_test"
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "environment.yml",
-        ),
-        "w",
-    ) as fh:
-        fh.write(yaml.dump(yaml_content))
-
-    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-    assert module_lint.failed[0].lint_test == "environment_yml_name"
-
-
-def test_modules_meta_yml_incorrect_licence_field(self):
-    """Test linting a module with an incorrect Licence field in meta.yml"""
-    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh:
-        meta_yml = yaml.safe_load(fh)
-    meta_yml["tools"][0]["bpipe"]["licence"] = "[MIT]"
-    with open(
-        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"),
-        "w",
-    ) as fh:
-        fh.write(yaml.dump(meta_yml))
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-
-    # reset changes
-    meta_yml["tools"][0]["bpipe"]["licence"] = ["MIT"]
-    with open(
-        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"),
-        "w",
-    ) as fh:
-        fh.write(yaml.dump(meta_yml))
-
-    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) >= 0
-    assert len(module_lint.warned) >= 0
-    assert module_lint.failed[0].lint_test == "meta_yml_valid"
-
-
-def test_modules_meta_yml_input_mismatch(self):
-    """Test linting a module with an extra entry in input fields in meta.yml compared to module.input"""
-    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh:
-        main_nf = fh.read()
-    main_nf_new = main_nf.replace("path bam", "path bai")
-    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
-        fh.write(main_nf_new)
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
-        fh.write(main_nf)
-    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) >= 0
-    assert len(module_lint.warned) == 2
-    lint_tests = [x.lint_test for x in module_lint.warned]
-    # check that it is there twice:
-    assert lint_tests.count("meta_input_meta_only") == 1
-    assert lint_tests.count("meta_input_main_only") == 1
-
-
-def test_modules_meta_yml_output_mismatch(self):
-    """Test linting a module with an extra entry in output fields in meta.yml compared to module.output"""
-    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh:
-        main_nf = fh.read()
-    main_nf_new = main_nf.replace("emit: bam", "emit: bai")
-    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
-        fh.write(main_nf_new)
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
-        fh.write(main_nf)
-    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) >= 0
-    assert len(module_lint.warned) == 2
-    lint_tests = [x.lint_test for x in module_lint.warned]
-    # check that it is there twice:
-    assert lint_tests.count("meta_output_meta_only") == 1
-    assert lint_tests.count("meta_output_main_only") == 1
-
-
-def test_modules_meta_yml_incorrect_name(self):
-    """Test linting a module with an incorrect name in meta.yml"""
-    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh:
-        meta_yml = yaml.safe_load(fh)
-    meta_yml["name"] = "bpipe/test"
-    # need to make the same change to the environment.yml file
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "environment.yml",
-        )
-    ) as fh:
-        environment_yml = yaml.safe_load(fh)
-    environment_yml["name"] = "bpipe/test"
-    with open(
-        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"),
-        "w",
-    ) as fh:
-        fh.write(yaml.dump(meta_yml))
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "environment.yml",
-        ),
-        "w",
-    ) as fh:
-        fh.write(yaml.dump(environment_yml))
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-
-    # reset changes
-    meta_yml["name"] = "bpipe_test"
-    with open(
-        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"),
-        "w",
-    ) as fh:
-        fh.write(yaml.dump(meta_yml))
-    environment_yml["name"] = "bpipe_test"
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "environment.yml",
-        ),
-        "w",
-    ) as fh:
-        fh.write(yaml.dump(environment_yml))
-
-    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) >= 0
-    assert len(module_lint.warned) >= 0
-    assert module_lint.failed[0].lint_test == "meta_name"
-
-
-def test_modules_missing_test_dir(self):
-    """Test linting a module with a missing test directory"""
-    Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests").rename(
-        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak")
-    )
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak").rename(
-        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests")
-    )
-    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) >= 0
-    assert len(module_lint.warned) >= 0
-    assert module_lint.failed[0].lint_test == "test_dir_exists"
-
-
-def test_modules_missing_test_main_nf(self):
-    """Test linting a module with a missing test/main.nf file"""
-    Path(
-        self.nfcore_modules,
-        "modules",
-        "nf-core",
-        "bpipe",
-        "test",
-        "tests",
-        "main.nf.test",
-    ).rename(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "tests",
-            "main.nf.test.bak",
-        )
-    )
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    Path(
-        self.nfcore_modules,
-        "modules",
-        "nf-core",
-        "bpipe",
-        "test",
-        "tests",
-        "main.nf.test.bak",
-    ).rename(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "tests",
-            "main.nf.test",
-        )
-    )
-    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) >= 0
-    assert len(module_lint.warned) >= 0
-    assert module_lint.failed[0].lint_test == "test_main_nf_exists"
-
-
-def test_modules_unused_pytest_files(self):
-    """Test linting a nf-test module with files still present in `tests/modules/`"""
-    Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").mkdir(parents=True, exist_ok=True)
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").rmdir()
-    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) >= 0
-    assert len(module_lint.warned) >= 0
-    assert module_lint.failed[0].lint_test == "test_old_test_dir"
-
-
-def test_nftest_failing_linting(self):
-    """Test linting a module which includes other modules in nf-test tests.
-    Linting tests"""
-    # Clone modules repo with testing modules
-    tmp_dir = self.nfcore_modules.parent
-    self.nfcore_modules = Path(tmp_dir, "modules-test")
-    Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_NFTEST_BRANCH)
-
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="kallisto/quant")
-
-    assert len(module_lint.failed) == 3, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) >= 0
-    assert len(module_lint.warned) >= 0
-    assert module_lint.failed[0].lint_test == "environment_yml_valid"
-    assert module_lint.failed[1].lint_test == "meta_yml_valid"
-    assert module_lint.failed[2].lint_test == "test_main_tags"
-    assert "kallisto/index" in module_lint.failed[2].message
-
-
-def test_modules_absent_version(self):
-    """Test linting a nf-test module if the versions is absent in the snapshot file `"""
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "tests",
-            "main.nf.test.snap",
-        )
-    ) as fh:
-        content = fh.read()
-        new_content = content.replace("versions", "foo")
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "tests",
-            "main.nf.test.snap",
-        ),
-        "w",
-    ) as fh:
-        fh.write(new_content)
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    with open(
-        Path(
-            self.nfcore_modules,
-            "modules",
-            "nf-core",
-            "bpipe",
-            "test",
-            "tests",
-            "main.nf.test.snap",
-        ),
-        "w",
-    ) as fh:
-        fh.write(content)
-    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) >= 0
-    assert len(module_lint.warned) >= 0
-    assert module_lint.failed[0].lint_test == "test_snap_versions"
-
-
-def test_modules_empty_file_in_snapshot(self):
-    """Test linting a nf-test module with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)"""
-    snap_file = Path(
-        self.nfcore_modules,
-        "modules",
-        "nf-core",
-        "bpipe",
-        "test",
-        "tests",
-        "main.nf.test.snap",
-    )
-    snap = json.load(snap_file.open())
-    content = snap_file.read_text()
-    snap["my test"]["content"][0]["0"] = "test:md5,d41d8cd98f00b204e9800998ecf8427e"
-
-    with open(snap_file, "w") as fh:
-        json.dump(snap, fh)
-
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-    assert module_lint.failed[0].lint_test == "test_snap_md5sum"
-
-    # reset the file
-    with open(snap_file, "w") as fh:
-        fh.write(content)
-
-
-def test_modules_empty_file_in_stub_snapshot(self):
-    """Test linting a nf-test module with an empty file sha sum in the stub test snapshot, which should make it not fail"""
-    snap_file = Path(
-        self.nfcore_modules,
-        "modules",
-        "nf-core",
-        "bpipe",
-        "test",
-        "tests",
-        "main.nf.test.snap",
-    )
-    snap = json.load(snap_file.open())
-    content = snap_file.read_text()
-    snap["my_test_stub"] = {"content": [{"0": "test:md5,d41d8cd98f00b204e9800998ecf8427e", "versions": {}}]}
-
-    with open(snap_file, "w") as fh:
-        json.dump(snap, fh)
-
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
-    module_lint.lint(print_results=False, module="bpipe/test")
-    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) > 0
-    assert len(module_lint.warned) >= 0
-    assert any(x.lint_test == "test_snap_md5sum" for x in module_lint.passed)
-
-    # reset the file
-    with open(snap_file, "w") as fh:
-        fh.write(content)
diff --git a/tests/modules/list.py b/tests/modules/list.py
deleted file mode 100644
index 3cb00a84d6..0000000000
--- a/tests/modules/list.py
+++ /dev/null
@@ -1,134 +0,0 @@
-import json
-from pathlib import Path
-
-import yaml
-from rich.console import Console
-
-import nf_core.modules
-
-from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL
-
-
-def test_modules_list_remote(self):
-    """Test listing available modules"""
-    mods_list = nf_core.modules.ModuleList(None, remote=True)
-    listed_mods = mods_list.list_components()
-    console = Console(record=True)
-    console.print(listed_mods)
-    output = console.export_text()
-    assert "fastqc" in output
-
-
-def test_modules_list_remote_gitlab(self):
-    """Test listing the modules in the remote gitlab repo"""
-    mods_list = nf_core.modules.ModuleList(None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH)
-    listed_mods = mods_list.list_components()
-    console = Console(record=True)
-    console.print(listed_mods)
-    output = console.export_text()
-    assert "fastqc" in output
-
-
-def test_modules_list_pipeline(self):
-    """Test listing locally installed modules"""
-    mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
-    listed_mods = mods_list.list_components()
-    console = Console(record=True)
-    console.print(listed_mods)
-    output = console.export_text()
-    assert "fastqc" in output
-    assert "multiqc" in output
-
-
-def test_modules_install_and_list_pipeline(self):
-    """Test listing locally installed modules"""
-    self.mods_install.install("trimgalore")
-    mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
-    listed_mods = mods_list.list_components()
-    console = Console(record=True)
-    console.print(listed_mods)
-    output = console.export_text()
-    assert "trimgalore" in output
-
-
-def test_modules_install_gitlab_and_list_pipeline(self):
-    """Test listing locally installed modules"""
-    self.mods_install_gitlab.install("fastqc")
-    mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
-    listed_mods = mods_list.list_components()
-    console = Console(record=True)
-    console.print(listed_mods)
-    output = console.export_text()
-    assert "fastqc" in output
-
-
-def test_modules_list_local_json(self):
-    """Test listing locally installed modules as JSON"""
-    mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
-    listed_mods = mods_list.list_components(print_json=True)
-    listed_mods = json.loads(listed_mods)
-    assert "fastqc" in listed_mods
-    assert "multiqc" in listed_mods
-
-
-def test_modules_list_remote_json(self):
-    """Test listing available modules as JSON"""
-    mods_list = nf_core.modules.ModuleList(None, remote=True)
-    listed_mods = mods_list.list_components(print_json=True)
-    listed_mods = json.loads(listed_mods)
-    assert "fastqc" in listed_mods
-    assert "multiqc" in listed_mods
-
-
-def test_modules_list_with_one_keyword(self):
-    """Test listing available modules with one keyword"""
-    mods_list = nf_core.modules.ModuleList(None, remote=True)
-    listed_mods = mods_list.list_components(keywords=["qc"])
-    console = Console(record=True)
-    console.print(listed_mods)
-    output = console.export_text()
-    assert "multiqc" in output
-
-
-def test_modules_list_with_keywords(self):
-    """Test listing available modules with multiple keywords"""
-    mods_list = nf_core.modules.ModuleList(None, remote=True)
-    listed_mods = mods_list.list_components(keywords=["fastq", "qc"])
-    console = Console(record=True)
-    console.print(listed_mods)
-    output = console.export_text()
-    assert "fastqc" in output
-
-
-def test_modules_list_with_unused_keyword(self):
-    """Test listing available modules with an unused keyword"""
-    mods_list = nf_core.modules.ModuleList(None, remote=True)
-    with self.assertLogs(level="INFO") as log:
-        listed_mods = mods_list.list_components(keywords=["you_will_never_find_me"])
-        self.assertIn("No available", log.output[0])
-        # expect empty list
-        assert listed_mods == ""
-
-
-def test_modules_list_in_wrong_repo_fail(self):
-    """Test listing available modules in a non-pipeline repo"""
-    # modify repotype in .nf-core.yml
-    with open(Path(self.pipeline_dir, ".nf-core.yml")) as fh:
-        nf_core_yml = yaml.safe_load(fh)
-    nf_core_yml_orig = nf_core_yml.copy()
-    nf_core_yml["repository_type"] = "modules"
-    nf_core_yml["org_path"] = "nf-core"
-
-    print(nf_core_yml)
-    with open(Path(self.pipeline_dir, ".nf-core.yml"), "w") as fh:
-        yaml.safe_dump(nf_core_yml, fh)
-    # expect error logged
-    with self.assertLogs(level="ERROR") as log:
-        mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
-        listed_mods = mods_list.list_components()
-        self.assertIn("must be run from a pipeline directory", log.output[0])
-        # expect empty list
-        assert listed_mods == ""
-    # restore .nf-core.yml
-    with open(Path(self.pipeline_dir, ".nf-core.yml"), "w") as fh:
-        yaml.safe_dump(nf_core_yml_orig, fh)
diff --git a/tests/modules/modules_json.py b/tests/modules/modules_json.py
deleted file mode 100644
index e0100adfb7..0000000000
--- a/tests/modules/modules_json.py
+++ /dev/null
@@ -1,253 +0,0 @@
-import copy
-import json
-import shutil
-from pathlib import Path
-
-from nf_core.modules.modules_json import ModulesJson
-from nf_core.modules.modules_repo import (
-    NF_CORE_MODULES_DEFAULT_BRANCH,
-    NF_CORE_MODULES_NAME,
-    NF_CORE_MODULES_REMOTE,
-    ModulesRepo,
-)
-from nf_core.modules.patch import ModulePatch
-
-
-def test_get_modules_json(self):
-    """Checks that the get_modules_json function returns the correct result"""
-    mod_json_path = Path(self.pipeline_dir, "modules.json")
-    with open(mod_json_path) as fh:
-        try:
-            mod_json_sb = json.load(fh)
-        except json.JSONDecodeError as e:
-            raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}")
-
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    mod_json = mod_json_obj.get_modules_json()
-
-    # Check that the modules.json hasn't changed
-    assert mod_json == mod_json_sb
-
-
-def test_mod_json_update(self):
-    """Checks whether the update function works properly"""
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    # Update the modules.json file
-    mod_repo_obj = ModulesRepo()
-    mod_json_obj.update("modules", mod_repo_obj, "MODULE_NAME", "GIT_SHA", "modules", write_file=False)
-    mod_json = mod_json_obj.get_modules_json()
-    assert "MODULE_NAME" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]
-    assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]
-    assert "GIT_SHA" == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["git_sha"]
-    assert (
-        NF_CORE_MODULES_DEFAULT_BRANCH
-        == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["branch"]
-    )
-    assert "modules" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["installed_by"]
-
-
-def test_mod_json_create(self):
-    """Test creating a modules.json file from scratch"""
-    mod_json_path = Path(self.pipeline_dir, "modules.json")
-    # Remove the existing modules.json file
-    mod_json_path.unlink()
-
-    # Create the new modules.json file
-    # (There are no prompts as long as there are only nf-core modules)
-    ModulesJson(self.pipeline_dir).create()
-
-    # Check that the file exists
-    assert (mod_json_path).exists()
-
-    # Get the contents of the file
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    mod_json = mod_json_obj.get_modules_json()
-
-    mods = ["fastqc", "multiqc"]
-    for mod in mods:
-        assert mod in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]
-        assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"][mod]
-        assert "branch" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"][mod]
-
-
-def modify_main_nf(path):
-    """Modify a file to test patch creation"""
-    with open(path) as fh:
-        lines = fh.readlines()
-    # Modify $meta.id to $meta.single_end
-    lines[1] = '    tag "$meta.single_end"\n'
-    with open(path, "w") as fh:
-        fh.writelines(lines)
-
-
-def test_mod_json_create_with_patch(self):
-    """Test creating a modules.json file from scratch when there are patched modules"""
-    mod_json_path = Path(self.pipeline_dir, "modules.json")
-
-    # Modify the module
-    module_path = Path(self.pipeline_dir, "modules", "nf-core", "fastqc")
-    modify_main_nf(module_path / "main.nf")
-
-    # Try creating a patch file
-    patch_obj = ModulePatch(self.pipeline_dir, NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_DEFAULT_BRANCH)
-    patch_obj.patch("fastqc")
-
-    # Remove the existing modules.json file
-    mod_json_path.unlink()
-
-    # Create the new modules.json file
-    ModulesJson(self.pipeline_dir).create()
-
-    # Check that the file exists
-    assert mod_json_path.is_file()
-
-    # Get the contents of the file
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    mod_json = mod_json_obj.get_modules_json()
-
-    # Check that fastqc is in the file
-    assert "fastqc" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]
-    assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["fastqc"]
-    assert "branch" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["fastqc"]
-
-    # Check that fastqc/main.nf maintains the changes
-    with open(module_path / "main.nf") as fh:
-        lines = fh.readlines()
-    assert lines[1] == '    tag "$meta.single_end"\n'
-
-
-def test_mod_json_up_to_date(self):
-    """
-    Checks if the modules.json file is up to date
-    when no changes have been made to the pipeline
-    """
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    mod_json_before = mod_json_obj.get_modules_json()
-    mod_json_obj.check_up_to_date()
-    mod_json_after = mod_json_obj.get_modules_json()
-
-    # Check that the modules.json hasn't changed
-    assert mod_json_before == mod_json_after
-
-
-def test_mod_json_up_to_date_module_removed(self):
-    """
-    Reinstall a module that has an entry in the modules.json
-    but is missing in the pipeline
-    """
-    # Remove the fastqc module
-    fastqc_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "fastqc")
-    shutil.rmtree(fastqc_path)
-
-    # Check that the modules.json file is up to date, and reinstall the module
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    mod_json_obj.check_up_to_date()
-
-    # Check that the module has been reinstalled
-    files = ["main.nf", "meta.yml"]
-    assert fastqc_path.exists()
-    for f in files:
-        assert Path(fastqc_path, f).exists()
-
-
-def test_mod_json_up_to_date_reinstall_fails(self):
-    """
-    Try reinstalling a module where the git_sha is invalid
-    """
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-
-    # Update the fastqc module entry to an invalid git_sha
-    mod_json_obj.update("modules", ModulesRepo(), "fastqc", "INVALID_GIT_SHA", "modules", write_file=True)
-
-    # Remove the fastqc module
-    fastqc_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "fastqc")
-    shutil.rmtree(fastqc_path)
-
-    # Check that the modules.json file is up to date, and remove the fastqc module entry
-    mod_json_obj.check_up_to_date()
-    mod_json = mod_json_obj.get_modules_json()
-
-    # Check that the module has been removed from the modules.json
-    assert "fastqc" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]
-
-
-def test_mod_json_repo_present(self):
-    """Tests the repo_present function"""
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-
-    assert mod_json_obj.repo_present(NF_CORE_MODULES_REMOTE) is True
-    assert mod_json_obj.repo_present("INVALID_REPO") is False
-
-
-def test_mod_json_module_present(self):
-    """Tests the module_present function"""
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-
-    assert mod_json_obj.module_present("fastqc", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) is True
-    assert mod_json_obj.module_present("INVALID_MODULE", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) is False
-    assert mod_json_obj.module_present("fastqc", "INVALID_REPO", "INVALID_DIR") is False
-    assert mod_json_obj.module_present("INVALID_MODULE", "INVALID_REPO", "INVALID_DIR") is False
-
-
-def test_mod_json_get_module_version(self):
-    """Test the get_module_version function"""
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    mod_json = mod_json_obj.get_modules_json()
-    assert (
-        mod_json_obj.get_module_version("fastqc", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME)
-        == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["fastqc"]["git_sha"]
-    )
-    assert mod_json_obj.get_module_version("INVALID_MODULE", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) is None
-
-
-def test_mod_json_dump(self):
-    """Tests the dump function"""
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    mod_json = mod_json_obj.get_modules_json()
-    # Remove the modules.json file
-    mod_json_path = Path(self.pipeline_dir, "modules.json")
-    mod_json_path.unlink()
-
-    # Check that the dump function creates the file
-    mod_json_obj.dump()
-    assert mod_json_path.exists()
-
-    # Check that the dump function writes the correct content
-    with open(mod_json_path) as f:
-        try:
-            mod_json_new = json.load(f)
-        except json.JSONDecodeError as e:
-            raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}")
-    assert mod_json == mod_json_new
-
-
-def test_mod_json_with_empty_modules_value(self):
-    # Load module.json and remove the modules entry
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    mod_json_obj.create()  # Create modules.json explicitly to get correct module sha
-    mod_json_orig = mod_json_obj.get_modules_json()
-    mod_json = copy.deepcopy(mod_json_orig)
-    mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"] = ""
-    # save the altered module.json and load it again to check if it will fix itself
-    mod_json_obj.modules_json = mod_json
-    mod_json_obj.dump()
-    mod_json_obj_new = ModulesJson(self.pipeline_dir)
-    mod_json_obj_new.check_up_to_date()
-    mod_json_new = mod_json_obj_new.get_modules_json()
-    assert mod_json_orig == mod_json_new
-
-
-def test_mod_json_with_missing_modules_entry(self):
-    # Load module.json and remove the modules entry
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    mod_json_obj.create()  # Create modules.json explicitly to get correct module sha
-    mod_json_orig = mod_json_obj.get_modules_json()
-    mod_json = copy.deepcopy(mod_json_orig)
-    mod_json["repos"][NF_CORE_MODULES_REMOTE].pop("modules")
-    # save the altered module.json and load it again to check if it will fix itself
-    mod_json_obj.modules_json = mod_json
-    mod_json_obj.dump()
-    mod_json_obj_new = ModulesJson(self.pipeline_dir)
-    mod_json_obj_new.check_up_to_date()
-    mod_json_new = mod_json_obj_new.get_modules_json()
-    assert mod_json_orig == mod_json_new
diff --git a/tests/modules/patch.py b/tests/modules/patch.py
deleted file mode 100644
index 513ea8a433..0000000000
--- a/tests/modules/patch.py
+++ /dev/null
@@ -1,360 +0,0 @@
-import os
-import tempfile
-from pathlib import Path
-from unittest import mock
-
-import pytest
-
-import nf_core.components.components_command
-import nf_core.modules
-
-from ..utils import GITLAB_URL
-
-"""
-Test the 'nf-core modules patch' command
-
-Uses a branch (patch-tester) in the GitLab nf-core/modules-test repo when
-testing if the update commands works correctly with patch files
-"""
-
-ORG_SHA = "002623ccc88a3b0cb302c7d8f13792a95354d9f2"
-CORRECT_SHA = "1dff30bfca2d98eb7ac7b09269a15e822451d99f"
-SUCCEED_SHA = "ba15c20c032c549d77c5773659f19c2927daf48e"
-FAIL_SHA = "67b642d4471c4005220a342cad3818d5ba2b5a73"
-BISMARK_ALIGN = "bismark/align"
-REPO_NAME = "nf-core-test"
-PATCH_BRANCH = "patch-tester"
-REPO_URL = "https://gitlab.com/nf-core/modules-test.git"
-
-
-def setup_patch(pipeline_dir, modify_module):
-    install_obj = nf_core.modules.ModuleInstall(
-        pipeline_dir, prompt=False, force=False, remote_url=GITLAB_URL, branch=PATCH_BRANCH, sha=ORG_SHA
-    )
-
-    # Install the module
-    install_obj.install(BISMARK_ALIGN)
-
-    if modify_module:
-        # Modify the module
-        module_path = Path(pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
-        modify_main_nf(module_path / "main.nf")
-
-
-def modify_main_nf(path):
-    """Modify a file to test patch creation"""
-    with open(path) as fh:
-        lines = fh.readlines()
-    # We want a patch file that looks something like:
-    # -    tuple val(meta), path(reads)
-    # -    path index
-    # +    tuple val(meta), path(reads), path(index)
-    for line_index in range(len(lines)):
-        if lines[line_index] == "    tuple val(meta), path(reads)\n":
-            lines[line_index] = "    tuple val(meta), path(reads), path(index)\n"
-        elif lines[line_index] == "    path index\n":
-            to_pop = line_index
-    lines.pop(to_pop)
-    with open(path, "w") as fh:
-        fh.writelines(lines)
-
-
-def test_create_patch_no_change(self):
-    """Test creating a patch when there is no change to the module"""
-    setup_patch(self.pipeline_dir, False)
-
-    # Try creating a patch file
-    patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
-    with pytest.raises(UserWarning):
-        patch_obj.patch(BISMARK_ALIGN)
-
-    module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
-
-    # Check that no patch file has been added to the directory
-    assert set(os.listdir(module_path)) == {"main.nf", "meta.yml"}
-
-    # Check the 'modules.json' contains no patch file for the module
-    modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
-    assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) is None
-
-
-def test_create_patch_change(self):
-    """Test creating a patch when there is a change to the module"""
-    setup_patch(self.pipeline_dir, True)
-
-    # Try creating a patch file
-    patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
-    patch_obj.patch(BISMARK_ALIGN)
-
-    module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
-
-    patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
-    # Check that a patch file with the correct name has been created
-    assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
-
-    # Check the 'modules.json' contains a patch file for the module
-    modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
-    assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path(
-        "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
-    )
-
-    # Check that the correct lines are in the patch file
-    with open(module_path / patch_fn) as fh:
-        patch_lines = fh.readlines()
-    module_relpath = module_path.relative_to(self.pipeline_dir)
-    assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines, module_relpath / "main.nf"
-    assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines
-    assert "-    tuple val(meta), path(reads)\n" in patch_lines
-    assert "-    path index\n" in patch_lines
-    assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
-
-
-def test_create_patch_try_apply_successful(self):
-    """
-    Test creating a patch file and applying it to a new version of the the files
-    """
-
-    setup_patch(self.pipeline_dir, True)
-    module_relpath = Path("modules", REPO_NAME, BISMARK_ALIGN)
-    module_path = Path(self.pipeline_dir, module_relpath)
-
-    # Try creating a patch file
-    patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
-    patch_obj.patch(BISMARK_ALIGN)
-
-    patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
-    # Check that a patch file with the correct name has been created
-    assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
-
-    # Check the 'modules.json' contains a patch file for the module
-    modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
-    assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path(
-        "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
-    )
-
-    update_obj = nf_core.modules.ModuleUpdate(
-        self.pipeline_dir, sha=SUCCEED_SHA, remote_url=GITLAB_URL, branch=PATCH_BRANCH
-    )
-    # Install the new files
-    install_dir = Path(tempfile.mkdtemp())
-    update_obj.install_component_files(BISMARK_ALIGN, SUCCEED_SHA, update_obj.modules_repo, install_dir)
-
-    # Try applying the patch
-    module_install_dir = install_dir / BISMARK_ALIGN
-    patch_relpath = module_relpath / patch_fn
-    assert update_obj.try_apply_patch(BISMARK_ALIGN, REPO_NAME, patch_relpath, module_path, module_install_dir) is True
-
-    # Move the files from the temporary directory
-    update_obj.move_files_from_tmp_dir(BISMARK_ALIGN, install_dir, REPO_NAME, SUCCEED_SHA)
-
-    # Check that a patch file with the correct name has been created
-    assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
-
-    # Check the 'modules.json' contains a patch file for the module
-    modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
-    assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path(
-        "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
-    )
-
-    # Check that the correct lines are in the patch file
-    with open(module_path / patch_fn) as fh:
-        patch_lines = fh.readlines()
-    module_relpath = module_path.relative_to(self.pipeline_dir)
-    assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines
-    assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines
-    assert "-    tuple val(meta), path(reads)\n" in patch_lines
-    assert "-    path index\n" in patch_lines
-    assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
-
-    # Check that 'main.nf' is updated correctly
-    with open(module_path / "main.nf") as fh:
-        main_nf_lines = fh.readlines()
-    # These lines should have been removed by the patch
-    assert "    tuple val(meta), path(reads)\n" not in main_nf_lines
-    assert "    path index\n" not in main_nf_lines
-    # This line should have been added
-    assert "    tuple val(meta), path(reads), path(index)\n" in main_nf_lines
-
-
-def test_create_patch_try_apply_failed(self):
-    """
-    Test creating a patch file and applying it to a new version of the the files
-    """
-
-    setup_patch(self.pipeline_dir, True)
-    module_relpath = Path("modules", REPO_NAME, BISMARK_ALIGN)
-    module_path = Path(self.pipeline_dir, module_relpath)
-
-    # Try creating a patch file
-    patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
-    patch_obj.patch(BISMARK_ALIGN)
-
-    patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
-    # Check that a patch file with the correct name has been created
-    assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
-
-    # Check the 'modules.json' contains a patch file for the module
-    modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
-    assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path(
-        "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
-    )
-
-    update_obj = nf_core.modules.ModuleUpdate(
-        self.pipeline_dir, sha=FAIL_SHA, remote_url=GITLAB_URL, branch=PATCH_BRANCH
-    )
-    # Install the new files
-    install_dir = Path(tempfile.mkdtemp())
-    update_obj.install_component_files(BISMARK_ALIGN, FAIL_SHA, update_obj.modules_repo, install_dir)
-
-    # Try applying the patch
-    module_install_dir = install_dir / BISMARK_ALIGN
-    patch_path = module_relpath / patch_fn
-    assert update_obj.try_apply_patch(BISMARK_ALIGN, REPO_NAME, patch_path, module_path, module_install_dir) is False
-
-
-def test_create_patch_update_success(self):
-    """
-    Test creating a patch file and the updating the module
-
-    Should have the same effect as 'test_create_patch_try_apply_successful'
-    but uses higher level api
-    """
-
-    setup_patch(self.pipeline_dir, True)
-    module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
-
-    # Try creating a patch file
-    patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
-    patch_obj.patch(BISMARK_ALIGN)
-
-    patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
-    # Check that a patch file with the correct name has been created
-    assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
-
-    # Check the 'modules.json' contains a patch file for the module
-    modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
-    assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, GITLAB_URL, REPO_NAME) == Path(
-        "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
-    )
-
-    # Update the module
-    update_obj = nf_core.modules.ModuleUpdate(
-        self.pipeline_dir,
-        sha=SUCCEED_SHA,
-        show_diff=False,
-        update_deps=True,
-        remote_url=GITLAB_URL,
-        branch=PATCH_BRANCH,
-    )
-    assert update_obj.update(BISMARK_ALIGN)
-
-    # Check that a patch file with the correct name has been created
-    assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
-
-    # Check the 'modules.json' contains a patch file for the module
-    modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
-    assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, GITLAB_URL, REPO_NAME) == Path(
-        "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
-    ), modules_json_obj.get_patch_fn(BISMARK_ALIGN, GITLAB_URL, REPO_NAME)
-
-    # Check that the correct lines are in the patch file
-    with open(module_path / patch_fn) as fh:
-        patch_lines = fh.readlines()
-    module_relpath = module_path.relative_to(self.pipeline_dir)
-    assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines
-    assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines
-    assert "-    tuple val(meta), path(reads)\n" in patch_lines
-    assert "-    path index\n" in patch_lines
-    assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
-
-    # Check that 'main.nf' is updated correctly
-    with open(module_path / "main.nf") as fh:
-        main_nf_lines = fh.readlines()
-    # These lines should have been removed by the patch
-    assert "    tuple val(meta), path(reads)\n" not in main_nf_lines
-    assert "    path index\n" not in main_nf_lines
-    # This line should have been added
-    assert "    tuple val(meta), path(reads), path(index)\n" in main_nf_lines
-
-
-def test_create_patch_update_fail(self):
-    """
-    Test creating a patch file and updating a module when there is a diff conflict
-    """
-
-    setup_patch(self.pipeline_dir, True)
-    module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
-
-    # Try creating a patch file
-    patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
-    patch_obj.patch(BISMARK_ALIGN)
-
-    patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
-    # Check that a patch file with the correct name has been created
-    assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
-
-    # Check the 'modules.json' contains a patch file for the module
-    modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
-    assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path(
-        "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
-    )
-
-    # Save the file contents for downstream comparison
-    with open(module_path / patch_fn) as fh:
-        patch_contents = fh.read()
-
-    update_obj = nf_core.modules.ModuleUpdate(
-        self.pipeline_dir, sha=FAIL_SHA, show_diff=False, update_deps=True, remote_url=GITLAB_URL, branch=PATCH_BRANCH
-    )
-    update_obj.update(BISMARK_ALIGN)
-
-    # Check that the installed files have not been affected by the attempted patch
-    temp_dir = Path(tempfile.mkdtemp())
-    nf_core.components.components_command.ComponentCommand(
-        "modules", self.pipeline_dir, GITLAB_URL, PATCH_BRANCH
-    ).install_component_files(BISMARK_ALIGN, FAIL_SHA, update_obj.modules_repo, temp_dir)
-
-    temp_module_dir = temp_dir / BISMARK_ALIGN
-    for file in os.listdir(temp_module_dir):
-        assert file in os.listdir(module_path)
-        with open(module_path / file) as fh:
-            installed = fh.read()
-        with open(temp_module_dir / file) as fh:
-            shouldbe = fh.read()
-        assert installed == shouldbe
-
-    # Check that the patch file is unaffected
-    with open(module_path / patch_fn) as fh:
-        new_patch_contents = fh.read()
-    assert patch_contents == new_patch_contents
-
-
-def test_remove_patch(self):
-    """Test creating a patch when there is no change to the module"""
-    setup_patch(self.pipeline_dir, True)
-
-    # Try creating a patch file
-    patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
-    patch_obj.patch(BISMARK_ALIGN)
-
-    module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
-
-    # Check that a patch file with the correct name has been created
-    patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
-    assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
-
-    # Check the 'modules.json' contains a patch file for the module
-    modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
-    assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path(
-        "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
-    )
-
-    with mock.patch.object(nf_core.components.patch.questionary, "confirm") as mock_questionary:
-        mock_questionary.unsafe_ask.return_value = True
-        patch_obj.remove(BISMARK_ALIGN)
-    # Check that the diff file has been removed
-    assert set(os.listdir(module_path)) == {"main.nf", "meta.yml"}
-
-    # Check that the 'modules.json' entry has been removed
-    modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
-    assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) is None
diff --git a/tests/modules/remove.py b/tests/modules/remove.py
deleted file mode 100644
index e412fd35a8..0000000000
--- a/tests/modules/remove.py
+++ /dev/null
@@ -1,22 +0,0 @@
-import os
-
-
-def test_modules_remove_trimgalore(self):
-    """Test removing TrimGalore! module after installing it"""
-    self.mods_install.install("trimgalore")
-    module_path = os.path.join(self.mods_install.dir, "modules", "nf-core", "modules", "trimgalore")
-    assert self.mods_remove.remove("trimgalore")
-    assert os.path.exists(module_path) is False
-
-
-def test_modules_remove_trimgalore_uninstalled(self):
-    """Test removing TrimGalore! module without installing it"""
-    assert self.mods_remove.remove("trimgalore") is False
-
-
-def test_modules_remove_multiqc_from_gitlab(self):
-    """Test removing multiqc module after installing it from an alternative source"""
-    self.mods_install_gitlab.install("multiqc")
-    module_path = os.path.join(self.mods_install_gitlab.dir, "modules", "nf-core-test", "multiqc")
-    assert self.mods_remove_gitlab.remove("multiqc", force=True)
-    assert os.path.exists(module_path) is False
diff --git a/tests/modules/test_bump_versions.py b/tests/modules/test_bump_versions.py
new file mode 100644
index 0000000000..29e030668d
--- /dev/null
+++ b/tests/modules/test_bump_versions.py
@@ -0,0 +1,50 @@
+import os
+import re
+
+import pytest
+
+import nf_core.modules
+from nf_core.modules.modules_utils import ModuleExceptionError
+
+from ..test_modules import TestModules
+
+
+class TestModulesBumpVersions(TestModules):
+    def test_modules_bump_versions_single_module(self):
+        """Test updating a single module"""
+        # Change the bpipe/test version to an older version
+        env_yml_path = os.path.join(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")
+        with open(env_yml_path) as fh:
+            content = fh.read()
+        new_content = re.sub(r"bioconda::star=\d.\d.\d\D?", r"bioconda::star=2.6.1d", content)
+        with open(env_yml_path, "w") as fh:
+            fh.write(new_content)
+        version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+        version_bumper.bump_versions(module="bpipe/test")
+        assert len(version_bumper.failed) == 0
+
+    def test_modules_bump_versions_all_modules(self):
+        """Test updating all modules"""
+        version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+        version_bumper.bump_versions(all_modules=True)
+        assert len(version_bumper.failed) == 0
+
+    def test_modules_bump_versions_fail(self):
+        """Fail updating a module with wrong name"""
+        version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+        with pytest.raises(ModuleExceptionError) as excinfo:
+            version_bumper.bump_versions(module="no/module")
+        assert "Could not find the specified module:" in str(excinfo.value)
+
+    def test_modules_bump_versions_fail_unknown_version(self):
+        """Fail because of an unknown version"""
+        # Change the bpipe/test version to an older version
+        env_yml_path = os.path.join(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")
+        with open(env_yml_path) as fh:
+            content = fh.read()
+        new_content = re.sub(r"bioconda::bpipe=\d.\d.\d\D?", r"bioconda::bpipe=xxx", content)
+        with open(env_yml_path, "w") as fh:
+            fh.write(new_content)
+        version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+        version_bumper.bump_versions(module="bpipe/test")
+        assert "Conda package had unknown version" in version_bumper.failed[0][0]
diff --git a/tests/modules/test_create.py b/tests/modules/test_create.py
new file mode 100644
index 0000000000..c847501830
--- /dev/null
+++ b/tests/modules/test_create.py
@@ -0,0 +1,164 @@
+import os
+import shutil
+from pathlib import Path
+from unittest import mock
+
+import pytest
+import requests_cache
+import responses
+import yaml
+from git.repo import Repo
+
+import nf_core.modules
+from tests.utils import (
+    GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH,
+    GITLAB_URL,
+    mock_anaconda_api_calls,
+    mock_biocontainers_api_calls,
+)
+
+from ..test_modules import TestModules
+
+
+class TestModulesCreate(TestModules):
+    def test_modules_create_succeed(self):
+        """Succeed at creating the TrimGalore! module"""
+        with responses.RequestsMock() as rsps:
+            mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7")
+            mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7")
+            module_create = nf_core.modules.ModuleCreate(
+                self.pipeline_dir, "trimgalore", "@author", "process_single", True, True, conda_name="trim-galore"
+            )
+            with requests_cache.disabled():
+                module_create.create()
+        assert os.path.exists(os.path.join(self.pipeline_dir, "modules", "local", "trimgalore.nf"))
+
+    def test_modules_create_fail_exists(self):
+        """Fail at creating the same module twice"""
+        with responses.RequestsMock() as rsps:
+            mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7")
+            mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7")
+            module_create = nf_core.modules.ModuleCreate(
+                self.pipeline_dir, "trimgalore", "@author", "process_single", False, False, conda_name="trim-galore"
+            )
+            with requests_cache.disabled():
+                module_create.create()
+            with pytest.raises(UserWarning) as excinfo:
+                with requests_cache.disabled():
+                    module_create.create()
+        assert "Module file exists already" in str(excinfo.value)
+
+    def test_modules_create_nfcore_modules(self):
+        """Create a module in nf-core/modules clone"""
+        with responses.RequestsMock() as rsps:
+            mock_anaconda_api_calls(rsps, "fastqc", "0.11.9")
+            mock_biocontainers_api_calls(rsps, "fastqc", "0.11.9")
+            module_create = nf_core.modules.ModuleCreate(
+                self.nfcore_modules, "fastqc", "@author", "process_low", False, False
+            )
+            with requests_cache.disabled():
+                module_create.create()
+        assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "fastqc", "main.nf"))
+        assert os.path.exists(
+            os.path.join(self.nfcore_modules, "modules", "nf-core", "fastqc", "tests", "main.nf.test")
+        )
+
+    def test_modules_create_nfcore_modules_subtool(self):
+        """Create a tool/subtool module in a nf-core/modules clone"""
+        with responses.RequestsMock() as rsps:
+            mock_anaconda_api_calls(rsps, "star", "2.8.10a")
+            mock_biocontainers_api_calls(rsps, "star", "2.8.10a")
+            module_create = nf_core.modules.ModuleCreate(
+                self.nfcore_modules, "star/index", "@author", "process_medium", False, False
+            )
+            with requests_cache.disabled():
+                module_create.create()
+        assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "star", "index", "main.nf"))
+        assert os.path.exists(
+            os.path.join(self.nfcore_modules, "modules", "nf-core", "star", "index", "tests", "main.nf.test")
+        )
+
+    @mock.patch("rich.prompt.Confirm.ask")
+    def test_modules_migrate(self, mock_rich_ask):
+        """Create a module with the --migrate-pytest option to convert pytest to nf-test"""
+        pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort")
+        module_dir = Path(self.nfcore_modules, "modules", "nf-core", "samtools", "sort")
+
+        # Clone modules repo with pytests
+        shutil.rmtree(self.nfcore_modules)
+        Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
+        with open(module_dir / "main.nf") as fh:
+            old_main_nf = fh.read()
+        with open(module_dir / "meta.yml") as fh:
+            old_meta_yml = fh.read()
+
+        # Create a module with --migrate-pytest
+        mock_rich_ask.return_value = True
+        module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
+        module_create.create()
+
+        with open(module_dir / "main.nf") as fh:
+            new_main_nf = fh.read()
+        with open(module_dir / "meta.yml") as fh:
+            new_meta_yml = fh.read()
+        nextflow_config = module_dir / "tests" / "nextflow.config"
+
+        # Check that old files have been copied to the new module
+        assert old_main_nf == new_main_nf
+        assert old_meta_yml == new_meta_yml
+        assert nextflow_config.is_file()
+
+        # Check that pytest folder is deleted
+        assert not pytest_dir.is_dir()
+
+        # Check that pytest_modules.yml is updated
+        with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
+            modules_yml = yaml.safe_load(fh)
+        assert "samtools/sort" not in modules_yml.keys()
+
+    @mock.patch("rich.prompt.Confirm.ask")
+    def test_modules_migrate_no_delete(self, mock_rich_ask):
+        """Create a module with the --migrate-pytest option to convert pytest to nf-test.
+        Test that pytest directory is not deleted."""
+        pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort")
+
+        # Clone modules repo with pytests
+        shutil.rmtree(self.nfcore_modules)
+        Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
+
+        # Create a module with --migrate-pytest
+        mock_rich_ask.return_value = False
+        module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
+        module_create.create()
+
+        # Check that pytest folder is not deleted
+        assert pytest_dir.is_dir()
+
+        # Check that pytest_modules.yml is updated
+        with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
+            modules_yml = yaml.safe_load(fh)
+        assert "samtools/sort" not in modules_yml.keys()
+
+    @mock.patch("rich.prompt.Confirm.ask")
+    def test_modules_migrate_symlink(self, mock_rich_ask):
+        """Create a module with the --migrate-pytest option to convert pytest with symlinks to nf-test.
+        Test that the symlink is deleted and the file is copied."""
+
+        pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort")
+        module_dir = Path(self.nfcore_modules, "modules", "nf-core", "samtools", "sort")
+
+        # Clone modules repo with pytests
+        shutil.rmtree(self.nfcore_modules)
+        Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
+
+        # Create a symlinked file in the pytest directory
+        symlink_file = pytest_dir / "symlink_file.txt"
+        symlink_file.symlink_to(module_dir / "main.nf")
+
+        # Create a module with --migrate-pytest
+        mock_rich_ask.return_value = True
+        module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
+        module_create.create()
+
+        # Check that symlink is deleted
+        assert not symlink_file.is_symlink()
diff --git a/tests/modules/test_info.py b/tests/modules/test_info.py
new file mode 100644
index 0000000000..8906854044
--- /dev/null
+++ b/tests/modules/test_info.py
@@ -0,0 +1,62 @@
+from rich.console import Console
+
+import nf_core.modules
+
+from ..test_modules import TestModules
+from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL
+
+
+class TestModulesCreate(TestModules):
+    def test_modules_info_remote(self):
+        """Test getting info about a remote module"""
+        mods_info = nf_core.modules.ModuleInfo(self.pipeline_dir, "fastqc")
+        mods_info_output = mods_info.get_component_info()
+        console = Console(record=True)
+        console.print(mods_info_output)
+        output = console.export_text()
+
+        assert "Module: fastqc" in output
+        assert "Inputs" in output
+        assert "Outputs" in output
+
+    def test_modules_info_remote_gitlab(self):
+        """Test getting info about a module in the remote gitlab repo"""
+        mods_info = nf_core.modules.ModuleInfo(
+            self.pipeline_dir, "fastqc", remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH
+        )
+        mods_info_output = mods_info.get_component_info()
+        console = Console(record=True)
+        console.print(mods_info_output)
+        output = console.export_text()
+
+        assert "Module: fastqc" in output
+        assert "Inputs" in output
+        assert "Outputs" in output
+        assert "--git-remote" in output
+
+    def test_modules_info_local(self):
+        """Test getting info about a locally installed module"""
+        self.mods_install.install("trimgalore")
+        mods_info = nf_core.modules.ModuleInfo(self.pipeline_dir, "trimgalore")
+        mods_info_output = mods_info.get_component_info()
+        console = Console(record=True)
+        console.print(mods_info_output)
+        output = console.export_text()
+
+        assert "Module: trimgalore" in output
+        assert "Inputs" in output
+        assert "Outputs" in output
+        assert "Location" in output
+
+    def test_modules_info_in_modules_repo(self):
+        """Test getting info about a module in the modules repo"""
+        mods_info = nf_core.modules.ModuleInfo(self.nfcore_modules, "fastqc")
+        mods_info.local = True
+        mods_info_output = mods_info.get_component_info()
+        console = Console(record=True)
+        console.print(mods_info_output)
+        output = console.export_text()
+
+        assert "Module: fastqc" in output
+        assert "Inputs" in output
+        assert "Outputs" in output
diff --git a/tests/modules/test_install.py b/tests/modules/test_install.py
new file mode 100644
index 0000000000..b90f01ee61
--- /dev/null
+++ b/tests/modules/test_install.py
@@ -0,0 +1,90 @@
+import os
+from pathlib import Path
+
+import pytest
+
+from nf_core.modules.install import ModuleInstall
+from nf_core.modules.modules_json import ModulesJson
+
+from ..test_modules import TestModules
+from ..utils import (
+    GITLAB_BRANCH_ORG_PATH_BRANCH,
+    GITLAB_BRANCH_TEST_BRANCH,
+    GITLAB_REPO,
+    GITLAB_URL,
+    with_temporary_folder,
+)
+
+
+class TestModulesCreate(TestModules):
+    def test_modules_install_nopipeline(self):
+        """Test installing a module - no pipeline given"""
+        self.mods_install.dir = None
+        assert self.mods_install.install("foo") is False
+
+    @with_temporary_folder
+    def test_modules_install_emptypipeline(self, tmpdir):
+        """Test installing a module - empty dir given"""
+        os.mkdir(os.path.join(tmpdir, "nf-core-pipe"))
+        self.mods_install.dir = os.path.join(tmpdir, "nf-core-pipe")
+        with pytest.raises(UserWarning) as excinfo:
+            self.mods_install.install("foo")
+        assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
+
+    def test_modules_install_nomodule(self):
+        """Test installing a module - unrecognised module given"""
+        assert self.mods_install.install("foo") is False
+
+    def test_modules_install_trimgalore(self):
+        """Test installing a module - TrimGalore!"""
+        assert self.mods_install.install("trimgalore") is not False
+        assert self.mods_install.dir is not None
+        module_path = Path(self.mods_install.dir, "modules", "nf-core", "trimgalore")
+        assert os.path.exists(module_path)
+
+    def test_modules_install_trimgalore_twice(self):
+        """Test installing a module - TrimGalore! already there"""
+        self.mods_install.install("trimgalore")
+        assert self.mods_install.install("trimgalore") is True
+
+    def test_modules_install_from_gitlab(self):
+        """Test installing a module from GitLab"""
+        assert self.mods_install_gitlab.install("fastqc") is True
+
+    def test_modules_install_different_branch_fail(self):
+        """Test installing a module from a different branch"""
+        install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH)
+        # The FastQC module does not exists in the branch-test branch
+        assert install_obj.install("fastqc") is False
+
+    def test_modules_install_different_branch_succeed(self):
+        """Test installing a module from a different branch"""
+        install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH)
+        # The fastp module does exists in the branch-test branch
+        assert install_obj.install("fastp") is True
+
+        # Verify that the branch entry was added correctly
+        modules_json = ModulesJson(self.pipeline_dir)
+        assert (
+            modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO)
+            == GITLAB_BRANCH_TEST_BRANCH
+        )
+
+    def test_modules_install_tracking(self):
+        """Test installing a module and finding 'modules' in the installed_by section of modules.json"""
+        self.mods_install.install("trimgalore")
+
+        # Verify that the installed_by entry was added correctly
+        modules_json = ModulesJson(self.pipeline_dir)
+        mod_json = modules_json.get_modules_json()
+        assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["trimgalore"][
+            "installed_by"
+        ] == ["modules"]
+
+    def test_modules_install_alternate_remote(self):
+        """Test installing a module from a different remote with the same organization path"""
+        install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_ORG_PATH_BRANCH)
+        # Install fastqc from GitLab which is also installed from GitHub with the same org_path
+        with pytest.raises(Exception) as excinfo:
+            install_obj.install("fastqc")
+            assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py
new file mode 100644
index 0000000000..6448916acf
--- /dev/null
+++ b/tests/modules/test_lint.py
@@ -0,0 +1,865 @@
+import json
+from pathlib import Path
+from typing import Union
+
+import pytest
+import yaml
+from git.repo import Repo
+
+import nf_core.modules
+from nf_core.modules.lint import main_nf
+from nf_core.utils import set_wd
+
+from ..test_modules import TestModules
+from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL
+from .test_patch import BISMARK_ALIGN, CORRECT_SHA, PATCH_BRANCH, REPO_NAME, modify_main_nf
+
+PROCESS_LABEL_GOOD = (
+    """
+    label 'process_high'
+    cpus 12
+    """,
+    1,
+    0,
+    0,
+)
+PROCESS_LABEL_NON_ALPHANUMERIC = (
+    """
+    label 'a:label:with:colons'
+    cpus 12
+    """,
+    0,
+    2,
+    0,
+)
+PROCESS_LABEL_GOOD_CONFLICTING = (
+    """
+    label 'process_high'
+    label 'process_low'
+    cpus 12
+    """,
+    0,
+    1,
+    0,
+)
+PROCESS_LABEL_GOOD_DUPLICATES = (
+    """
+    label 'process_high'
+    label 'process_high'
+    cpus 12
+    """,
+    0,
+    2,
+    0,
+)
+PROCESS_LABEL_GOOD_AND_NONSTANDARD = (
+    """
+    label 'process_high'
+    label 'process_extra_label'
+    cpus 12
+    """,
+    1,
+    1,
+    0,
+)
+PROCESS_LABEL_NONSTANDARD = (
+    """
+    label 'process_extra_label'
+    cpus 12
+    """,
+    0,
+    2,
+    0,
+)
+PROCESS_LABEL_NONSTANDARD_DUPLICATES = (
+    """
+    label process_extra_label
+    label process_extra_label
+    cpus 12
+    """,
+    0,
+    3,
+    0,
+)
+PROCESS_LABEL_NONE_FOUND = (
+    """
+    cpus 12
+    """,
+    0,
+    1,
+    0,
+)
+
+PROCESS_LABEL_TEST_CASES = [
+    PROCESS_LABEL_GOOD,
+    PROCESS_LABEL_NON_ALPHANUMERIC,
+    PROCESS_LABEL_GOOD_CONFLICTING,
+    PROCESS_LABEL_GOOD_DUPLICATES,
+    PROCESS_LABEL_GOOD_AND_NONSTANDARD,
+    PROCESS_LABEL_NONSTANDARD,
+    PROCESS_LABEL_NONSTANDARD_DUPLICATES,
+    PROCESS_LABEL_NONE_FOUND,
+]
+
+
+# Test cases for linting the container definitions
+
+CONTAINER_SINGLE_GOOD = (
+    "Single-line container definition should pass",
+    """
+    container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package
+    """,
+    2,  # passed
+    0,  # warned
+    0,  # failed
+)
+
+CONTAINER_TWO_LINKS_GOOD = (
+    "Multi-line container definition should pass",
+    """
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
+        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
+    """,
+    6,
+    0,
+    0,
+)
+
+CONTAINER_WITH_SPACE_BAD = (
+    "Space in container URL should fail",
+    """
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ':
+        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
+    """,
+    5,
+    0,
+    1,
+)
+
+CONTAINER_MULTIPLE_DBLQUOTES_BAD = (
+    "Incorrect quoting of container string should fail",
+    """
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ':
+        "biocontainers/gatk4:4.4.0.0--py36hdfd78af_0" }"
+    """,
+    4,
+    0,
+    1,
+)
+
+CONTAINER_TEST_CASES = [
+    CONTAINER_SINGLE_GOOD,
+    CONTAINER_TWO_LINKS_GOOD,
+    CONTAINER_WITH_SPACE_BAD,
+    CONTAINER_MULTIPLE_DBLQUOTES_BAD,
+]
+
+
+class TestModulesCreate(TestModules):
+    def _setup_patch(self, pipeline_dir: Union[str, Path], modify_module: bool):
+        install_obj = nf_core.modules.ModuleInstall(
+            pipeline_dir,
+            prompt=False,
+            force=False,
+            remote_url=GITLAB_URL,
+            branch=PATCH_BRANCH,
+            sha=CORRECT_SHA,
+        )
+
+        # Install the module
+        install_obj.install(BISMARK_ALIGN)
+
+        if modify_module:
+            # Modify the module
+            module_path = Path(pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
+            modify_main_nf(module_path / "main.nf")
+
+    def test_modules_lint_trimgalore(self):
+        """Test linting the TrimGalore! module"""
+        self.mods_install.install("trimgalore")
+        module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
+        module_lint.lint(print_results=False, module="trimgalore")
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
+    def test_modules_lint_empty(self):
+        """Test linting a pipeline with no modules installed"""
+        self.mods_remove.remove("fastqc", force=True)
+        self.mods_remove.remove("multiqc", force=True)
+        with pytest.raises(LookupError):
+            nf_core.modules.ModuleLint(dir=self.pipeline_dir)
+
+    def test_modules_lint_new_modules(self):
+        """lint a new module"""
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, all_modules=True)
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
+    def test_modules_lint_no_gitlab(self):
+        """Test linting a pipeline with no modules installed"""
+        self.mods_remove.remove("fastqc", force=True)
+        self.mods_remove.remove("multiqc", force=True)
+        with pytest.raises(LookupError):
+            nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+
+    def test_modules_lint_gitlab_modules(self):
+        """Lint modules from a different remote"""
+        self.mods_install_gitlab.install("fastqc")
+        self.mods_install_gitlab.install("multiqc")
+        module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+        module_lint.lint(print_results=False, all_modules=True)
+        assert len(module_lint.failed) == 2
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
+    def test_modules_lint_multiple_remotes(self):
+        """Lint modules from a different remote"""
+        self.mods_install_gitlab.install("multiqc")
+        module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+        module_lint.lint(print_results=False, all_modules=True)
+        assert len(module_lint.failed) == 1
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
+    def test_modules_lint_registry(self):
+        """Test linting the samtools module and alternative registry"""
+        self.mods_install.install("samtools")
+        module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, registry="public.ecr.aws")
+        module_lint.lint(print_results=False, module="samtools")
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+        module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
+        module_lint.lint(print_results=False, module="samtools")
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
+    def test_modules_lint_patched_modules(self):
+        """
+        Test creating a patch file and applying it to a new version of the the files
+        """
+        self._setup_patch(str(self.pipeline_dir), True)
+
+        # Create a patch file
+        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj.patch(BISMARK_ALIGN)
+
+        # change temporarily working directory to the pipeline directory
+        # to avoid error from try_apply_patch() during linting
+        with set_wd(self.pipeline_dir):
+            module_lint = nf_core.modules.ModuleLint(
+                dir=self.pipeline_dir,
+                remote_url=GITLAB_URL,
+                branch=PATCH_BRANCH,
+                hide_progress=True,
+            )
+            module_lint.lint(
+                print_results=False,
+                all_modules=True,
+            )
+
+        assert len(module_lint.failed) == 1
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
+    def test_modules_lint_check_process_labels(self):
+        for test_case in PROCESS_LABEL_TEST_CASES:
+            process, passed, warned, failed = test_case
+            mocked_ModuleLint = MockModuleLint()
+            main_nf.check_process_labels(mocked_ModuleLint, process.splitlines())
+            assert len(mocked_ModuleLint.passed) == passed
+            assert len(mocked_ModuleLint.warned) == warned
+            assert len(mocked_ModuleLint.failed) == failed
+
+    def test_modules_lint_check_url(self):
+        for test_case in CONTAINER_TEST_CASES:
+            test, process, passed, warned, failed = test_case
+            mocked_ModuleLint = MockModuleLint()
+            for line in process.splitlines():
+                if line.strip():
+                    main_nf.check_container_link_line(mocked_ModuleLint, line, registry="quay.io")
+
+            assert (
+                len(mocked_ModuleLint.passed) == passed
+            ), f"{test}: Expected {passed} PASS, got {len(mocked_ModuleLint.passed)}."
+            assert (
+                len(mocked_ModuleLint.warned) == warned
+            ), f"{test}: Expected {warned} WARN, got {len(mocked_ModuleLint.warned)}."
+            assert (
+                len(mocked_ModuleLint.failed) == failed
+            ), f"{test}: Expected {failed} FAIL, got {len(mocked_ModuleLint.failed)}."
+
+    def test_modules_lint_snapshot_file(self):
+        """Test linting a module with a snapshot file"""
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
+    def test_modules_lint_snapshot_file_missing_fail(self):
+        """Test linting a module with a snapshot file missing, which should fail"""
+        Path(
+            self.nfcore_modules,
+            "modules",
+            "nf-core",
+            "bpipe",
+            "test",
+            "tests",
+            "main.nf.test.snap",
+        ).unlink()
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        Path(
+            self.nfcore_modules,
+            "modules",
+            "nf-core",
+            "bpipe",
+            "test",
+            "tests",
+            "main.nf.test.snap",
+        ).touch()
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+        assert module_lint.failed[0].lint_test == "test_snapshot_exists"
+
+    def test_modules_lint_snapshot_file_not_needed(self):
+        """Test linting a module which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file"""
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "tests",
+                "main.nf.test",
+            )
+        ) as fh:
+            content = fh.read()
+            new_content = content.replace("snapshot(", "snap (")
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "tests",
+                "main.nf.test",
+            ),
+            "w",
+        ) as fh:
+            fh.write(new_content)
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
+    def test_modules_environment_yml_file_doesnt_exists(self):
+        """Test linting a module with an environment.yml file"""
+        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml").rename(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml.bak",
+            )
+        )
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        Path(
+            self.nfcore_modules,
+            "modules",
+            "nf-core",
+            "bpipe",
+            "test",
+            "environment.yml.bak",
+        ).rename(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            )
+        )
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+        assert module_lint.failed[0].lint_test == "environment_yml_exists"
+
+    def test_modules_environment_yml_file_sorted_correctly(self):
+        """Test linting a module with a correctly sorted environment.yml file"""
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
+    def test_modules_environment_yml_file_sorted_incorrectly(self):
+        """Test linting a module with an incorrectly sorted environment.yml file"""
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            )
+        ) as fh:
+            yaml_content = yaml.safe_load(fh)
+        # Add a new dependency to the environment.yml file and reverse the order
+        yaml_content["dependencies"].append("z")
+        yaml_content["dependencies"].reverse()
+        yaml_content = yaml.dump(yaml_content)
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            ),
+            "w",
+        ) as fh:
+            fh.write(yaml_content)
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        # we fix the sorting on the fly, so this should pass
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
+    def test_modules_environment_yml_file_not_array(self):
+        """Test linting a module with an incorrectly formatted environment.yml file"""
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            )
+        ) as fh:
+            yaml_content = yaml.safe_load(fh)
+        yaml_content["dependencies"] = "z"
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            ),
+            "w",
+        ) as fh:
+            fh.write(yaml.dump(yaml_content))
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+        assert module_lint.failed[0].lint_test == "environment_yml_valid"
+
+    def test_modules_environment_yml_file_name_mismatch(self):
+        """Test linting a module with a different name in the environment.yml file"""
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            )
+        ) as fh:
+            yaml_content = yaml.safe_load(fh)
+        yaml_content["name"] = "bpipe-test"
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            ),
+            "w",
+        ) as fh:
+            fh.write(yaml.dump(yaml_content))
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        # reset changes
+        yaml_content["name"] = "bpipe_test"
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            ),
+            "w",
+        ) as fh:
+            fh.write(yaml.dump(yaml_content))
+
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+        assert module_lint.failed[0].lint_test == "environment_yml_name"
+
+    def test_modules_meta_yml_incorrect_licence_field(self):
+        """Test linting a module with an incorrect Licence field in meta.yml"""
+        with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh:
+            meta_yml = yaml.safe_load(fh)
+        meta_yml["tools"][0]["bpipe"]["licence"] = "[MIT]"
+        with open(
+            Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"),
+            "w",
+        ) as fh:
+            fh.write(yaml.dump(meta_yml))
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+
+        # reset changes
+        meta_yml["tools"][0]["bpipe"]["licence"] = ["MIT"]
+        with open(
+            Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"),
+            "w",
+        ) as fh:
+            fh.write(yaml.dump(meta_yml))
+
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) >= 0
+        assert len(module_lint.warned) >= 0
+        assert module_lint.failed[0].lint_test == "meta_yml_valid"
+
+    def test_modules_meta_yml_input_mismatch(self):
+        """Test linting a module with an extra entry in input fields in meta.yml compared to module.input"""
+        with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh:
+            main_nf = fh.read()
+        main_nf_new = main_nf.replace("path bam", "path bai")
+        with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
+            fh.write(main_nf_new)
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
+            fh.write(main_nf)
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) >= 0
+        assert len(module_lint.warned) == 2
+        lint_tests = [x.lint_test for x in module_lint.warned]
+        # check that it is there twice:
+        assert lint_tests.count("meta_input_meta_only") == 1
+        assert lint_tests.count("meta_input_main_only") == 1
+
+    def test_modules_meta_yml_output_mismatch(self):
+        """Test linting a module with an extra entry in output fields in meta.yml compared to module.output"""
+        with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh:
+            main_nf = fh.read()
+        main_nf_new = main_nf.replace("emit: bam", "emit: bai")
+        with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
+            fh.write(main_nf_new)
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
+            fh.write(main_nf)
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) >= 0
+        assert len(module_lint.warned) == 2
+        lint_tests = [x.lint_test for x in module_lint.warned]
+        # check that it is there twice:
+        assert lint_tests.count("meta_output_meta_only") == 1
+        assert lint_tests.count("meta_output_main_only") == 1
+
+    def test_modules_meta_yml_incorrect_name(self):
+        """Test linting a module with an incorrect name in meta.yml"""
+        with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh:
+            meta_yml = yaml.safe_load(fh)
+        meta_yml["name"] = "bpipe/test"
+        # need to make the same change to the environment.yml file
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            )
+        ) as fh:
+            environment_yml = yaml.safe_load(fh)
+        environment_yml["name"] = "bpipe/test"
+        with open(
+            Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"),
+            "w",
+        ) as fh:
+            fh.write(yaml.dump(meta_yml))
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            ),
+            "w",
+        ) as fh:
+            fh.write(yaml.dump(environment_yml))
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+
+        # reset changes
+        meta_yml["name"] = "bpipe_test"
+        with open(
+            Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"),
+            "w",
+        ) as fh:
+            fh.write(yaml.dump(meta_yml))
+        environment_yml["name"] = "bpipe_test"
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "environment.yml",
+            ),
+            "w",
+        ) as fh:
+            fh.write(yaml.dump(environment_yml))
+
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) >= 0
+        assert len(module_lint.warned) >= 0
+        assert module_lint.failed[0].lint_test == "meta_name"
+
+    def test_modules_missing_test_dir(self):
+        """Test linting a module with a missing test directory"""
+        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests").rename(
+            Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak")
+        )
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak").rename(
+            Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests")
+        )
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) >= 0
+        assert len(module_lint.warned) >= 0
+        assert module_lint.failed[0].lint_test == "test_dir_exists"
+
+    def test_modules_missing_test_main_nf(self):
+        """Test linting a module with a missing test/main.nf file"""
+        Path(
+            self.nfcore_modules,
+            "modules",
+            "nf-core",
+            "bpipe",
+            "test",
+            "tests",
+            "main.nf.test",
+        ).rename(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "tests",
+                "main.nf.test.bak",
+            )
+        )
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        Path(
+            self.nfcore_modules,
+            "modules",
+            "nf-core",
+            "bpipe",
+            "test",
+            "tests",
+            "main.nf.test.bak",
+        ).rename(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "tests",
+                "main.nf.test",
+            )
+        )
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) >= 0
+        assert len(module_lint.warned) >= 0
+        assert module_lint.failed[0].lint_test == "test_main_nf_exists"
+
+    def test_modules_unused_pytest_files(self):
+        """Test linting a nf-test module with files still present in `tests/modules/`"""
+        Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").mkdir(parents=True, exist_ok=True)
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").rmdir()
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) >= 0
+        assert len(module_lint.warned) >= 0
+        assert module_lint.failed[0].lint_test == "test_old_test_dir"
+
+    def test_nftest_failing_linting(self):
+        """Test linting a module which includes other modules in nf-test tests.
+        Linting tests"""
+        # Clone modules repo with testing modules
+        tmp_dir = self.nfcore_modules.parent
+        self.nfcore_modules = Path(tmp_dir, "modules-test")
+        Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_NFTEST_BRANCH)
+
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="kallisto/quant")
+
+        assert len(module_lint.failed) == 3, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) >= 0
+        assert len(module_lint.warned) >= 0
+        assert module_lint.failed[0].lint_test == "environment_yml_valid"
+        assert module_lint.failed[1].lint_test == "meta_yml_valid"
+        assert module_lint.failed[2].lint_test == "test_main_tags"
+        assert "kallisto/index" in module_lint.failed[2].message
+
+    def test_modules_absent_version(self):
+        """Test linting a nf-test module if the versions is absent in the snapshot file `"""
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "tests",
+                "main.nf.test.snap",
+            )
+        ) as fh:
+            content = fh.read()
+            new_content = content.replace("versions", "foo")
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "tests",
+                "main.nf.test.snap",
+            ),
+            "w",
+        ) as fh:
+            fh.write(new_content)
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        with open(
+            Path(
+                self.nfcore_modules,
+                "modules",
+                "nf-core",
+                "bpipe",
+                "test",
+                "tests",
+                "main.nf.test.snap",
+            ),
+            "w",
+        ) as fh:
+            fh.write(content)
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) >= 0
+        assert len(module_lint.warned) >= 0
+        assert module_lint.failed[0].lint_test == "test_snap_versions"
+
+    def test_modules_empty_file_in_snapshot(self):
+        """Test linting a nf-test module with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)"""
+        snap_file = Path(
+            self.nfcore_modules,
+            "modules",
+            "nf-core",
+            "bpipe",
+            "test",
+            "tests",
+            "main.nf.test.snap",
+        )
+        snap = json.load(snap_file.open())
+        content = snap_file.read_text()
+        snap["my test"]["content"][0]["0"] = "test:md5,d41d8cd98f00b204e9800998ecf8427e"
+
+        with open(snap_file, "w") as fh:
+            json.dump(snap, fh)
+
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+        assert module_lint.failed[0].lint_test == "test_snap_md5sum"
+
+        # reset the file
+        with open(snap_file, "w") as fh:
+            fh.write(content)
+
+    def test_modules_empty_file_in_stub_snapshot(self):
+        """Test linting a nf-test module with an empty file sha sum in the stub test snapshot, which should make it not fail"""
+        snap_file = Path(
+            self.nfcore_modules,
+            "modules",
+            "nf-core",
+            "bpipe",
+            "test",
+            "tests",
+            "main.nf.test.snap",
+        )
+        snap = json.load(snap_file.open())
+        content = snap_file.read_text()
+        snap["my_test_stub"] = {"content": [{"0": "test:md5,d41d8cd98f00b204e9800998ecf8427e", "versions": {}}]}
+
+        with open(snap_file, "w") as fh:
+            json.dump(snap, fh)
+
+        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+        assert any(x.lint_test == "test_snap_md5sum" for x in module_lint.passed)
+
+        # reset the file
+        with open(snap_file, "w") as fh:
+            fh.write(content)
+
+
+# A skeleton object with the passed/warned/failed list attrs
+# Use this in place of a ModuleLint object to test behaviour of
+# linting methods which don't need the full setup
+class MockModuleLint:
+    def __init__(self):
+        self.passed = []
+        self.warned = []
+        self.failed = []
+
+        self.main_nf = "main_nf"
diff --git a/tests/modules/test_list.py b/tests/modules/test_list.py
new file mode 100644
index 0000000000..81484cc8f0
--- /dev/null
+++ b/tests/modules/test_list.py
@@ -0,0 +1,126 @@
+import json
+from pathlib import Path
+
+import yaml
+from rich.console import Console
+
+import nf_core.modules
+
+from ..test_modules import TestModules
+from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL
+
+
+class TestModulesCreate(TestModules):
+    def test_modules_list_remote(self):
+        """Test listing available modules"""
+        mods_list = nf_core.modules.ModuleList(None, remote=True)
+        listed_mods = mods_list.list_components()
+        console = Console(record=True)
+        console.print(listed_mods)
+        output = console.export_text()
+        assert "fastqc" in output
+
+    def test_modules_list_remote_gitlab(self):
+        """Test listing the modules in the remote gitlab repo"""
+        mods_list = nf_core.modules.ModuleList(None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH)
+        listed_mods = mods_list.list_components()
+        console = Console(record=True)
+        console.print(listed_mods)
+        output = console.export_text()
+        assert "fastqc" in output
+
+    def test_modules_list_pipeline(self):
+        """Test listing locally installed modules"""
+        mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
+        listed_mods = mods_list.list_components()
+        console = Console(record=True)
+        console.print(listed_mods)
+        output = console.export_text()
+        assert "fastqc" in output
+        assert "multiqc" in output
+
+    def test_modules_install_and_list_pipeline(self):
+        """Test listing locally installed modules"""
+        self.mods_install.install("trimgalore")
+        mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
+        listed_mods = mods_list.list_components()
+        console = Console(record=True)
+        console.print(listed_mods)
+        output = console.export_text()
+        assert "trimgalore" in output
+
+    def test_modules_install_gitlab_and_list_pipeline(self):
+        """Test listing locally installed modules"""
+        self.mods_install_gitlab.install("fastqc")
+        mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
+        listed_mods = mods_list.list_components()
+        console = Console(record=True)
+        console.print(listed_mods)
+        output = console.export_text()
+        assert "fastqc" in output
+
+    def test_modules_list_local_json(self):
+        """Test listing locally installed modules as JSON"""
+        mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
+        listed_mods = mods_list.list_components(print_json=True)
+        listed_mods = json.loads(listed_mods)
+        assert "fastqc" in listed_mods
+        assert "multiqc" in listed_mods
+
+    def test_modules_list_remote_json(self):
+        """Test listing available modules as JSON"""
+        mods_list = nf_core.modules.ModuleList(None, remote=True)
+        listed_mods = mods_list.list_components(print_json=True)
+        listed_mods = json.loads(listed_mods)
+        assert "fastqc" in listed_mods
+        assert "multiqc" in listed_mods
+
+    def test_modules_list_with_one_keyword(self):
+        """Test listing available modules with one keyword"""
+        mods_list = nf_core.modules.ModuleList(None, remote=True)
+        listed_mods = mods_list.list_components(keywords=["qc"])
+        console = Console(record=True)
+        console.print(listed_mods)
+        output = console.export_text()
+        assert "multiqc" in output
+
+    def test_modules_list_with_keywords(self):
+        """Test listing available modules with multiple keywords"""
+        mods_list = nf_core.modules.ModuleList(None, remote=True)
+        listed_mods = mods_list.list_components(keywords=["fastq", "qc"])
+        console = Console(record=True)
+        console.print(listed_mods)
+        output = console.export_text()
+        assert "fastqc" in output
+
+    def test_modules_list_with_unused_keyword(self):
+        """Test listing available modules with an unused keyword"""
+        mods_list = nf_core.modules.ModuleList(None, remote=True)
+        with self.assertLogs(level="INFO") as log:
+            listed_mods = mods_list.list_components(keywords=["you_will_never_find_me"])
+            self.assertIn("No available", log.output[0])
+            # expect empty list
+            assert listed_mods == ""
+
+    def test_modules_list_in_wrong_repo_fail(self):
+        """Test listing available modules in a non-pipeline repo"""
+        # modify repotype in .nf-core.yml
+        with open(Path(self.pipeline_dir, ".nf-core.yml")) as fh:
+            nf_core_yml = yaml.safe_load(fh)
+        nf_core_yml_orig = nf_core_yml.copy()
+        nf_core_yml["repository_type"] = "modules"
+        nf_core_yml["org_path"] = "nf-core"
+
+        print(nf_core_yml)
+        with open(Path(self.pipeline_dir, ".nf-core.yml"), "w") as fh:
+            yaml.safe_dump(nf_core_yml, fh)
+        # expect error logged
+        with self.assertLogs(level="ERROR") as log:
+            mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
+            listed_mods = mods_list.list_components()
+            self.assertIn("must be run from a pipeline directory", log.output[0])
+            # expect empty list
+            assert listed_mods == ""
+        # restore .nf-core.yml
+        with open(Path(self.pipeline_dir, ".nf-core.yml"), "w") as fh:
+            yaml.safe_dump(nf_core_yml_orig, fh)
diff --git a/tests/modules/test_modules_json.py b/tests/modules/test_modules_json.py
new file mode 100644
index 0000000000..319b5ad657
--- /dev/null
+++ b/tests/modules/test_modules_json.py
@@ -0,0 +1,245 @@
+import copy
+import json
+import shutil
+from pathlib import Path
+
+from nf_core.modules.modules_json import ModulesJson
+from nf_core.modules.modules_repo import (
+    NF_CORE_MODULES_DEFAULT_BRANCH,
+    NF_CORE_MODULES_NAME,
+    NF_CORE_MODULES_REMOTE,
+    ModulesRepo,
+)
+from nf_core.modules.patch import ModulePatch
+
+from ..test_modules import TestModules
+
+
+class TestModulesCreate(TestModules):
+    def test_get_modules_json(self):
+        """Checks that the get_modules_json function returns the correct result"""
+        mod_json_path = Path(self.pipeline_dir, "modules.json")
+        with open(mod_json_path) as fh:
+            try:
+                mod_json_sb = json.load(fh)
+            except json.JSONDecodeError as e:
+                raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}")
+
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+        mod_json = mod_json_obj.get_modules_json()
+
+        # Check that the modules.json hasn't changed
+        assert mod_json == mod_json_sb
+
+    def test_mod_json_update(self):
+        """Checks whether the update function works properly"""
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+        # Update the modules.json file
+        mod_repo_obj = ModulesRepo()
+        mod_json_obj.update("modules", mod_repo_obj, "MODULE_NAME", "GIT_SHA", "modules", write_file=False)
+        mod_json = mod_json_obj.get_modules_json()
+        assert "MODULE_NAME" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]
+        assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]
+        assert "GIT_SHA" == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["git_sha"]
+        assert (
+            NF_CORE_MODULES_DEFAULT_BRANCH
+            == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["branch"]
+        )
+        assert (
+            "modules" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["installed_by"]
+        )
+
+    def test_mod_json_create(self):
+        """Test creating a modules.json file from scratch"""
+        mod_json_path = Path(self.pipeline_dir, "modules.json")
+        # Remove the existing modules.json file
+        mod_json_path.unlink()
+
+        # Create the new modules.json file
+        # (There are no prompts as long as there are only nf-core modules)
+        ModulesJson(self.pipeline_dir).create()
+
+        # Check that the file exists
+        assert (mod_json_path).exists()
+
+        # Get the contents of the file
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+        mod_json = mod_json_obj.get_modules_json()
+
+        mods = ["fastqc", "multiqc"]
+        for mod in mods:
+            assert mod in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]
+            assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"][mod]
+            assert "branch" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"][mod]
+
+    def _modify_main_nf(self, path):
+        """Modify a file to test patch creation"""
+        with open(path) as fh:
+            lines = fh.readlines()
+        # Modify $meta.id to $meta.single_end
+        lines[1] = '    tag "$meta.single_end"\n'
+        with open(path, "w") as fh:
+            fh.writelines(lines)
+
+    def test_mod_json_create_with_patch(self):
+        """Test creating a modules.json file from scratch when there are patched modules"""
+        mod_json_path = Path(self.pipeline_dir, "modules.json")
+
+        # Modify the module
+        module_path = Path(self.pipeline_dir, "modules", "nf-core", "fastqc")
+        self._modify_main_nf(module_path / "main.nf")
+
+        # Try creating a patch file
+        patch_obj = ModulePatch(self.pipeline_dir, NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_DEFAULT_BRANCH)
+        patch_obj.patch("fastqc")
+
+        # Remove the existing modules.json file
+        mod_json_path.unlink()
+
+        # Create the new modules.json file
+        ModulesJson(self.pipeline_dir).create()
+
+        # Check that the file exists
+        assert mod_json_path.is_file()
+
+        # Get the contents of the file
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+        mod_json = mod_json_obj.get_modules_json()
+
+        # Check that fastqc is in the file
+        assert "fastqc" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]
+        assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["fastqc"]
+        assert "branch" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["fastqc"]
+
+        # Check that fastqc/main.nf maintains the changes
+        with open(module_path / "main.nf") as fh:
+            lines = fh.readlines()
+        assert lines[1] == '    tag "$meta.single_end"\n'
+
+    def test_mod_json_up_to_date(self):
+        """
+        Checks if the modules.json file is up to date
+        when no changes have been made to the pipeline
+        """
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+        mod_json_before = mod_json_obj.get_modules_json()
+        mod_json_obj.check_up_to_date()
+        mod_json_after = mod_json_obj.get_modules_json()
+
+        # Check that the modules.json hasn't changed
+        assert mod_json_before == mod_json_after
+
+    def test_mod_json_up_to_date_module_removed(self):
+        """
+        Reinstall a module that has an entry in the modules.json
+        but is missing in the pipeline
+        """
+        # Remove the fastqc module
+        fastqc_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "fastqc")
+        shutil.rmtree(fastqc_path)
+
+        # Check that the modules.json file is up to date, and reinstall the module
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+        mod_json_obj.check_up_to_date()
+
+        # Check that the module has been reinstalled
+        files = ["main.nf", "meta.yml"]
+        assert fastqc_path.exists()
+        for f in files:
+            assert Path(fastqc_path, f).exists()
+
+    def test_mod_json_up_to_date_reinstall_fails(self):
+        """
+        Try reinstalling a module where the git_sha is invalid
+        """
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+
+        # Update the fastqc module entry to an invalid git_sha
+        mod_json_obj.update("modules", ModulesRepo(), "fastqc", "INVALID_GIT_SHA", "modules", write_file=True)
+
+        # Remove the fastqc module
+        fastqc_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "fastqc")
+        shutil.rmtree(fastqc_path)
+
+        # Check that the modules.json file is up to date, and remove the fastqc module entry
+        mod_json_obj.check_up_to_date()
+        mod_json = mod_json_obj.get_modules_json()
+
+        # Check that the module has been removed from the modules.json
+        assert "fastqc" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]
+
+    def test_mod_json_repo_present(self):
+        """Tests the repo_present function"""
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+
+        assert mod_json_obj.repo_present(NF_CORE_MODULES_REMOTE) is True
+        assert mod_json_obj.repo_present("INVALID_REPO") is False
+
+    def test_mod_json_module_present(self):
+        """Tests the module_present function"""
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+
+        assert mod_json_obj.module_present("fastqc", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) is True
+        assert mod_json_obj.module_present("INVALID_MODULE", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) is False
+        assert mod_json_obj.module_present("fastqc", "INVALID_REPO", "INVALID_DIR") is False
+        assert mod_json_obj.module_present("INVALID_MODULE", "INVALID_REPO", "INVALID_DIR") is False
+
+    def test_mod_json_get_module_version(self):
+        """Test the get_module_version function"""
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+        mod_json = mod_json_obj.get_modules_json()
+        assert (
+            mod_json_obj.get_module_version("fastqc", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME)
+            == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["fastqc"]["git_sha"]
+        )
+        assert mod_json_obj.get_module_version("INVALID_MODULE", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) is None
+
+    def test_mod_json_dump(self):
+        """Tests the dump function"""
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+        mod_json = mod_json_obj.get_modules_json()
+        # Remove the modules.json file
+        mod_json_path = Path(self.pipeline_dir, "modules.json")
+        mod_json_path.unlink()
+
+        # Check that the dump function creates the file
+        mod_json_obj.dump()
+        assert mod_json_path.exists()
+
+        # Check that the dump function writes the correct content
+        with open(mod_json_path) as f:
+            try:
+                mod_json_new = json.load(f)
+            except json.JSONDecodeError as e:
+                raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}")
+        assert mod_json == mod_json_new
+
+    def test_mod_json_with_empty_modules_value(self):
+        # Load module.json and remove the modules entry
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+        mod_json_obj.create()  # Create modules.json explicitly to get correct module sha
+        mod_json_orig = mod_json_obj.get_modules_json()
+        mod_json = copy.deepcopy(mod_json_orig)
+        mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"] = ""
+        # save the altered module.json and load it again to check if it will fix itself
+        mod_json_obj.modules_json = mod_json
+        mod_json_obj.dump()
+        mod_json_obj_new = ModulesJson(self.pipeline_dir)
+        mod_json_obj_new.check_up_to_date()
+        mod_json_new = mod_json_obj_new.get_modules_json()
+        assert mod_json_orig == mod_json_new
+
+    def test_mod_json_with_missing_modules_entry(self):
+        # Load module.json and remove the modules entry
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+        mod_json_obj.create()  # Create modules.json explicitly to get correct module sha
+        mod_json_orig = mod_json_obj.get_modules_json()
+        mod_json = copy.deepcopy(mod_json_orig)
+        mod_json["repos"][NF_CORE_MODULES_REMOTE].pop("modules")
+        # save the altered module.json and load it again to check if it will fix itself
+        mod_json_obj.modules_json = mod_json
+        mod_json_obj.dump()
+        mod_json_obj_new = ModulesJson(self.pipeline_dir)
+        mod_json_obj_new.check_up_to_date()
+        mod_json_new = mod_json_obj_new.get_modules_json()
+        assert mod_json_orig == mod_json_new
diff --git a/tests/modules/test_patch.py b/tests/modules/test_patch.py
new file mode 100644
index 0000000000..230bb1ce8f
--- /dev/null
+++ b/tests/modules/test_patch.py
@@ -0,0 +1,365 @@
+import os
+import tempfile
+from pathlib import Path
+from unittest import mock
+
+import pytest
+
+import nf_core.components.components_command
+import nf_core.modules
+
+from ..test_modules import TestModules
+from ..utils import GITLAB_URL
+
+"""
+Test the 'nf-core modules patch' command
+
+Uses a branch (patch-tester) in the GitLab nf-core/modules-test repo when
+testing if the update commands works correctly with patch files
+"""
+
+ORG_SHA = "002623ccc88a3b0cb302c7d8f13792a95354d9f2"
+CORRECT_SHA = "1dff30bfca2d98eb7ac7b09269a15e822451d99f"
+SUCCEED_SHA = "ba15c20c032c549d77c5773659f19c2927daf48e"
+FAIL_SHA = "67b642d4471c4005220a342cad3818d5ba2b5a73"
+BISMARK_ALIGN = "bismark/align"
+REPO_NAME = "nf-core-test"
+PATCH_BRANCH = "patch-tester"
+REPO_URL = "https://gitlab.com/nf-core/modules-test.git"
+
+
+def setup_patch(pipeline_dir, modify_module):
+    install_obj = nf_core.modules.ModuleInstall(
+        pipeline_dir, prompt=False, force=False, remote_url=GITLAB_URL, branch=PATCH_BRANCH, sha=ORG_SHA
+    )
+
+    # Install the module
+    install_obj.install(BISMARK_ALIGN)
+
+    if modify_module:
+        # Modify the module
+        module_path = Path(pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
+        modify_main_nf(module_path / "main.nf")
+
+
+def modify_main_nf(path):
+    """Modify a file to test patch creation"""
+    with open(path) as fh:
+        lines = fh.readlines()
+    # We want a patch file that looks something like:
+    # -    tuple val(meta), path(reads)
+    # -    path index
+    # +    tuple val(meta), path(reads), path(index)
+    for line_index in range(len(lines)):
+        if lines[line_index] == "    tuple val(meta), path(reads)\n":
+            lines[line_index] = "    tuple val(meta), path(reads), path(index)\n"
+        elif lines[line_index] == "    path index\n":
+            to_pop = line_index
+    lines.pop(to_pop)
+    with open(path, "w") as fh:
+        fh.writelines(lines)
+
+
+class TestModulesCreate(TestModules):
+    def test_create_patch_no_change(self):
+        """Test creating a patch when there is no change to the module"""
+        setup_patch(self.pipeline_dir, False)
+
+        # Try creating a patch file
+        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        with pytest.raises(UserWarning):
+            patch_obj.patch(BISMARK_ALIGN)
+
+        module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
+
+        # Check that no patch file has been added to the directory
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml"}
+
+        # Check the 'modules.json' contains no patch file for the module
+        modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
+        assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) is None
+
+    def test_create_patch_change(self):
+        """Test creating a patch when there is a change to the module"""
+        setup_patch(self.pipeline_dir, True)
+
+        # Try creating a patch file
+        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj.patch(BISMARK_ALIGN)
+
+        module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
+
+        patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
+        # Check that a patch file with the correct name has been created
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+
+        # Check the 'modules.json' contains a patch file for the module
+        modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
+        assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path(
+            "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
+        )
+
+        # Check that the correct lines are in the patch file
+        with open(module_path / patch_fn) as fh:
+            patch_lines = fh.readlines()
+        module_relpath = module_path.relative_to(self.pipeline_dir)
+        assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines, module_relpath / "main.nf"
+        assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines
+        assert "-    tuple val(meta), path(reads)\n" in patch_lines
+        assert "-    path index\n" in patch_lines
+        assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
+
+    def test_create_patch_try_apply_successful(self):
+        """
+        Test creating a patch file and applying it to a new version of the the files
+        """
+
+        setup_patch(self.pipeline_dir, True)
+        module_relpath = Path("modules", REPO_NAME, BISMARK_ALIGN)
+        module_path = Path(self.pipeline_dir, module_relpath)
+
+        # Try creating a patch file
+        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj.patch(BISMARK_ALIGN)
+
+        patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
+        # Check that a patch file with the correct name has been created
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+
+        # Check the 'modules.json' contains a patch file for the module
+        modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
+        assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path(
+            "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
+        )
+
+        update_obj = nf_core.modules.ModuleUpdate(
+            self.pipeline_dir, sha=SUCCEED_SHA, remote_url=GITLAB_URL, branch=PATCH_BRANCH
+        )
+        # Install the new files
+        install_dir = Path(tempfile.mkdtemp())
+        update_obj.install_component_files(BISMARK_ALIGN, SUCCEED_SHA, update_obj.modules_repo, install_dir)
+
+        # Try applying the patch
+        module_install_dir = install_dir / BISMARK_ALIGN
+        patch_relpath = module_relpath / patch_fn
+        assert (
+            update_obj.try_apply_patch(BISMARK_ALIGN, REPO_NAME, patch_relpath, module_path, module_install_dir) is True
+        )
+
+        # Move the files from the temporary directory
+        update_obj.move_files_from_tmp_dir(BISMARK_ALIGN, install_dir, REPO_NAME, SUCCEED_SHA)
+
+        # Check that a patch file with the correct name has been created
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+
+        # Check the 'modules.json' contains a patch file for the module
+        modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
+        assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path(
+            "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
+        )
+
+        # Check that the correct lines are in the patch file
+        with open(module_path / patch_fn) as fh:
+            patch_lines = fh.readlines()
+        module_relpath = module_path.relative_to(self.pipeline_dir)
+        assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines
+        assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines
+        assert "-    tuple val(meta), path(reads)\n" in patch_lines
+        assert "-    path index\n" in patch_lines
+        assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
+
+        # Check that 'main.nf' is updated correctly
+        with open(module_path / "main.nf") as fh:
+            main_nf_lines = fh.readlines()
+        # These lines should have been removed by the patch
+        assert "    tuple val(meta), path(reads)\n" not in main_nf_lines
+        assert "    path index\n" not in main_nf_lines
+        # This line should have been added
+        assert "    tuple val(meta), path(reads), path(index)\n" in main_nf_lines
+
+    def test_create_patch_try_apply_failed(self):
+        """
+        Test creating a patch file and applying it to a new version of the the files
+        """
+
+        setup_patch(self.pipeline_dir, True)
+        module_relpath = Path("modules", REPO_NAME, BISMARK_ALIGN)
+        module_path = Path(self.pipeline_dir, module_relpath)
+
+        # Try creating a patch file
+        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj.patch(BISMARK_ALIGN)
+
+        patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
+        # Check that a patch file with the correct name has been created
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+
+        # Check the 'modules.json' contains a patch file for the module
+        modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
+        assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path(
+            "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
+        )
+
+        update_obj = nf_core.modules.ModuleUpdate(
+            self.pipeline_dir, sha=FAIL_SHA, remote_url=GITLAB_URL, branch=PATCH_BRANCH
+        )
+        # Install the new files
+        install_dir = Path(tempfile.mkdtemp())
+        update_obj.install_component_files(BISMARK_ALIGN, FAIL_SHA, update_obj.modules_repo, install_dir)
+
+        # Try applying the patch
+        module_install_dir = install_dir / BISMARK_ALIGN
+        patch_path = module_relpath / patch_fn
+        assert (
+            update_obj.try_apply_patch(BISMARK_ALIGN, REPO_NAME, patch_path, module_path, module_install_dir) is False
+        )
+
+    def test_create_patch_update_success(self):
+        """
+        Test creating a patch file and the updating the module
+
+        Should have the same effect as 'test_create_patch_try_apply_successful'
+        but uses higher level api
+        """
+
+        setup_patch(self.pipeline_dir, True)
+        module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
+
+        # Try creating a patch file
+        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj.patch(BISMARK_ALIGN)
+
+        patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
+        # Check that a patch file with the correct name has been created
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+
+        # Check the 'modules.json' contains a patch file for the module
+        modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
+        assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, GITLAB_URL, REPO_NAME) == Path(
+            "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
+        )
+
+        # Update the module
+        update_obj = nf_core.modules.ModuleUpdate(
+            self.pipeline_dir,
+            sha=SUCCEED_SHA,
+            show_diff=False,
+            update_deps=True,
+            remote_url=GITLAB_URL,
+            branch=PATCH_BRANCH,
+        )
+        assert update_obj.update(BISMARK_ALIGN)
+
+        # Check that a patch file with the correct name has been created
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+
+        # Check the 'modules.json' contains a patch file for the module
+        modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
+        assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, GITLAB_URL, REPO_NAME) == Path(
+            "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
+        ), modules_json_obj.get_patch_fn(BISMARK_ALIGN, GITLAB_URL, REPO_NAME)
+
+        # Check that the correct lines are in the patch file
+        with open(module_path / patch_fn) as fh:
+            patch_lines = fh.readlines()
+        module_relpath = module_path.relative_to(self.pipeline_dir)
+        assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines
+        assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines
+        assert "-    tuple val(meta), path(reads)\n" in patch_lines
+        assert "-    path index\n" in patch_lines
+        assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
+
+        # Check that 'main.nf' is updated correctly
+        with open(module_path / "main.nf") as fh:
+            main_nf_lines = fh.readlines()
+        # These lines should have been removed by the patch
+        assert "    tuple val(meta), path(reads)\n" not in main_nf_lines
+        assert "    path index\n" not in main_nf_lines
+        # This line should have been added
+        assert "    tuple val(meta), path(reads), path(index)\n" in main_nf_lines
+
+    def test_create_patch_update_fail(self):
+        """
+        Test creating a patch file and updating a module when there is a diff conflict
+        """
+
+        setup_patch(self.pipeline_dir, True)
+        module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
+
+        # Try creating a patch file
+        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj.patch(BISMARK_ALIGN)
+
+        patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
+        # Check that a patch file with the correct name has been created
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+
+        # Check the 'modules.json' contains a patch file for the module
+        modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
+        assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path(
+            "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
+        )
+
+        # Save the file contents for downstream comparison
+        with open(module_path / patch_fn) as fh:
+            patch_contents = fh.read()
+
+        update_obj = nf_core.modules.ModuleUpdate(
+            self.pipeline_dir,
+            sha=FAIL_SHA,
+            show_diff=False,
+            update_deps=True,
+            remote_url=GITLAB_URL,
+            branch=PATCH_BRANCH,
+        )
+        update_obj.update(BISMARK_ALIGN)
+
+        # Check that the installed files have not been affected by the attempted patch
+        temp_dir = Path(tempfile.mkdtemp())
+        nf_core.components.components_command.ComponentCommand(
+            "modules", self.pipeline_dir, GITLAB_URL, PATCH_BRANCH
+        ).install_component_files(BISMARK_ALIGN, FAIL_SHA, update_obj.modules_repo, temp_dir)
+
+        temp_module_dir = temp_dir / BISMARK_ALIGN
+        for file in os.listdir(temp_module_dir):
+            assert file in os.listdir(module_path)
+            with open(module_path / file) as fh:
+                installed = fh.read()
+            with open(temp_module_dir / file) as fh:
+                shouldbe = fh.read()
+            assert installed == shouldbe
+
+        # Check that the patch file is unaffected
+        with open(module_path / patch_fn) as fh:
+            new_patch_contents = fh.read()
+        assert patch_contents == new_patch_contents
+
+    def test_remove_patch(self):
+        """Test creating a patch when there is no change to the module"""
+        setup_patch(self.pipeline_dir, True)
+
+        # Try creating a patch file
+        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj.patch(BISMARK_ALIGN)
+
+        module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
+
+        # Check that a patch file with the correct name has been created
+        patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+
+        # Check the 'modules.json' contains a patch file for the module
+        modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
+        assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path(
+            "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
+        )
+
+        with mock.patch.object(nf_core.components.patch.questionary, "confirm") as mock_questionary:
+            mock_questionary.unsafe_ask.return_value = True
+            patch_obj.remove(BISMARK_ALIGN)
+        # Check that the diff file has been removed
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml"}
+
+        # Check that the 'modules.json' entry has been removed
+        modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
+        assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) is None
diff --git a/tests/modules/test_remove.py b/tests/modules/test_remove.py
new file mode 100644
index 0000000000..a80c8b0986
--- /dev/null
+++ b/tests/modules/test_remove.py
@@ -0,0 +1,26 @@
+import os
+from pathlib import Path
+
+from ..test_modules import TestModules
+
+
+class TestModulesRemove(TestModules):
+    def test_modules_remove_trimgalore(self):
+        """Test removing TrimGalore! module after installing it"""
+        self.mods_install.install("trimgalore")
+        assert self.mods_install.dir is not None
+        module_path = Path(self.mods_install.dir, "modules", "nf-core", "modules", "trimgalore")
+        assert self.mods_remove.remove("trimgalore")
+        assert os.path.exists(module_path) is False
+
+    def test_modules_remove_trimgalore_uninstalled(self):
+        """Test removing TrimGalore! module without installing it"""
+        assert self.mods_remove.remove("trimgalore") is False
+
+    def test_modules_remove_multiqc_from_gitlab(self):
+        """Test removing multiqc module after installing it from an alternative source"""
+        self.mods_install_gitlab.install("multiqc")
+        assert self.mods_install.dir is not None
+        module_path = Path(self.mods_install_gitlab.dir, "modules", "nf-core-test", "multiqc")
+        assert self.mods_remove_gitlab.remove("multiqc", force=True)
+        assert os.path.exists(module_path) is False
diff --git a/tests/modules/test_update.py b/tests/modules/test_update.py
new file mode 100644
index 0000000000..a33aac3775
--- /dev/null
+++ b/tests/modules/test_update.py
@@ -0,0 +1,435 @@
+import logging
+import shutil
+import tempfile
+from pathlib import Path
+from unittest import mock
+
+import questionary
+import yaml
+
+import nf_core.utils
+from nf_core.modules.install import ModuleInstall
+from nf_core.modules.modules_json import ModulesJson
+from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
+from nf_core.modules.patch import ModulePatch
+from nf_core.modules.update import ModuleUpdate
+
+from ..test_modules import TestModules
+from ..utils import (
+    GITLAB_BRANCH_TEST_BRANCH,
+    GITLAB_BRANCH_TEST_NEW_SHA,
+    GITLAB_BRANCH_TEST_OLD_SHA,
+    GITLAB_DEFAULT_BRANCH,
+    GITLAB_REPO,
+    GITLAB_URL,
+    OLD_TRIMGALORE_BRANCH,
+    OLD_TRIMGALORE_SHA,
+    cmp_component,
+)
+
+
+class TestModulesInstall(TestModules):
+    def test_install_and_update(self):
+        """Installs a module in the pipeline and updates it (no change)"""
+        self.mods_install.install("trimgalore")
+        update_obj = ModuleUpdate(self.pipeline_dir, show_diff=False)
+
+        # Copy the module files and check that they are unaffected by the update
+        tmpdir = Path(tempfile.TemporaryDirectory().name)
+        trimgalore_tmpdir = tmpdir / "trimgalore"
+        trimgalore_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "trimgalore")
+        shutil.copytree(trimgalore_path, trimgalore_tmpdir)
+
+        assert update_obj.update("trimgalore") is True
+        assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True
+
+    def test_install_at_hash_and_update(self):
+        """Installs an old version of a module in the pipeline and updates it"""
+        assert self.mods_install_old.install("trimgalore")
+        update_obj = ModuleUpdate(
+            self.pipeline_dir, show_diff=False, update_deps=True, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH
+        )
+
+        # Copy the module files and check that they are affected by the update
+        tmpdir = Path(tempfile.TemporaryDirectory().name)
+        trimgalore_tmpdir = tmpdir / "trimgalore"
+        trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
+        shutil.copytree(trimgalore_path, trimgalore_tmpdir)
+
+        assert update_obj.update("trimgalore") is True
+        assert cmp_component(trimgalore_tmpdir, trimgalore_path) is False
+
+        # Check that the modules.json is correctly updated
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+        mod_json = mod_json_obj.get_modules_json()
+        # Get the up-to-date git_sha for the module from the ModulesRepo object
+        correct_git_sha = update_obj.modules_repo.get_latest_component_version("trimgalore", "modules")
+        current_git_sha = mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"]
+        assert correct_git_sha == current_git_sha
+
+    # Mock questionary answer: do not update module, only show diffs
+    @mock.patch.object(questionary.Question, "unsafe_ask", return_value=True)
+    def test_install_at_hash_and_update_limit_output(self, mock_prompt):
+        """Installs an old version of a module in the pipeline and updates it with limited output reporting"""
+        self.caplog.set_level(logging.INFO)
+        assert self.mods_install_old.install("trimgalore")
+
+        update_obj = ModuleUpdate(
+            self.pipeline_dir,
+            show_diff=True,
+            update_deps=True,
+            remote_url=GITLAB_URL,
+            branch=OLD_TRIMGALORE_BRANCH,
+            limit_output=True,
+        )
+        assert update_obj.update("trimgalore")
+
+        # Check changes not shown for non-.nf files
+        assert "Changes in 'trimgalore/meta.yml' but not shown" in self.caplog.text
+        # Check changes shown for .nf files
+        assert "Changes in 'trimgalore/main.nf'" in self.caplog.text
+        for line in self.caplog.text.split("\n"):
+            if line.startswith("---"):
+                assert line.endswith("main.nf")
+
+    def test_install_at_hash_and_update_and_save_diff_to_file(self):
+        """Installs an old version of a module in the pipeline and updates it"""
+        self.mods_install_old.install("trimgalore")
+        patch_path = Path(self.pipeline_dir, "trimgalore.patch")
+        update_obj = ModuleUpdate(
+            self.pipeline_dir,
+            save_diff_fn=patch_path,
+            sha=OLD_TRIMGALORE_SHA,
+            remote_url=GITLAB_URL,
+            branch=OLD_TRIMGALORE_BRANCH,
+        )
+
+        # Copy the module files and check that they are affected by the update
+        tmpdir = Path(tempfile.TemporaryDirectory().name)
+        trimgalore_tmpdir = tmpdir / "trimgalore"
+        trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
+        shutil.copytree(trimgalore_path, trimgalore_tmpdir)
+
+        assert update_obj.update("trimgalore") is True
+        assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True
+
+        # TODO: Apply the patch to the module
+
+    def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self):
+        """Installs an old version of a module in the pipeline and updates it"""
+        # Install old version of trimgalore
+        self.mods_install_old.install("trimgalore")
+        patch_path = Path(self.pipeline_dir, "trimgalore.patch")
+        # Update saving the differences to a patch file and with `limit_output`
+        update_obj = ModuleUpdate(
+            self.pipeline_dir,
+            save_diff_fn=patch_path,
+            remote_url=GITLAB_URL,
+            branch=OLD_TRIMGALORE_BRANCH,
+            limit_output=True,
+        )
+        assert update_obj.update("trimgalore")
+
+        # Check that the patch file was created
+        assert patch_path.exists(), f"Patch file was not created at {patch_path}"
+
+        # Read the contents of the patch file
+        with open(patch_path) as fh:
+            patch_content = fh.read()
+            # Check changes not shown for non-.nf files
+            assert "Changes in 'trimgalore/meta.yml' but not shown" in patch_content
+            # Check changes only shown for main.nf
+            assert "Changes in 'trimgalore/main.nf'" in patch_content
+            for line in patch_content:
+                if line.startswith("---"):
+                    assert line.endswith("main.nf")
+
+    def test_update_all(self):
+        """Updates all modules present in the pipeline"""
+        update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=False)
+        # Get the current modules.json
+        assert update_obj.update() is True
+
+        # We must reload the modules.json to get the updated version
+        mod_json_obj = ModulesJson(self.pipeline_dir)
+        mod_json = mod_json_obj.get_modules_json()
+        # Loop through all modules and check that they are updated (according to the modules.json file)
+        for mod in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]:
+            correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"]
+            current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
+            assert correct_git_sha == current_git_sha
+
+    def test_update_with_config_fixed_version(self):
+        """Try updating when there are entries in the .nf-core.yml"""
+        # Install trimgalore at the latest version
+        assert self.mods_install_trimgalore.install("trimgalore")
+
+        # Fix the trimgalore version in the .nf-core.yml to an old version
+        update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": OLD_TRIMGALORE_SHA}}}
+        config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
+        tools_config["update"] = update_config
+        with open(Path(self.pipeline_dir, config_fn), "w") as f:
+            yaml.dump(tools_config, f)
+
+        # Update all modules in the pipeline
+        update_obj = ModuleUpdate(
+            self.pipeline_dir, update_all=True, show_diff=False, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH
+        )
+        assert update_obj.update() is True
+
+        # Check that the git sha for trimgalore is correctly downgraded
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        assert "trimgalore" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]
+        assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]
+        assert mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] == OLD_TRIMGALORE_SHA
+
+    def test_update_with_config_dont_update(self):
+        """Try updating when module is to be ignored"""
+        # Install an old version of trimgalore
+        self.mods_install_old.install("trimgalore")
+
+        # Set the trimgalore field to no update in the .nf-core.yml
+        update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": False}}}
+        config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
+        tools_config["update"] = update_config
+        with open(Path(self.pipeline_dir, config_fn), "w") as f:
+            yaml.dump(tools_config, f)
+
+        # Update all modules in the pipeline
+        update_obj = ModuleUpdate(
+            self.pipeline_dir,
+            update_all=True,
+            show_diff=False,
+            sha=OLD_TRIMGALORE_SHA,
+            remote_url=GITLAB_URL,
+            branch=OLD_TRIMGALORE_BRANCH,
+        )
+        assert update_obj.update() is True
+
+        # Check that the git sha for trimgalore is correctly downgraded
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        assert "trimgalore" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]
+        assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]
+        assert mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] == OLD_TRIMGALORE_SHA
+
+    def test_update_with_config_fix_all(self):
+        """Fix the version of all nf-core modules"""
+        self.mods_install_trimgalore.install("trimgalore")
+
+        # Fix the version of all nf-core modules in the .nf-core.yml to an old version
+        update_config = {GITLAB_URL: OLD_TRIMGALORE_SHA}
+        config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
+        tools_config["update"] = update_config
+        with open(Path(self.pipeline_dir, config_fn), "w") as f:
+            yaml.dump(tools_config, f)
+
+        # Update all modules in the pipeline
+        update_obj = ModuleUpdate(
+            self.pipeline_dir, update_all=True, show_diff=False, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH
+        )
+        assert update_obj.update() is True
+
+        # Check that the git sha for trimgalore is correctly downgraded
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]
+        assert mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] == OLD_TRIMGALORE_SHA
+
+    def test_update_with_config_no_updates(self):
+        """Don't update any nf-core modules"""
+        assert self.mods_install_old.install("trimgalore")
+        old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+
+        # Fix the version of all nf-core modules in the .nf-core.yml to an old version
+        update_config = {GITLAB_URL: False}
+        config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
+        tools_config["update"] = update_config
+        with open(Path(self.pipeline_dir, config_fn), "w") as f:
+            yaml.dump(tools_config, f)
+
+        # Update all modules in the pipeline
+        update_obj = ModuleUpdate(
+            self.pipeline_dir,
+            update_all=True,
+            show_diff=False,
+            sha=OLD_TRIMGALORE_SHA,
+            remote_url=GITLAB_URL,
+            branch=OLD_TRIMGALORE_BRANCH,
+        )
+        assert update_obj.update() is True
+
+        # Check that the git sha for trimgalore is correctly downgraded and none of the modules has changed
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        for module in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]:
+            assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO][module]
+            assert (
+                mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO][module]["git_sha"]
+                == old_mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO][module]["git_sha"]
+            )
+
+    def test_update_different_branch_single_module(self):
+        """Try updating a module in a specific branch"""
+        install_obj = ModuleInstall(
+            self.pipeline_dir,
+            prompt=False,
+            force=False,
+            remote_url=GITLAB_URL,
+            branch=GITLAB_BRANCH_TEST_BRANCH,
+            sha=GITLAB_BRANCH_TEST_OLD_SHA,
+        )
+        assert install_obj.install("fastp")
+
+        update_obj = ModuleUpdate(
+            self.pipeline_dir,
+            update_deps=True,
+            remote_url=GITLAB_URL,
+            branch=GITLAB_BRANCH_TEST_BRANCH,
+            show_diff=False,
+        )
+        update_obj.update("fastp")
+
+        # Verify that the branch entry was updated correctly
+        modules_json = ModulesJson(self.pipeline_dir)
+        assert (
+            modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO)
+            == GITLAB_BRANCH_TEST_BRANCH
+        )
+        assert modules_json.get_module_version("fastp", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA
+
+    def test_update_different_branch_mixed_modules_main(self):
+        """Try updating all modules where MultiQC is installed from main branch"""
+        # Install fastp
+        assert self.mods_install_gitlab_old.install("fastp")
+
+        # Install MultiQC from gitlab default branch
+        assert self.mods_install_gitlab.install("multiqc")
+
+        # Try updating
+        update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=False)
+        assert update_obj.update() is True
+
+        modules_json = ModulesJson(self.pipeline_dir)
+        # Verify that the branch entry was updated correctly
+        assert (
+            modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO)
+            == GITLAB_BRANCH_TEST_BRANCH
+        )
+        assert modules_json.get_module_version("fastp", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA
+        # MultiQC is present in both branches but should've been updated using the 'main' branch
+        assert (
+            modules_json.get_component_branch(self.component_type, "multiqc", GITLAB_URL, GITLAB_REPO)
+            == GITLAB_DEFAULT_BRANCH
+        )
+
+    def test_update_different_branch_mix_modules_branch_test(self):
+        """Try updating all modules where MultiQC is installed from branch-test branch"""
+        # Install multiqc from the branch-test branch
+        assert self.mods_install_gitlab_old.install(
+            "multiqc"
+        )  # Force as the same module is installed from github nf-core modules repo
+        modules_json = ModulesJson(self.pipeline_dir)
+        update_obj = ModuleUpdate(
+            self.pipeline_dir,
+            update_all=True,
+            show_diff=False,
+            remote_url=GITLAB_URL,
+            branch=GITLAB_BRANCH_TEST_BRANCH,
+            sha=GITLAB_BRANCH_TEST_NEW_SHA,
+        )
+        assert update_obj.update()
+
+        assert (
+            modules_json.get_component_branch(self.component_type, "multiqc", GITLAB_URL, GITLAB_REPO)
+            == GITLAB_BRANCH_TEST_BRANCH
+        )
+        assert modules_json.get_module_version("multiqc", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA
+
+    # Mock questionary answer: do not update module, only show diffs
+    @mock.patch.object(questionary.Question, "unsafe_ask", return_value=False)
+    def test_update_only_show_differences(self, mock_prompt):
+        """Try updating all modules showing differences.
+        Only show diffs, don't actually save any updated files.
+        Check that the sha in modules.json is not changed."""
+
+        # Update modules to a fixed old SHA
+        update_old = ModuleUpdate(
+            self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+        )
+        update_old.update()
+
+        tmpdir = Path(tempfile.TemporaryDirectory().name)
+        shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir)
+
+        update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True)
+        assert ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True).update()
+
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        # Loop through all modules and check that they are NOT updated (according to the modules.json file)
+        # A module that can be updated but shouldn't is fastqc
+        # Module multiqc is already up to date so don't check
+        mod = "fastqc"
+        non_updated_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"]
+        current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
+        assert non_updated_git_sha != current_git_sha
+        assert cmp_component(Path(tmpdir, mod), Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, mod)) is True
+
+    # Mock questionary answer: do not update module, only show diffs
+    @mock.patch.object(questionary.Question, "unsafe_ask", return_value=False)
+    def test_update_only_show_differences_when_patch(self, mock_prompt):
+        """Try updating all modules showing differences when there's a patched module.
+        Don't update some of them.
+        Check that the sha in modules.json is not changed."""
+        modules_json = ModulesJson(self.pipeline_dir)
+        update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True)
+
+        # Update modules to a fixed old SHA
+        update_old = ModuleUpdate(
+            self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+        )
+        assert update_old.update()
+
+        # Modify fastqc module, it will have a patch which will be applied during update
+        # We modify fastqc because it's one of the modules that can be updated and there's another one before it (custom/dumpsoftwareversions)
+        module_path = Path(self.pipeline_dir, "modules", "nf-core", "fastqc")
+        main_path = Path(module_path, "main.nf")
+        with open(main_path) as fh:
+            lines = fh.readlines()
+        for line_index in range(len(lines)):
+            if lines[line_index] == "    label 'process_medium'\n":
+                lines[line_index] = "    label 'process_low'\n"
+                break
+        with open(main_path, "w") as fh:
+            fh.writelines(lines)
+        # Create a patch file
+        patch_obj = ModulePatch(self.pipeline_dir)
+        patch_obj.patch("fastqc")
+        # Check that a patch file with the correct name has been created
+        assert "fastqc.diff" in [f.name for f in module_path.glob("*.diff")]
+
+        # Update all modules
+        assert update_obj.update() is True
+
+        mod_json = modules_json.get_modules_json()
+        # Loop through all modules and check that they are NOT updated (according to the modules.json file)
+        # A module that can be updated but shouldn't is fastqc
+        # Module multiqc is already up to date so don't check
+        mod = "fastqc"
+        correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"]
+        current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
+        assert correct_git_sha != current_git_sha
+
+    def test_update_module_with_extra_config_file(self):
+        """Try updating a module with a config file"""
+        # Install the module
+        assert self.mods_install.install("trimgalore")
+        # Add a nextflow_test.config file to the module
+        trimgalore_path = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore")
+        Path(trimgalore_path, "nextflow_test.config").touch()
+        with open(Path(trimgalore_path, "nextflow_test.config"), "w") as fh:
+            fh.write("params.my_param = 'my_value'\n")
+        # Update the module
+        update_obj = ModuleUpdate(self.pipeline_dir, show_diff=False)
+        assert update_obj.update("trimgalore")
+        # Check that the nextflow_test.config file is still there
+        assert Path(trimgalore_path, "nextflow_test.config").exists()
+        with open(Path(trimgalore_path, "nextflow_test.config")) as fh:
+            assert "params.my_param = 'my_value'" in fh.read()
diff --git a/tests/modules/update.py b/tests/modules/update.py
deleted file mode 100644
index e02b058fbb..0000000000
--- a/tests/modules/update.py
+++ /dev/null
@@ -1,444 +0,0 @@
-import logging
-import shutil
-import tempfile
-from pathlib import Path
-from unittest import mock
-
-import questionary
-import yaml
-
-import nf_core.utils
-from nf_core.modules.install import ModuleInstall
-from nf_core.modules.modules_json import ModulesJson
-from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
-from nf_core.modules.patch import ModulePatch
-from nf_core.modules.update import ModuleUpdate
-
-from ..utils import (
-    GITLAB_BRANCH_TEST_BRANCH,
-    GITLAB_BRANCH_TEST_NEW_SHA,
-    GITLAB_BRANCH_TEST_OLD_SHA,
-    GITLAB_DEFAULT_BRANCH,
-    GITLAB_REPO,
-    GITLAB_URL,
-    OLD_TRIMGALORE_BRANCH,
-    OLD_TRIMGALORE_SHA,
-    cmp_component,
-)
-
-
-def test_install_and_update(self):
-    """Installs a module in the pipeline and updates it (no change)"""
-    self.mods_install.install("trimgalore")
-    update_obj = ModuleUpdate(self.pipeline_dir, show_diff=False)
-
-    # Copy the module files and check that they are unaffected by the update
-    tmpdir = Path(tempfile.TemporaryDirectory().name)
-    trimgalore_tmpdir = tmpdir / "trimgalore"
-    trimgalore_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "trimgalore")
-    shutil.copytree(trimgalore_path, trimgalore_tmpdir)
-
-    assert update_obj.update("trimgalore") is True
-    assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True
-
-
-def test_install_at_hash_and_update(self):
-    """Installs an old version of a module in the pipeline and updates it"""
-    assert self.mods_install_old.install("trimgalore")
-    update_obj = ModuleUpdate(
-        self.pipeline_dir, show_diff=False, update_deps=True, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH
-    )
-
-    # Copy the module files and check that they are affected by the update
-    tmpdir = Path(tempfile.TemporaryDirectory().name)
-    trimgalore_tmpdir = tmpdir / "trimgalore"
-    trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
-    shutil.copytree(trimgalore_path, trimgalore_tmpdir)
-
-    assert update_obj.update("trimgalore") is True
-    assert cmp_component(trimgalore_tmpdir, trimgalore_path) is False
-
-    # Check that the modules.json is correctly updated
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    mod_json = mod_json_obj.get_modules_json()
-    # Get the up-to-date git_sha for the module from the ModulesRepo object
-    correct_git_sha = update_obj.modules_repo.get_latest_component_version("trimgalore", "modules")
-    current_git_sha = mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"]
-    assert correct_git_sha == current_git_sha
-
-
-# Mock questionary answer: do not update module, only show diffs
-@mock.patch.object(questionary.Question, "unsafe_ask", return_value=True)
-def test_install_at_hash_and_update_limit_output(self, mock_prompt):
-    """Installs an old version of a module in the pipeline and updates it with limited output reporting"""
-    self.caplog.set_level(logging.INFO)
-    assert self.mods_install_old.install("trimgalore")
-
-    update_obj = ModuleUpdate(
-        self.pipeline_dir,
-        show_diff=True,
-        update_deps=True,
-        remote_url=GITLAB_URL,
-        branch=OLD_TRIMGALORE_BRANCH,
-        limit_output=True,
-    )
-    assert update_obj.update("trimgalore")
-
-    # Check changes not shown for non-.nf files
-    assert "Changes in 'trimgalore/meta.yml' but not shown" in self.caplog.text
-    # Check changes shown for .nf files
-    assert "Changes in 'trimgalore/main.nf'" in self.caplog.text
-    for line in self.caplog.text.split("\n"):
-        if line.startswith("---"):
-            assert line.endswith("main.nf")
-
-
-def test_install_at_hash_and_update_and_save_diff_to_file(self):
-    """Installs an old version of a module in the pipeline and updates it"""
-    self.mods_install_old.install("trimgalore")
-    patch_path = Path(self.pipeline_dir, "trimgalore.patch")
-    update_obj = ModuleUpdate(
-        self.pipeline_dir,
-        save_diff_fn=patch_path,
-        sha=OLD_TRIMGALORE_SHA,
-        remote_url=GITLAB_URL,
-        branch=OLD_TRIMGALORE_BRANCH,
-    )
-
-    # Copy the module files and check that they are affected by the update
-    tmpdir = Path(tempfile.TemporaryDirectory().name)
-    trimgalore_tmpdir = tmpdir / "trimgalore"
-    trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore")
-    shutil.copytree(trimgalore_path, trimgalore_tmpdir)
-
-    assert update_obj.update("trimgalore") is True
-    assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True
-
-    # TODO: Apply the patch to the module
-
-
-def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self):
-    """Installs an old version of a module in the pipeline and updates it"""
-    # Install old version of trimgalore
-    self.mods_install_old.install("trimgalore")
-    patch_path = Path(self.pipeline_dir, "trimgalore.patch")
-    # Update saving the differences to a patch file and with `limit_output`
-    update_obj = ModuleUpdate(
-        self.pipeline_dir,
-        save_diff_fn=patch_path,
-        remote_url=GITLAB_URL,
-        branch=OLD_TRIMGALORE_BRANCH,
-        limit_output=True,
-    )
-    assert update_obj.update("trimgalore")
-
-    # Check that the patch file was created
-    assert patch_path.exists(), f"Patch file was not created at {patch_path}"
-
-    # Read the contents of the patch file
-    with open(patch_path) as fh:
-        patch_content = fh.read()
-        # Check changes not shown for non-.nf files
-        assert "Changes in 'trimgalore/meta.yml' but not shown" in patch_content
-        # Check changes only shown for main.nf
-        assert "Changes in 'trimgalore/main.nf'" in patch_content
-        for line in patch_content:
-            if line.startswith("---"):
-                assert line.endswith("main.nf")
-
-
-def test_update_all(self):
-    """Updates all modules present in the pipeline"""
-    update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=False)
-    # Get the current modules.json
-    assert update_obj.update() is True
-
-    # We must reload the modules.json to get the updated version
-    mod_json_obj = ModulesJson(self.pipeline_dir)
-    mod_json = mod_json_obj.get_modules_json()
-    # Loop through all modules and check that they are updated (according to the modules.json file)
-    for mod in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]:
-        correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"]
-        current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
-        assert correct_git_sha == current_git_sha
-
-
-def test_update_with_config_fixed_version(self):
-    """Try updating when there are entries in the .nf-core.yml"""
-    # Install trimgalore at the latest version
-    assert self.mods_install_trimgalore.install("trimgalore")
-
-    # Fix the trimgalore version in the .nf-core.yml to an old version
-    update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": OLD_TRIMGALORE_SHA}}}
-    config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-    tools_config["update"] = update_config
-    with open(Path(self.pipeline_dir, config_fn), "w") as f:
-        yaml.dump(tools_config, f)
-
-    # Update all modules in the pipeline
-    update_obj = ModuleUpdate(
-        self.pipeline_dir, update_all=True, show_diff=False, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH
-    )
-    assert update_obj.update() is True
-
-    # Check that the git sha for trimgalore is correctly downgraded
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    assert "trimgalore" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]
-    assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]
-    assert mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] == OLD_TRIMGALORE_SHA
-
-
-def test_update_with_config_dont_update(self):
-    """Try updating when module is to be ignored"""
-    # Install an old version of trimgalore
-    self.mods_install_old.install("trimgalore")
-
-    # Set the trimgalore field to no update in the .nf-core.yml
-    update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": False}}}
-    config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-    tools_config["update"] = update_config
-    with open(Path(self.pipeline_dir, config_fn), "w") as f:
-        yaml.dump(tools_config, f)
-
-    # Update all modules in the pipeline
-    update_obj = ModuleUpdate(
-        self.pipeline_dir,
-        update_all=True,
-        show_diff=False,
-        sha=OLD_TRIMGALORE_SHA,
-        remote_url=GITLAB_URL,
-        branch=OLD_TRIMGALORE_BRANCH,
-    )
-    assert update_obj.update() is True
-
-    # Check that the git sha for trimgalore is correctly downgraded
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    assert "trimgalore" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]
-    assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]
-    assert mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] == OLD_TRIMGALORE_SHA
-
-
-def test_update_with_config_fix_all(self):
-    """Fix the version of all nf-core modules"""
-    self.mods_install_trimgalore.install("trimgalore")
-
-    # Fix the version of all nf-core modules in the .nf-core.yml to an old version
-    update_config = {GITLAB_URL: OLD_TRIMGALORE_SHA}
-    config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-    tools_config["update"] = update_config
-    with open(Path(self.pipeline_dir, config_fn), "w") as f:
-        yaml.dump(tools_config, f)
-
-    # Update all modules in the pipeline
-    update_obj = ModuleUpdate(
-        self.pipeline_dir, update_all=True, show_diff=False, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH
-    )
-    assert update_obj.update() is True
-
-    # Check that the git sha for trimgalore is correctly downgraded
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]
-    assert mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] == OLD_TRIMGALORE_SHA
-
-
-def test_update_with_config_no_updates(self):
-    """Don't update any nf-core modules"""
-    assert self.mods_install_old.install("trimgalore")
-    old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-
-    # Fix the version of all nf-core modules in the .nf-core.yml to an old version
-    update_config = {GITLAB_URL: False}
-    config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-    tools_config["update"] = update_config
-    with open(Path(self.pipeline_dir, config_fn), "w") as f:
-        yaml.dump(tools_config, f)
-
-    # Update all modules in the pipeline
-    update_obj = ModuleUpdate(
-        self.pipeline_dir,
-        update_all=True,
-        show_diff=False,
-        sha=OLD_TRIMGALORE_SHA,
-        remote_url=GITLAB_URL,
-        branch=OLD_TRIMGALORE_BRANCH,
-    )
-    assert update_obj.update() is True
-
-    # Check that the git sha for trimgalore is correctly downgraded and none of the modules has changed
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    for module in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]:
-        assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO][module]
-        assert (
-            mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO][module]["git_sha"]
-            == old_mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO][module]["git_sha"]
-        )
-
-
-def test_update_different_branch_single_module(self):
-    """Try updating a module in a specific branch"""
-    install_obj = ModuleInstall(
-        self.pipeline_dir,
-        prompt=False,
-        force=False,
-        remote_url=GITLAB_URL,
-        branch=GITLAB_BRANCH_TEST_BRANCH,
-        sha=GITLAB_BRANCH_TEST_OLD_SHA,
-    )
-    assert install_obj.install("fastp")
-
-    update_obj = ModuleUpdate(
-        self.pipeline_dir, update_deps=True, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH, show_diff=False
-    )
-    update_obj.update("fastp")
-
-    # Verify that the branch entry was updated correctly
-    modules_json = ModulesJson(self.pipeline_dir)
-    assert (
-        modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO)
-        == GITLAB_BRANCH_TEST_BRANCH
-    )
-    assert modules_json.get_module_version("fastp", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA
-
-
-def test_update_different_branch_mixed_modules_main(self):
-    """Try updating all modules where MultiQC is installed from main branch"""
-    # Install fastp
-    assert self.mods_install_gitlab_old.install("fastp")
-
-    # Install MultiQC from gitlab default branch
-    assert self.mods_install_gitlab.install("multiqc")
-
-    # Try updating
-    update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=False)
-    assert update_obj.update() is True
-
-    modules_json = ModulesJson(self.pipeline_dir)
-    # Verify that the branch entry was updated correctly
-    assert (
-        modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO)
-        == GITLAB_BRANCH_TEST_BRANCH
-    )
-    assert modules_json.get_module_version("fastp", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA
-    # MultiQC is present in both branches but should've been updated using the 'main' branch
-    assert (
-        modules_json.get_component_branch(self.component_type, "multiqc", GITLAB_URL, GITLAB_REPO)
-        == GITLAB_DEFAULT_BRANCH
-    )
-
-
-def test_update_different_branch_mix_modules_branch_test(self):
-    """Try updating all modules where MultiQC is installed from branch-test branch"""
-    # Install multiqc from the branch-test branch
-    assert self.mods_install_gitlab_old.install(
-        "multiqc"
-    )  # Force as the same module is installed from github nf-core modules repo
-    modules_json = ModulesJson(self.pipeline_dir)
-    update_obj = ModuleUpdate(
-        self.pipeline_dir,
-        update_all=True,
-        show_diff=False,
-        remote_url=GITLAB_URL,
-        branch=GITLAB_BRANCH_TEST_BRANCH,
-        sha=GITLAB_BRANCH_TEST_NEW_SHA,
-    )
-    assert update_obj.update()
-
-    assert (
-        modules_json.get_component_branch(self.component_type, "multiqc", GITLAB_URL, GITLAB_REPO)
-        == GITLAB_BRANCH_TEST_BRANCH
-    )
-    assert modules_json.get_module_version("multiqc", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA
-
-
-# Mock questionary answer: do not update module, only show diffs
-@mock.patch.object(questionary.Question, "unsafe_ask", return_value=False)
-def test_update_only_show_differences(self, mock_prompt):
-    """Try updating all modules showing differences.
-    Only show diffs, don't actually save any updated files.
-    Check that the sha in modules.json is not changed."""
-
-    # Update modules to a fixed old SHA
-    update_old = ModuleUpdate(
-        self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905"
-    )
-    update_old.update()
-
-    tmpdir = Path(tempfile.TemporaryDirectory().name)
-    shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir)
-
-    update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True)
-    assert ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True).update()
-
-    mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
-    # Loop through all modules and check that they are NOT updated (according to the modules.json file)
-    # A module that can be updated but shouldn't is fastqc
-    # Module multiqc is already up to date so don't check
-    mod = "fastqc"
-    non_updated_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"]
-    current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
-    assert non_updated_git_sha != current_git_sha
-    assert cmp_component(Path(tmpdir, mod), Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, mod)) is True
-
-
-# Mock questionary answer: do not update module, only show diffs
-@mock.patch.object(questionary.Question, "unsafe_ask", return_value=False)
-def test_update_only_show_differences_when_patch(self, mock_prompt):
-    """Try updating all modules showing differences when there's a patched module.
-    Don't update some of them.
-    Check that the sha in modules.json is not changed."""
-    modules_json = ModulesJson(self.pipeline_dir)
-    update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True)
-
-    # Update modules to a fixed old SHA
-    update_old = ModuleUpdate(
-        self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905"
-    )
-    assert update_old.update()
-
-    # Modify fastqc module, it will have a patch which will be applied during update
-    # We modify fastqc because it's one of the modules that can be updated and there's another one before it (custom/dumpsoftwareversions)
-    module_path = Path(self.pipeline_dir, "modules", "nf-core", "fastqc")
-    main_path = Path(module_path, "main.nf")
-    with open(main_path) as fh:
-        lines = fh.readlines()
-    for line_index in range(len(lines)):
-        if lines[line_index] == "    label 'process_medium'\n":
-            lines[line_index] = "    label 'process_low'\n"
-            break
-    with open(main_path, "w") as fh:
-        fh.writelines(lines)
-    # Create a patch file
-    patch_obj = ModulePatch(self.pipeline_dir)
-    patch_obj.patch("fastqc")
-    # Check that a patch file with the correct name has been created
-    assert "fastqc.diff" in [f.name for f in module_path.glob("*.diff")]
-
-    # Update all modules
-    assert update_obj.update() is True
-
-    mod_json = modules_json.get_modules_json()
-    # Loop through all modules and check that they are NOT updated (according to the modules.json file)
-    # A module that can be updated but shouldn't is fastqc
-    # Module multiqc is already up to date so don't check
-    mod = "fastqc"
-    correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"]
-    current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"]
-    assert correct_git_sha != current_git_sha
-
-
-def test_update_module_with_extra_config_file(self):
-    """Try updating a module with a config file"""
-    # Install the module
-    assert self.mods_install.install("trimgalore")
-    # Add a nextflow_test.config file to the module
-    trimgalore_path = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore")
-    Path(trimgalore_path, "nextflow_test.config").touch()
-    with open(Path(trimgalore_path, "nextflow_test.config"), "w") as fh:
-        fh.write("params.my_param = 'my_value'\n")
-    # Update the module
-    update_obj = ModuleUpdate(self.pipeline_dir, show_diff=False)
-    assert update_obj.update("trimgalore")
-    # Check that the nextflow_test.config file is still there
-    assert Path(trimgalore_path, "nextflow_test.config").exists()
-    with open(Path(trimgalore_path, "nextflow_test.config")) as fh:
-        assert "params.my_param = 'my_value'" in fh.read()
diff --git a/tests/test_modules.py b/tests/test_modules.py
index 6e601ce7ad..13bf32f971 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -160,131 +160,3 @@ def test_modulesrepo_class(self):
     @pytest.fixture(autouse=True)
     def _use_caplog(self, caplog):
         self.caplog = caplog
-
-    ############################################
-    # Test of the individual modules commands. #
-    ############################################
-
-    from .modules.bump_versions import (  # type: ignore[misc]
-        test_modules_bump_versions_all_modules,
-        test_modules_bump_versions_fail,
-        test_modules_bump_versions_fail_unknown_version,
-        test_modules_bump_versions_single_module,
-    )
-    from .modules.create import (  # type: ignore[misc]
-        test_modules_create_fail_exists,
-        test_modules_create_nfcore_modules,
-        test_modules_create_nfcore_modules_subtool,
-        test_modules_create_succeed,
-        test_modules_migrate,
-        test_modules_migrate_no_delete,
-        test_modules_migrate_symlink,
-    )
-    from .modules.info import (  # type: ignore[misc]
-        test_modules_info_in_modules_repo,
-        test_modules_info_local,
-        test_modules_info_remote,
-        test_modules_info_remote_gitlab,
-    )
-    from .modules.install import (  # type: ignore[misc]
-        test_modules_install_alternate_remote,
-        test_modules_install_different_branch_fail,
-        test_modules_install_different_branch_succeed,
-        test_modules_install_emptypipeline,
-        test_modules_install_from_gitlab,
-        test_modules_install_nomodule,
-        test_modules_install_nopipeline,
-        test_modules_install_tracking,
-        test_modules_install_trimgalore,
-        test_modules_install_trimgalore_twice,
-    )
-    from .modules.lint import (  # type: ignore[misc]
-        test_modules_absent_version,
-        test_modules_empty_file_in_snapshot,
-        test_modules_empty_file_in_stub_snapshot,
-        test_modules_environment_yml_file_doesnt_exists,
-        test_modules_environment_yml_file_name_mismatch,
-        test_modules_environment_yml_file_not_array,
-        test_modules_environment_yml_file_sorted_correctly,
-        test_modules_environment_yml_file_sorted_incorrectly,
-        test_modules_lint_check_process_labels,
-        test_modules_lint_check_url,
-        test_modules_lint_empty,
-        test_modules_lint_gitlab_modules,
-        test_modules_lint_multiple_remotes,
-        test_modules_lint_new_modules,
-        test_modules_lint_no_gitlab,
-        test_modules_lint_patched_modules,
-        test_modules_lint_snapshot_file,
-        test_modules_lint_snapshot_file_missing_fail,
-        test_modules_lint_snapshot_file_not_needed,
-        test_modules_lint_trimgalore,
-        test_modules_meta_yml_incorrect_licence_field,
-        test_modules_meta_yml_incorrect_name,
-        test_modules_meta_yml_input_mismatch,
-        test_modules_meta_yml_output_mismatch,
-        test_modules_missing_test_dir,
-        test_modules_missing_test_main_nf,
-        test_modules_unused_pytest_files,
-        test_nftest_failing_linting,
-    )
-    from .modules.list import (  # type: ignore[misc]
-        test_modules_install_and_list_pipeline,
-        test_modules_install_gitlab_and_list_pipeline,
-        test_modules_list_in_wrong_repo_fail,
-        test_modules_list_local_json,
-        test_modules_list_pipeline,
-        test_modules_list_remote,
-        test_modules_list_remote_gitlab,
-        test_modules_list_remote_json,
-        test_modules_list_with_keywords,
-        test_modules_list_with_one_keyword,
-        test_modules_list_with_unused_keyword,
-    )
-    from .modules.modules_json import (  # type: ignore[misc]
-        test_get_modules_json,
-        test_mod_json_create,
-        test_mod_json_create_with_patch,
-        test_mod_json_dump,
-        test_mod_json_get_module_version,
-        test_mod_json_module_present,
-        test_mod_json_repo_present,
-        test_mod_json_up_to_date,
-        test_mod_json_up_to_date_module_removed,
-        test_mod_json_up_to_date_reinstall_fails,
-        test_mod_json_update,
-        test_mod_json_with_empty_modules_value,
-        test_mod_json_with_missing_modules_entry,
-    )
-    from .modules.patch import (  # type: ignore[misc]
-        test_create_patch_change,
-        test_create_patch_no_change,
-        test_create_patch_try_apply_failed,
-        test_create_patch_try_apply_successful,
-        test_create_patch_update_fail,
-        test_create_patch_update_success,
-        test_remove_patch,
-    )
-    from .modules.remove import (  # type: ignore[misc]
-        test_modules_remove_multiqc_from_gitlab,
-        test_modules_remove_trimgalore,
-        test_modules_remove_trimgalore_uninstalled,
-    )
-    from .modules.update import (  # type: ignore[misc]
-        test_install_and_update,
-        test_install_at_hash_and_update,
-        test_install_at_hash_and_update_and_save_diff_to_file,
-        test_install_at_hash_and_update_and_save_diff_to_file_limit_output,
-        test_install_at_hash_and_update_limit_output,
-        test_update_all,
-        test_update_different_branch_mix_modules_branch_test,
-        test_update_different_branch_mixed_modules_main,
-        test_update_different_branch_single_module,
-        test_update_module_with_extra_config_file,
-        test_update_only_show_differences,
-        test_update_only_show_differences_when_patch,
-        test_update_with_config_dont_update,
-        test_update_with_config_fix_all,
-        test_update_with_config_fixed_version,
-        test_update_with_config_no_updates,
-    )

From 772ff5244af03351e35584a28154a94818f2cd5f Mon Sep 17 00:00:00 2001
From: LaurenceKuhl <laurence.kuhlburger@gmail.com>
Date: Thu, 18 Jul 2024 11:25:23 +0200
Subject: [PATCH 093/414] Update CHANGELOG.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 CHANGELOG.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8cda88788b..b80a63c6a0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,6 @@
 - Run awsfulltest on PRs to `master` with two PR approvals ([#3042](https://github.com/nf-core/tools/pull/3042))
 - Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046))
 - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055))
-- Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055))
 - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072))
 
 ### Linting

From d95f7f8631f0605319f8a80d4ab2199b08e6fea4 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 18 Jul 2024 10:14:54 +0200
Subject: [PATCH 094/414] avoid naming collision with variable name `dir`

---
 nf_core/commands_pipelines.py            |  8 ++--
 nf_core/components/components_command.py | 52 +++++++++++------------
 nf_core/components/components_test.py    |  4 +-
 nf_core/components/install.py            | 16 +++----
 nf_core/components/lint/__init__.py      | 54 +++++++++++++-----------
 nf_core/components/update.py             | 49 ++++++++++++---------
 nf_core/modules/lint/__init__.py         |  9 ++--
 nf_core/modules/modules_json.py          | 18 ++++----
 nf_core/pipelines/create_logo.py         | 14 +++---
 9 files changed, 121 insertions(+), 103 deletions(-)

diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py
index 3f569bfe35..deb1f691a5 100644
--- a/nf_core/commands_pipelines.py
+++ b/nf_core/commands_pipelines.py
@@ -308,7 +308,7 @@ def pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, usern
 
 
 # nf-core pipelines create-logo
-def pipelines_create_logo(logo_text, dir, name, theme, width, format, force):
+def pipelines_create_logo(logo_text, directory, name, theme, width, format, force):
     """
     Generate a logo with the nf-core logo template.
 
@@ -317,9 +317,9 @@ def pipelines_create_logo(logo_text, dir, name, theme, width, format, force):
     from nf_core.pipelines.create_logo import create_logo
 
     try:
-        if dir == ".":
-            dir = Path.cwd()
-        logo_path = create_logo(logo_text, dir, name, theme, width, format, force)
+        if directory == ".":
+            directory = Path.cwd()
+        logo_path = create_logo(logo_text, directory, name, theme, width, format, force)
         # Print path to logo relative to current working directory
         try:
             logo_path = Path(logo_path).relative_to(Path.cwd())
diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index aa1dccc0d4..bf80b46113 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -22,7 +22,7 @@ class ComponentCommand:
     def __init__(
         self,
         component_type: str,
-        dir: Union[str, Path],
+        directory: Union[str, Path],
         remote_url: Optional[str] = None,
         branch: Optional[str] = None,
         no_pull: bool = False,
@@ -33,7 +33,7 @@ def __init__(
         Initialise the ComponentClass object
         """
         self.component_type = component_type
-        self.dir = Path(dir) if dir else None
+        self.directory = Path(directory) if directory else None
         self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)
         self.hide_progress = hide_progress
         self.no_prompts = no_prompts
@@ -49,8 +49,8 @@ def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
         """
 
         try:
-            if self.dir:
-                self.dir, self.repo_type, self.org = get_repo_info(self.dir, use_prompt=not self.no_prompts)
+            if self.directory:
+                self.directory, self.repo_type, self.org = get_repo_info(self.directory, use_prompt=not self.no_prompts)
             else:
                 self.repo_type = None
                 self.org = ""
@@ -68,7 +68,7 @@ def get_local_components(self) -> List[str]:
         """
         Get the local modules/subworkflows in a pipeline
         """
-        local_component_dir = Path(self.dir, self.component_type, "local")
+        local_component_dir = Path(self.directory, self.component_type, "local")
         return [
             str(path.relative_to(local_component_dir)) for path in local_component_dir.iterdir() if path.suffix == ".nf"
         ]
@@ -78,9 +78,9 @@ def get_components_clone_modules(self) -> List[str]:
         Get the modules/subworkflows repository available in a clone of nf-core/modules
         """
         if self.component_type == "modules":
-            component_base_path = Path(self.dir, self.default_modules_path)
+            component_base_path = Path(self.directory, self.default_modules_path)
         elif self.component_type == "subworkflows":
-            component_base_path = Path(self.dir, self.default_subworkflows_path)
+            component_base_path = Path(self.directory, self.default_subworkflows_path)
         return [
             str(Path(dir).relative_to(component_base_path))
             for dir, _, files in os.walk(component_base_path)
@@ -91,23 +91,23 @@ def has_valid_directory(self) -> bool:
         """Check that we were given a pipeline or clone of nf-core/modules"""
         if self.repo_type == "modules":
             return True
-        if self.dir is None or not os.path.exists(self.dir):
-            log.error(f"Could not find directory: {self.dir}")
+        if self.directory is None or not os.path.exists(self.directory):
+            log.error(f"Could not find directory: {self.directory}")
             return False
-        main_nf = os.path.join(self.dir, "main.nf")
-        nf_config = os.path.join(self.dir, "nextflow.config")
+        main_nf = os.path.join(self.directory, "main.nf")
+        nf_config = os.path.join(self.directory, "nextflow.config")
         if not os.path.exists(main_nf) and not os.path.exists(nf_config):
-            if Path(self.dir).resolve().parts[-1].startswith("nf-core"):
-                raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'")
-            log.warning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'")
+            if Path(self.directory).resolve().parts[-1].startswith("nf-core"):
+                raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'")
+            log.warning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'")
         return True
 
     def has_modules_file(self) -> None:
         """Checks whether a module.json file has been created and creates one if it is missing"""
-        modules_json_path = os.path.join(self.dir, "modules.json")
+        modules_json_path = os.path.join(self.directory, "modules.json")
         if not os.path.exists(modules_json_path):
             log.info("Creating missing 'module.json' file.")
-            ModulesJson(self.dir).create()
+            ModulesJson(self.directory).create()
 
     def clear_component_dir(self, component_name: str, component_dir: str) -> bool:
         """
@@ -122,7 +122,7 @@ def clear_component_dir(self, component_name: str, component_dir: str) -> bool:
         try:
             shutil.rmtree(component_dir)
             # remove all empty directories
-            for dir_path, dir_names, filenames in os.walk(self.dir, topdown=False):
+            for dir_path, dir_names, filenames in os.walk(self.directory, topdown=False):
                 if not dir_names and not filenames:
                     try:
                         os.rmdir(dir_path)
@@ -147,7 +147,7 @@ def components_from_repo(self, install_dir: str) -> List[str]:
         Returns:
             [str]: The names of the modules/subworkflows
         """
-        repo_dir = Path(self.dir, self.component_type, install_dir)
+        repo_dir = Path(self.directory, self.component_type, install_dir)
         if not repo_dir.exists():
             raise LookupError(f"Nothing installed from {install_dir} in pipeline")
 
@@ -180,7 +180,7 @@ def load_lint_config(self) -> None:
 
         Add parsed config to the `self.lint_config` class attribute.
         """
-        _, tools_config = nf_core.utils.load_tools_config(self.dir)
+        _, tools_config = nf_core.utils.load_tools_config(self.directory)
         self.lint_config = tools_config.get("lint", {})
 
     def check_modules_structure(self) -> None:
@@ -193,9 +193,9 @@ def check_modules_structure(self) -> None:
         """
         if self.repo_type == "pipeline":
             wrong_location_modules: List[Path] = []
-            for directory, _, files in os.walk(Path(self.dir, "modules")):
+            for directory, _, files in os.walk(Path(self.directory, "modules")):
                 if "main.nf" in files:
-                    module_path = Path(directory).relative_to(Path(self.dir, "modules"))
+                    module_path = Path(directory).relative_to(Path(self.directory, "modules"))
                     parts = module_path.parts
                     # Check that there are modules installed directly under the 'modules' directory
                     if parts[1] == "modules":
@@ -215,9 +215,9 @@ def check_modules_structure(self) -> None:
                     wrong_dir = Path(modules_dir, module)
                     shutil.move(str(wrong_dir), str(correct_dir))
                     log.info(f"Moved {wrong_dir} to {correct_dir}.")
-                shutil.rmtree(Path(self.dir, "modules", self.modules_repo.repo_path, "modules"))
+                shutil.rmtree(Path(self.directory, "modules", self.modules_repo.repo_path, "modules"))
                 # Regenerate modules.json file
-                modules_json = ModulesJson(self.dir)
+                modules_json = ModulesJson(self.directory)
                 modules_json.check_up_to_date()
 
     def check_patch_paths(self, patch_path: Path, module_name: str) -> None:
@@ -243,12 +243,12 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None:
                     for line in lines:
                         fh.write(line)
                 # Update path in modules.json if the file is in the correct format
-                modules_json = ModulesJson(self.dir)
+                modules_json = ModulesJson(self.directory)
                 modules_json.load()
                 if modules_json.has_git_url_and_modules() and modules_json.modules_json is not None:
                     modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][
                         self.modules_repo.repo_path
-                    ][module_name]["patch"] = str(patch_path.relative_to(Path(self.dir).resolve()))
+                    ][module_name]["patch"] = str(patch_path.relative_to(Path(self.directory).resolve()))
                 modules_json.dump()
 
     def check_if_in_include_stmts(self, component_path: str) -> Dict[str, List[Dict[str, Union[int, str]]]]:
@@ -262,7 +262,7 @@ def check_if_in_include_stmts(self, component_path: str) -> Dict[str, List[Dict[
         """
         include_stmts: Dict[str, List[Dict[str, Union[int, str]]]] = {}
         if self.repo_type == "pipeline":
-            workflow_files = Path(self.dir, "workflows").glob("*.nf")
+            workflow_files = Path(self.directory, "workflows").glob("*.nf")
             for workflow_file in workflow_files:
                 with open(workflow_file) as fh:
                     # Check if component path is in the file using mmap
diff --git a/nf_core/components/components_test.py b/nf_core/components/components_test.py
index 9b81f54f06..f9b891004a 100644
--- a/nf_core/components/components_test.py
+++ b/nf_core/components/components_test.py
@@ -93,7 +93,7 @@ def run(self) -> None:
         os.environ["NFT_DIFF_ARGS"] = (
             "--line-numbers --expand-tabs=2"  # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences
         )
-        with nf_core.utils.set_wd(Path(self.dir)):
+        with nf_core.utils.set_wd(Path(self.directory)):
             self.check_snapshot_stability()
         if len(self.errors) > 0:
             errors = "\n - ".join(self.errors)
@@ -126,7 +126,7 @@ def check_inputs(self) -> None:
         self.component_dir = Path(self.component_type, self.modules_repo.repo_path, *self.component_name.split("/"))
 
         # First, sanity check that the module directory exists
-        if not Path(self.dir, self.component_dir).is_dir():
+        if not Path(self.directory, self.component_dir).is_dir():
             raise UserWarning(
                 f"Cannot find directory '{self.component_dir}'.{' Should be TOOL/SUBTOOL or TOOL' if self.component_type == 'modules' else ''}"
             )
diff --git a/nf_core/components/install.py b/nf_core/components/install.py
index 6385ee4092..dddc3f93ec 100644
--- a/nf_core/components/install.py
+++ b/nf_core/components/install.py
@@ -54,7 +54,7 @@ def install(self, component, silent=False):
             self.check_modules_structure()
 
         # Verify that 'modules.json' is consistent with the installed modules and subworkflows
-        modules_json = ModulesJson(self.dir)
+        modules_json = ModulesJson(self.directory)
         if not silent:
             modules_json.check_up_to_date()
 
@@ -79,7 +79,7 @@ def install(self, component, silent=False):
         )
 
         # Set the install folder based on the repository name
-        install_folder = Path(self.dir, self.component_type, self.modules_repo.repo_path)
+        install_folder = Path(self.directory, self.component_type, self.modules_repo.repo_path)
 
         # Compute the component directory
         component_dir = Path(install_folder, component)
@@ -134,14 +134,14 @@ def install(self, component, silent=False):
             log.info(f"Use the following statement to include this {self.component_type[:-1]}:")
             Console().print(
                 Syntax(
-                    f"include {{ {component_name} }} from '../{Path(install_folder, component).relative_to(self.dir)}/main'",
+                    f"include {{ {component_name} }} from '../{Path(install_folder, component).relative_to(self.directory)}/main'",
                     "groovy",
                     theme="ansi_dark",
                     padding=1,
                 )
             )
             if self.component_type == "subworkflows":
-                subworkflow_config = Path(install_folder, component, "nextflow.config").relative_to(self.dir)
+                subworkflow_config = Path(install_folder, component, "nextflow.config").relative_to(self.directory)
                 if os.path.isfile(subworkflow_config):
                     log.info("Add the following config statement to use this subworkflow:")
                     Console().print(
@@ -261,9 +261,9 @@ def clean_modules_json(self, component, modules_repo, modules_json):
         Remove installed version of module/subworkflow from modules.json
         """
         for repo_url, repo_content in modules_json.modules_json["repos"].items():
-            for dir, dir_components in repo_content[self.component_type].items():
+            for directory, dir_components in repo_content[self.component_type].items():
                 for name, component_values in dir_components.items():
-                    if name == component and dir == modules_repo.repo_path:
+                    if name == component and directory == modules_repo.repo_path:
                         repo_to_remove = repo_url
                         log.debug(
                             f"Removing {self.component_type[:-1]} '{modules_repo.repo_path}/{component}' from repo '{repo_to_remove}' from modules.json."
@@ -285,7 +285,7 @@ def check_alternate_remotes(self, modules_json):
         modules_json.load()
         for repo_url, repo_content in modules_json.modules_json.get("repos", dict()).items():
             for component_type in repo_content:
-                for dir in repo_content.get(component_type, dict()).keys():
-                    if dir == self.modules_repo.repo_path and repo_url != self.modules_repo.remote_url:
+                for directory in repo_content.get(component_type, dict()).keys():
+                    if directory == self.modules_repo.repo_path and repo_url != self.modules_repo.remote_url:
                         return True
         return False
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index 6d47f1e7a8..7dd39bd904 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -7,6 +7,7 @@
 import operator
 import os
 from pathlib import Path
+from typing import List, Optional, Union
 
 import rich.box
 import rich.console
@@ -53,18 +54,18 @@ class ComponentLint(ComponentCommand):
 
     def __init__(
         self,
-        component_type,
-        dir,
-        fail_warned=False,
-        remote_url=None,
-        branch=None,
-        no_pull=False,
-        registry=None,
-        hide_progress=False,
+        component_type: str,
+        directory: Union[str, Path],
+        fail_warned: bool = False,
+        remote_url: Optional[str] = None,
+        branch: Optional[str] = None,
+        no_pull: bool = False,
+        registry: Optional[str] = None,
+        hide_progress: bool = False,
     ):
         super().__init__(
             component_type,
-            dir=dir,
+            directory=directory,
             remote_url=remote_url,
             branch=branch,
             no_pull=no_pull,
@@ -72,18 +73,18 @@ def __init__(
         )
 
         self.fail_warned = fail_warned
-        self.passed = []
-        self.warned = []
-        self.failed = []
+        self.passed: List[str] = []
+        self.warned: List[str] = []
+        self.failed: List[str] = []
         if self.component_type == "modules":
             self.lint_tests = self.get_all_module_lint_tests(self.repo_type == "pipeline")
         else:
             self.lint_tests = self.get_all_subworkflow_lint_tests(self.repo_type == "pipeline")
 
         if self.repo_type == "pipeline":
-            modules_json = ModulesJson(self.dir)
+            modules_json = ModulesJson(self.directory)
             modules_json.check_up_to_date()
-            self.all_remote_components = []
+            self.all_remote_components: List[NFCoreComponent] = []
             for repo_url, components in modules_json.get_all_components(self.component_type).items():
                 if remote_url is not None and remote_url != repo_url:
                     continue
@@ -92,9 +93,9 @@ def __init__(
                         NFCoreComponent(
                             comp,
                             repo_url,
-                            Path(self.dir, self.component_type, org, comp),
+                            Path(self.directory, self.component_type, org, comp),
                             self.repo_type,
-                            Path(self.dir),
+                            Path(self.directory),
                             self.component_type,
                         )
                     )
@@ -102,7 +103,7 @@ def __init__(
                 raise LookupError(
                     f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline."
                 )
-            local_component_dir = Path(self.dir, self.component_type, "local")
+            local_component_dir = Path(self.directory, self.component_type, "local")
             self.all_local_components = []
             if local_component_dir.exists():
                 self.all_local_components = [
@@ -111,20 +112,20 @@ def __init__(
                         None,
                         Path(local_component_dir, comp),
                         self.repo_type,
-                        Path(self.dir),
+                        Path(self.directory),
                         self.component_type,
                         remote_component=False,
                     )
                     for comp in self.get_local_components()
                 ]
-            self.config = nf_core.utils.fetch_wf_config(Path(self.dir), cache_config=True)
+            self.config = nf_core.utils.fetch_wf_config(Path(self.directory), cache_config=True)
         else:
             component_dir = Path(
-                self.dir,
+                self.directory,
                 self.default_modules_path if self.component_type == "modules" else self.default_subworkflows_path,
             )
             self.all_remote_components = [
-                NFCoreComponent(m, None, component_dir / m, self.repo_type, Path(self.dir), self.component_type)
+                NFCoreComponent(m, None, component_dir / m, self.repo_type, Path(self.directory), self.component_type)
                 for m in self.get_components_clone_modules()
             ]
             self.all_local_components = []
@@ -132,7 +133,9 @@ def __init__(
                 raise LookupError(f"No {self.component_type} in '{self.component_type}' directory")
 
             # This could be better, perhaps glob for all nextflow.config files in?
-            self.config = nf_core.utils.fetch_wf_config(Path(self.dir).joinpath("tests", "config"), cache_config=True)
+            self.config = nf_core.utils.fetch_wf_config(
+                Path(self.directory).joinpath("tests", "config"), cache_config=True
+            )
 
         if registry is None:
             self.registry = self.config.get("docker.registry", "quay.io")
@@ -143,6 +146,9 @@ def __init__(
         self.lint_config = None
         self.modules_json = None
 
+    def __repr__(self) -> str:
+        return f"ComponentLint({self.component_type}, {self.directory})"
+
     @staticmethod
     def get_all_module_lint_tests(is_pipeline):
         if is_pipeline:
@@ -168,7 +174,7 @@ def get_all_subworkflow_lint_tests(is_pipeline):
 
     def set_up_pipeline_files(self):
         self.load_lint_config()
-        self.modules_json = ModulesJson(self.dir)
+        self.modules_json = ModulesJson(self.directory)
         self.modules_json.load()
 
         # Only continue if a lint config has been loaded
@@ -243,7 +249,7 @@ def format_result(test_results, table):
                     module_name = lint_result.component_name
 
                 # Make the filename clickable to open in VSCode
-                file_path = os.path.relpath(lint_result.file_path, self.dir)
+                file_path = os.path.relpath(lint_result.file_path, self.directory)
                 file_path_link = f"[link=vscode://file/{os.path.abspath(file_path)}]{file_path}[/link]"
 
                 table.add_row(
diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index 1e31e56271..9b24b6c0c9 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -51,7 +51,7 @@ def __init__(
         self.update_deps = update_deps
         self.component = None
         self.update_config = None
-        self.modules_json = ModulesJson(self.dir)
+        self.modules_json = ModulesJson(self.directory)
         self.branch = branch
 
     def _parameter_checks(self):
@@ -96,9 +96,12 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
         if updated is None:
             updated = []
 
-        _, tool_config = nf_core.utils.load_tools_config(self.dir)
+        _, tool_config = nf_core.utils.load_tools_config(self.directory)
         self.update_config = tool_config.get("update", {})
 
+        if self.update_config is None:
+            raise UserWarning("Could not find '.nf-core.yml' file in pipeline directory")
+
         self._parameter_checks()
 
         # Check modules directory structure
@@ -171,7 +174,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
             component_install_dir = install_tmp_dir / component
 
             # Compute the component directory
-            component_dir = os.path.join(self.dir, self.component_type, modules_repo.repo_path, component)
+            component_dir = Path(self.directory, self.component_type, modules_repo.repo_path, component)
 
             if sha is not None:
                 version = sha
@@ -318,7 +321,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                 self.save_diff_fn,
                 old_modules_json,
                 self.modules_json.get_modules_json(),
-                Path(self.dir, "modules.json"),
+                Path(self.directory, "modules.json"),
             )
             if exit_value and not silent:
                 log.info(
@@ -479,7 +482,9 @@ def get_all_components_info(self, branch=None):
         # Loop through all the modules/subworkflows in the pipeline
         # and check if they have an entry in the '.nf-core.yml' file
         for repo_name, components in self.modules_json.get_all_components(self.component_type).items():
-            if repo_name not in self.update_config or self.update_config[repo_name] is True:
+            if isinstance(self.update_config, dict) and (
+                repo_name not in self.update_config or self.update_config[repo_name] is True
+            ):
                 # There aren't restrictions for the repository in .nf-core.yml file
                 components_info[repo_name] = {}
                 for component_dir, component in components:
@@ -503,7 +508,7 @@ def get_all_components_info(self, branch=None):
                                 ),
                             )
                         ]
-            elif isinstance(self.update_config[repo_name], dict):
+            elif isinstance(self.update_config, dict) and isinstance(self.update_config[repo_name], dict):
                 # If it is a dict, then there are entries for individual components or component directories
                 for component_dir in set([dir for dir, _ in components]):
                     if isinstance(self.update_config[repo_name][component_dir], str):
@@ -535,8 +540,8 @@ def get_all_components_info(self, branch=None):
                         if self.sha is not None:
                             overridden_repos.append(repo_name)
                     elif self.update_config[repo_name][component_dir] is False:
-                        for dir, component in components:
-                            if dir == component_dir:
+                        for directory, component in components:
+                            if directory == component_dir:
                                 skipped_components.append(f"{component_dir}/{components}")
                     elif isinstance(self.update_config[repo_name][component_dir], dict):
                         # If it's a dict, there are entries for individual components
@@ -596,7 +601,7 @@ def get_all_components_info(self, branch=None):
                                 raise UserWarning(
                                     f"{self.component_type[:-1].title()} '{component}' in '{component_dir}' has an invalid entry in '.nf-core.yml'"
                                 )
-            elif isinstance(self.update_config[repo_name], str):
+            elif isinstance(self.update_config, dict) and isinstance(self.update_config[repo_name], str):
                 # If a string is given it is the commit SHA to which we should update to
                 custom_sha = self.update_config[repo_name]
                 components_info[repo_name] = {}
@@ -623,8 +628,10 @@ def get_all_components_info(self, branch=None):
                         ]
                 if self.sha is not None:
                     overridden_repos.append(repo_name)
-            elif self.update_config[repo_name] is False:
+            elif isinstance(self.update_config, dict) and self.update_config[repo_name] is False:
                 skipped_repos.append(repo_name)
+            elif not isinstance(self.update_config, dict):
+                raise UserWarning("`.nf-core.yml` is not correctly formatted.")
             else:
                 raise UserWarning(f"Repo '{repo_name}' has an invalid entry in '.nf-core.yml'")
 
@@ -712,8 +719,10 @@ def setup_diff_file(self, check_diff_exist=True):
             self.save_diff_fn = questionary.path(
                 "Enter the filename: ", style=nf_core.utils.nfcore_question_style
             ).unsafe_ask()
-
-        self.save_diff_fn = Path(self.save_diff_fn)
+        if self.save_diff_fn is not None:
+            self.save_diff_fn = Path(self.save_diff_fn)
+        else:
+            raise UserWarning("No filename provided for saving the diff file")
 
         if not check_diff_exist:
             # This guarantees that the file exists after calling the function
@@ -744,7 +753,7 @@ def move_files_from_tmp_dir(self, component: str, install_folder: str, repo_path
         """
         temp_component_dir = Path(install_folder, component)
         files = [file_path for file_path in temp_component_dir.rglob("*") if file_path.is_file()]
-        pipeline_path = Path(self.dir, self.component_type, repo_path, component)
+        pipeline_path = Path(self.directory, self.component_type, repo_path, component)
 
         if pipeline_path.exists():
             pipeline_files = [f.name for f in pipeline_path.iterdir() if f.is_file()]
@@ -795,7 +804,7 @@ def try_apply_patch(
         component_fullname = str(Path(repo_path, component))
         log.info(f"Found patch for  {self.component_type[:-1]} '{component_fullname}'. Trying to apply it to new files")
 
-        patch_path = Path(self.dir / patch_relpath)
+        patch_path = Path(self.directory / patch_relpath)
         component_relpath = Path(self.component_type, repo_path, component)
 
         # Check that paths in patch file are updated
@@ -928,29 +937,31 @@ def update_linked_components(
     def manage_changes_in_linked_components(self, component, modules_to_update, subworkflows_to_update):
         """Check for linked components added or removed in the new subworkflow version"""
         if self.component_type == "subworkflows":
-            subworkflow_directory = Path(self.dir, self.component_type, self.modules_repo.repo_path, component)
+            subworkflow_directory = Path(self.directory, self.component_type, self.modules_repo.repo_path, component)
             included_modules, included_subworkflows = get_components_to_install(subworkflow_directory)
             # If a module/subworkflow has been removed from the subworkflow
             for module in modules_to_update:
                 if module not in included_modules:
                     log.info(f"Removing module '{module}' which is not included in '{component}' anymore.")
-                    remove_module_object = ComponentRemove("modules", self.dir)
+                    remove_module_object = ComponentRemove("modules", self.directory)
                     remove_module_object.remove(module, removed_by=component)
             for subworkflow in subworkflows_to_update:
                 if subworkflow not in included_subworkflows:
                     log.info(f"Removing subworkflow '{subworkflow}' which is not included in '{component}' anymore.")
-                    remove_subworkflow_object = ComponentRemove("subworkflows", self.dir)
+                    remove_subworkflow_object = ComponentRemove("subworkflows", self.directory)
                     remove_subworkflow_object.remove(subworkflow, removed_by=component)
             # If a new module/subworkflow is included in the subworklfow and wasn't included before
             for module in included_modules:
                 if module not in modules_to_update:
                     log.info(f"Installing newly included module '{module}' for '{component}'")
-                    install_module_object = ComponentInstall(self.dir, "modules", installed_by=component)
+                    install_module_object = ComponentInstall(self.directory, "modules", installed_by=component)
                     install_module_object.install(module, silent=True)
             for subworkflow in included_subworkflows:
                 if subworkflow not in subworkflows_to_update:
                     log.info(f"Installing newly included subworkflow '{subworkflow}' for '{component}'")
-                    install_subworkflow_object = ComponentInstall(self.dir, "subworkflows", installed_by=component)
+                    install_subworkflow_object = ComponentInstall(
+                        self.directory, "subworkflows", installed_by=component
+                    )
                     install_subworkflow_object.install(subworkflow, silent=True)
 
     def _change_component_type(self, new_component_type):
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index b780144ef7..90d39104d2 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -11,6 +11,7 @@
 
 import questionary
 import rich
+import rich.progress
 
 import nf_core.modules.modules_utils
 import nf_core.utils
@@ -39,7 +40,7 @@ class ModuleLint(ComponentLint):
 
     def __init__(
         self,
-        dir,
+        directory,
         fail_warned=False,
         remote_url=None,
         branch=None,
@@ -49,7 +50,7 @@ def __init__(
     ):
         super().__init__(
             component_type="modules",
-            dir=dir,
+            directory=directory,
             fail_warned=fail_warned,
             remote_url=remote_url,
             branch=branch,
@@ -127,9 +128,9 @@ def lint(
             remote_modules = self.all_remote_components
 
         if self.repo_type == "modules":
-            log.info(f"Linting modules repo: [magenta]'{self.dir}'")
+            log.info(f"Linting modules repo: [magenta]'{self.directory}'")
         else:
-            log.info(f"Linting pipeline: [magenta]'{self.dir}'")
+            log.info(f"Linting pipeline: [magenta]'{self.directory}'")
         if module:
             log.info(f"Linting module: [magenta]'{module}'")
 
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 2c2f1a32c9..63c356a79a 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -39,10 +39,10 @@ def __init__(self, pipeline_dir: Union[str, Path]):
         Args:
             pipeline_dir (str): The pipeline directory
         """
-        self.dir = Path(pipeline_dir)
-        self.modules_dir = self.dir / "modules"
-        self.subworkflows_dir = self.dir / "subworkflows"
-        self.modules_json_path = self.dir / "modules.json"
+        self.directory = Path(pipeline_dir)
+        self.modules_dir = self.directory / "modules"
+        self.subworkflows_dir = self.directory / "subworkflows"
+        self.modules_json_path = self.directory / "modules.json"
         self.modules_json = None
         self.pipeline_modules = None
         self.pipeline_subworkflows = None
@@ -63,7 +63,7 @@ def create(self):
         Raises:
             UserWarning: If the creation fails
         """
-        pipeline_config = nf_core.utils.fetch_wf_config(self.dir)
+        pipeline_config = nf_core.utils.fetch_wf_config(self.directory)
         pipeline_name = pipeline_config.get("manifest.name", "")
         pipeline_url = pipeline_config.get("manifest.homePage", "")
         new_modules_json = {"name": pipeline_name.strip("'"), "homePage": pipeline_url.strip("'"), "repos": {}}
@@ -72,7 +72,7 @@ def create(self):
             if rich.prompt.Confirm.ask(
                 "[bold][blue]?[/] Can't find a ./modules directory. Would you like me to create one?", default=True
             ):
-                log.info(f"Creating ./modules directory in '{self.dir}'")
+                log.info(f"Creating ./modules directory in '{self.directory}'")
                 self.modules_dir.mkdir()
             else:
                 raise UserWarning("Cannot proceed without a ./modules directory.")
@@ -153,7 +153,7 @@ def get_pipeline_module_repositories(self, component_type, directory, repos=None
         # The function might rename some directories, keep track of them
         renamed_dirs = {}
         # Check if there are any untracked repositories
-        dirs_not_covered = self.dir_tree_uncovered(directory, [Path(ModulesRepo(url).repo_path) for url in repos])
+        dirs_not_covered = self.directory_tree_uncovered(directory, [Path(ModulesRepo(url).repo_path) for url in repos])
         if len(dirs_not_covered) > 0:
             log.info(f"Found custom {component_type[:-1]} repositories when creating 'modules.json'")
             # Loop until all directories in the base directory are covered by a remote
@@ -203,7 +203,7 @@ def get_pipeline_module_repositories(self, component_type, directory, repos=None
                 if component_type not in repos[nrepo_remote]:
                     repos[nrepo_remote][component_type] = {}
                 repos[nrepo_remote][component_type][nrepo_name] = {}
-                dirs_not_covered = self.dir_tree_uncovered(
+                dirs_not_covered = self.directory_tree_uncovered(
                     directory, [Path(name) for url in repos for name in repos[url][component_type]]
                 )
 
@@ -816,7 +816,7 @@ def try_apply_patch_reverse(self, module, repo_name, patch_relpath, module_dir):
             LookupError: If patch was not applied
         """
         module_fullname = str(Path(repo_name, module))
-        patch_path = Path(self.dir / patch_relpath)
+        patch_path = Path(self.directory / patch_relpath)
 
         try:
             new_files = ModulesDiffer.try_apply_patch(module, repo_name, patch_path, module_dir, reverse=True)
diff --git a/nf_core/pipelines/create_logo.py b/nf_core/pipelines/create_logo.py
index 0643d2e295..f49e98e93c 100644
--- a/nf_core/pipelines/create_logo.py
+++ b/nf_core/pipelines/create_logo.py
@@ -12,7 +12,7 @@
 
 def create_logo(
     text: str,
-    dir: Union[Path, str],
+    directory: Union[Path, str],
     filename: str = "",
     theme: str = "light",
     width: int = 2300,
@@ -22,10 +22,10 @@ def create_logo(
     """Create a logo for a pipeline."""
     if not text:
         raise UserWarning("Please provide the name of the text to put on the logo.")
-    dir = Path(dir)
-    if not dir.is_dir():
-        log.debug(f"Creating directory {dir}")
-        dir.mkdir(parents=True, exist_ok=True)
+    directory = Path(directory)
+    if not directory.is_dir():
+        log.debug(f"Creating directory {directory}")
+        directory.mkdir(parents=True, exist_ok=True)
     assets = Path(nf_core.__file__).parent / "assets/logo"
 
     if format == "svg":
@@ -43,7 +43,7 @@ def create_logo(
         # save the svg
         logo_filename = f"nf-core-{text}_logo_{theme}.svg" if not filename else filename
         logo_filename = f"{logo_filename}.svg" if not logo_filename.lower().endswith(".svg") else logo_filename
-        logo_path = Path(dir, logo_filename)
+        logo_path = Path(directory, logo_filename)
         with open(logo_path, "w") as fh:
             fh.write(svg)
 
@@ -51,7 +51,7 @@ def create_logo(
         logo_filename = f"nf-core-{text}_logo_{theme}.png" if not filename else filename
         logo_filename = f"{logo_filename}.png" if not logo_filename.lower().endswith(".png") else logo_filename
         cache_name = f"nf-core-{text}_logo_{theme}_{width}.png"
-        logo_path = Path(dir, logo_filename)
+        logo_path = Path(directory, logo_filename)
 
         # Check if we haven't already created this logo
         if logo_path.is_file() and not force:

From 089bb672b13265d40b5cd5cc7e96146943288402 Mon Sep 17 00:00:00 2001
From: laurencekuhl <laurence.kuhlburger@gmail.com>
Date: Thu, 18 Jul 2024 16:31:08 +0200
Subject: [PATCH 095/414] Fix the command_create by putting the plain param
 again

---
 nf_core/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 192c7cd139..1892189964 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -2181,7 +2181,7 @@ def command_lint(
     help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)",
 )
 @click.pass_context
-def command_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation):
+def command_create(ctx, name, description, author, version, force, outdir, template_yaml, plain, organisation):
     """
     Use `nf-core pipelines create` instead.
     """

From dcb1dc0b6802d39494389bfb401d75647b201e83 Mon Sep 17 00:00:00 2001
From: laurencekuhl <laurence.kuhlburger@gmail.com>
Date: Thu, 18 Jul 2024 16:41:38 +0200
Subject: [PATCH 096/414] Automatically add a default version in
 pipelines_create

---
 nf_core/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 1892189964..152814c9cc 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -2188,7 +2188,7 @@ def command_create(ctx, name, description, author, version, force, outdir, templ
     log.warning(
         "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead."
     )
-    pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation)
+    pipelines_create(ctx, name, description, author, version="1.0.0dev", force, outdir, template_yaml, organisation)
 
 
 # Main script is being run - launch the CLI

From 9dc96b8768e4a289cb6784924c7f29e07ed4a39c Mon Sep 17 00:00:00 2001
From: laurencekuhl <laurence.kuhlburger@gmail.com>
Date: Thu, 18 Jul 2024 17:03:45 +0200
Subject: [PATCH 097/414] Add default version

---
 nf_core/__main__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 152814c9cc..cb99bdedcc 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -2169,7 +2169,7 @@ def command_lint(
 )
 @click.option("-d", "--description", type=str, help="A short description of your pipeline")
 @click.option("-a", "--author", type=str, help="Name of the main author(s)")
-@click.option("--version", type=str, help="The initial version number to use")
+@click.option("--version", type=str, default="1.0.0dev", help="The initial version number to use")
 @click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output directory if it already exists")
 @click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)")
 @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
@@ -2188,7 +2188,7 @@ def command_create(ctx, name, description, author, version, force, outdir, templ
     log.warning(
         "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead."
     )
-    pipelines_create(ctx, name, description, author, version="1.0.0dev", force, outdir, template_yaml, organisation)
+    pipelines_create(ctx, name, description, author, force, outdir, template_yaml, organisation)
 
 
 # Main script is being run - launch the CLI

From 60973a19a2381f89b11ff6c408c9f150ff6a1d55 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 19 Jul 2024 06:45:58 +0200
Subject: [PATCH 098/414] fix ALL the mypy errors

---
 nf_core/commands_pipelines.py                 |   2 +-
 nf_core/components/components_command.py      |  10 +-
 nf_core/components/components_utils.py        |   8 +-
 nf_core/components/create.py                  |   2 +-
 nf_core/components/info.py                    |  66 +++++----
 nf_core/components/install.py                 |  42 +++---
 nf_core/components/lint/__init__.py           |  38 +++---
 nf_core/components/list.py                    |  10 +-
 nf_core/components/nfcore_component.py        |  51 ++++---
 nf_core/components/patch.py                   |   4 +
 nf_core/components/remove.py                  |  19 ++-
 nf_core/modules/bump_versions.py              |  12 +-
 nf_core/modules/lint/__init__.py              |  60 ++++++---
 nf_core/modules/lint/environment_yml.py       |   6 +-
 nf_core/modules/lint/main_nf.py               |  21 ++-
 nf_core/modules/lint/meta_yml.py              |   6 +-
 nf_core/modules/modules_differ.py             |  16 ++-
 nf_core/modules/modules_json.py               | 126 ++++++++++++------
 nf_core/modules/modules_repo.py               |   9 +-
 nf_core/modules/modules_utils.py              |  12 +-
 .../subworkflows/lint/subworkflow_tests.py    |   7 +-
 nf_core/synced_repo.py                        |  58 +++++---
 nf_core/utils.py                              |  16 ++-
 23 files changed, 381 insertions(+), 220 deletions(-)

diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py
index deb1f691a5..432a36aaee 100644
--- a/nf_core/commands_pipelines.py
+++ b/nf_core/commands_pipelines.py
@@ -284,7 +284,7 @@ def pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, usern
     Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template.
 
     To keep nf-core pipelines up to date with improvements in the main
-    template, we use a method of synchronisation that uses a special
+    template, we use a method of w that uses a special
     git branch called [cyan i]TEMPLATE[/].
 
     This command updates the [cyan i]TEMPLATE[/] branch with the latest version of
diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index bf80b46113..13a6fed338 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -33,7 +33,7 @@ def __init__(
         Initialise the ComponentClass object
         """
         self.component_type = component_type
-        self.directory = Path(directory) if directory else None
+        self.directory = Path(directory)
         self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)
         self.hide_progress = hide_progress
         self.no_prompts = no_prompts
@@ -109,13 +109,13 @@ def has_modules_file(self) -> None:
             log.info("Creating missing 'module.json' file.")
             ModulesJson(self.directory).create()
 
-    def clear_component_dir(self, component_name: str, component_dir: str) -> bool:
+    def clear_component_dir(self, component_name: str, component_dir: Union[str, Path]) -> bool:
         """
         Removes all files in the module/subworkflow directory
 
         Args:
             component_name (str): The name of the module/subworkflow
-            component_dir (str): The path to the module/subworkflow in the module repository
+            component_dir (str, Path): The path to the module/subworkflow
 
         """
 
@@ -156,7 +156,7 @@ def components_from_repo(self, install_dir: str) -> List[str]:
         ]
 
     def install_component_files(
-        self, component_name: str, component_version: str, modules_repo: ModulesRepo, install_dir: str
+        self, component_name: str, component_version: str, modules_repo: ModulesRepo, install_dir: Union[str, Path]
     ) -> bool:
         """
         Installs a module/subworkflow into the given directory
@@ -165,7 +165,7 @@ def install_component_files(
             component_name (str): The name of the module/subworkflow
             component_version (str): Git SHA for the version of the module/subworkflow to be installed
             modules_repo (ModulesRepo): A correctly configured ModulesRepo object
-            install_dir (str): The path to where the module/subworkflow should be installed (should be the 'modules/' or 'subworkflows/' dir of the pipeline)
+            install_dir (str, Path): The path to where the module/subworkflow should be installed (should be the 'modules/' or 'subworkflows/' dir of the pipeline)
 
         Returns:
             (bool): Whether the operation was successful of not
diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py
index 01650a643d..32f6c0fc11 100644
--- a/nf_core/components/components_utils.py
+++ b/nf_core/components/components_utils.py
@@ -1,7 +1,7 @@
 import logging
 import re
 from pathlib import Path
-from typing import List, Optional, Tuple
+from typing import List, Optional, Tuple, Union
 
 import questionary
 import rich.prompt
@@ -12,7 +12,7 @@
 log = logging.getLogger(__name__)
 
 
-def get_repo_info(directory: str, use_prompt: Optional[bool] = True) -> Tuple[str, Optional[str], str]:
+def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[Path, Optional[str], str]:
     """
     Determine whether this is a pipeline repository or a clone of
     nf-core/modules
@@ -23,7 +23,7 @@ def get_repo_info(directory: str, use_prompt: Optional[bool] = True) -> Tuple[st
         raise UserWarning(f"Could not find directory: {directory}")
 
     # Try to find the root directory
-    base_dir: str = nf_core.utils.determine_base_dir(directory)
+    base_dir: Path = nf_core.utils.determine_base_dir(directory)
 
     # Figure out the repository type from the .nf-core.yml config file if we can
     config_fn, tools_config = nf_core.utils.load_tools_config(base_dir)
@@ -132,7 +132,7 @@ def prompt_component_version_sha(
     return git_sha
 
 
-def get_components_to_install(subworkflow_dir: str) -> Tuple[List[str], List[str]]:
+def get_components_to_install(subworkflow_dir: Union[str, Path]) -> Tuple[List[str], List[str]]:
     """
     Parse the subworkflow main.nf file to retrieve all imported modules and subworkflows.
     """
diff --git a/nf_core/components/create.py b/nf_core/components/create.py
index 5d6c411bdc..532c2a46d6 100644
--- a/nf_core/components/create.py
+++ b/nf_core/components/create.py
@@ -29,7 +29,7 @@ class ComponentCreate(ComponentCommand):
     def __init__(
         self,
         component_type: str,
-        directory: str = ".",
+        directory: Path = Path("."),
         component: str = "",
         author: Optional[str] = None,
         process_label: Optional[str] = None,
diff --git a/nf_core/components/info.py b/nf_core/components/info.py
index 54fc0004dc..8597875af4 100644
--- a/nf_core/components/info.py
+++ b/nf_core/components/info.py
@@ -1,6 +1,7 @@
 import logging
 import os
 from pathlib import Path
+from typing import Dict, Optional, Union
 
 import questionary
 import yaml
@@ -57,25 +58,26 @@ class ComponentInfo(ComponentCommand):
 
     def __init__(
         self,
-        component_type,
-        pipeline_dir,
-        component_name,
-        remote_url=None,
-        branch=None,
-        no_pull=False,
+        component_type: str,
+        pipeline_dir: Union[str, Path],
+        component_name: str,
+        remote_url: Optional[str] = None,
+        branch: Optional[str] = None,
+        no_pull: bool = False,
     ):
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
-        self.meta = None
-        self.local_path = None
-        self.remote_location = None
-        self.local = None
+        self.meta: Optional[Dict] = None
+        self.local_path: Optional[Path] = None
+        self.remote_location: Optional[str] = None
+        self.local: bool = False
+        self.modules_json: Optional[ModulesJson] = None
 
         if self.repo_type == "pipeline":
             # Check modules directory structure
             if self.component_type == "modules":
                 self.check_modules_structure()
             # Check modules.json up to date
-            self.modules_json = ModulesJson(self.dir)
+            self.modules_json = ModulesJson(self.directory)
             self.modules_json.check_up_to_date()
         else:
             self.modules_json = None
@@ -95,6 +97,7 @@ def init_mod_name(self, component):
         Args:
             module: str: Module name to check
         """
+        assert self.modules_json is not None  # mypy
         if component is None:
             self.local = questionary.confirm(
                 f"Is the {self.component_type[:-1]} locally installed?", style=nf_core.utils.nfcore_question_style
@@ -103,12 +106,12 @@ def init_mod_name(self, component):
                 if self.repo_type == "modules":
                     components = self.get_components_clone_modules()
                 else:
-                    components = self.modules_json.get_all_components(self.component_type).get(
-                        self.modules_repo.remote_url, {}
+                    all_components = self.modules_json.get_all_components(self.component_type).get(
+                        self.modules_repo.remote_url, []
                     )
                     components = [
                         component if directory == self.modules_repo.repo_path else f"{directory}/{component}"
-                        for directory, component in components
+                        for directory, component in all_components
                     ]
                     if not components:
                         raise UserWarning(
@@ -133,11 +136,13 @@ def init_mod_name(self, component):
             if self.repo_type == "pipeline":
                 # check if the module is locally installed
                 local_paths = self.modules_json.get_all_components(self.component_type).get(
-                    self.modules_repo.remote_url, {}
-                )
+                    self.modules_repo.remote_url
+                )  # type: ignore
+                if local_paths is None:
+                    raise LookupError(f"No {self.component_type[:-1]} installed from {self.modules_repo.remote_url}")
                 for directory, comp in local_paths:
                     if comp == component:
-                        component_base_path = Path(self.dir, self.component_type)
+                        component_base_path = Path(self.directory, self.component_type)
                         self.local_path = Path(component_base_path, directory, component)
                         break
                 if self.local_path:
@@ -166,20 +171,22 @@ def get_local_yaml(self):
         """Attempt to get the meta.yml file from a locally installed module/subworkflow.
 
         Returns:
-            dict or bool: Parsed meta.yml found, False otherwise
+            Optional[dict]: Parsed meta.yml if found, None otherwise
         """
 
+        assert self.modules_json is not None  # mypy
         if self.repo_type == "pipeline":
             # Try to find and load the meta.yml file
-            component_base_path = Path(self.dir, self.component_type)
+            component_base_path = Path(self.directory, self.component_type)
             # Check that we have any modules/subworkflows installed from this repo
             components = self.modules_json.get_all_components(self.component_type).get(self.modules_repo.remote_url)
-            component_names = [component for _, component in components]
             if components is None:
                 raise LookupError(f"No {self.component_type[:-1]} installed from {self.modules_repo.remote_url}")
 
+            component_names = [component for _, component in components]
+
             if self.component in component_names:
-                install_dir = [dir for dir, module in components if module == self.component][0]
+                install_dir = [directory for directory, module in components if module == self.component][0]
                 comp_dir = Path(component_base_path, install_dir, self.component)
                 meta_fn = Path(comp_dir, "meta.yml")
                 if meta_fn.exists():
@@ -190,7 +197,7 @@ def get_local_yaml(self):
 
             log.debug(f"{self.component_type[:-1].title()} '{self.component}' meta.yml not found locally")
         else:
-            component_base_path = Path(self.dir, self.component_type, self.org)
+            component_base_path = Path(self.directory, self.component_type, self.org)
             if self.component in os.listdir(component_base_path):
                 comp_dir = Path(component_base_path, self.component)
                 meta_fn = Path(comp_dir, "meta.yml")
@@ -203,7 +210,7 @@ def get_local_yaml(self):
 
         return None
 
-    def get_remote_yaml(self):
+    def get_remote_yaml(self) -> Optional[dict]:
         """Attempt to get the meta.yml file from a remote repo.
 
         Returns:
@@ -211,11 +218,11 @@ def get_remote_yaml(self):
         """
         # Check if our requested module/subworkflow is there
         if self.component not in self.modules_repo.get_avail_components(self.component_type):
-            return False
+            return None
 
         file_contents = self.modules_repo.get_meta_yml(self.component_type, self.component)
         if file_contents is None:
-            return False
+            return None
         self.remote_location = self.modules_repo.remote_url
         return yaml.safe_load(file_contents)
 
@@ -242,7 +249,8 @@ def generate_component_info_help(self):
                     "\n"
                 )
             )
-
+        if self.meta is None:
+            raise UserWarning("No meta.yml file found")
         if self.meta.get("tools"):
             tools_strings = []
             for tool in self.meta["tools"]:
@@ -307,21 +315,21 @@ def generate_component_info_help(self):
 
         # Print include statement
         if self.local_path:
-            install_folder = Path(self.dir, self.component_type, self.modules_repo.repo_path)
+            install_folder = Path(self.directory, self.component_type, self.modules_repo.repo_path)
             component_name = "_".join(self.component.upper().split("/"))
             renderables.append(
                 Text.from_markup(f"\n [blue]Use the following statement to include this {self.component_type[:-1]}:")
             )
             renderables.append(
                 Syntax(
-                    f"include {{ {component_name} }} from '../{Path(install_folder, self.component).relative_to(self.dir)}/main'",
+                    f"include {{ {component_name} }} from '../{Path(install_folder, self.component).relative_to(self.directory)}/main'",
                     "groovy",
                     theme="ansi_dark",
                     padding=1,
                 )
             )
             if self.component_type == "subworkflows":
-                subworkflow_config = Path(install_folder, self.component, "nextflow.config").relative_to(self.dir)
+                subworkflow_config = Path(install_folder, self.component, "nextflow.config").relative_to(self.directory)
                 if os.path.isfile(subworkflow_config):
                     renderables.append(
                         Text.from_markup("\n [blue]Add the following config statement to use this subworkflow:")
diff --git a/nf_core/components/install.py b/nf_core/components/install.py
index dddc3f93ec..e6c31b3cbb 100644
--- a/nf_core/components/install.py
+++ b/nf_core/components/install.py
@@ -1,11 +1,13 @@
 import logging
 import os
 from pathlib import Path
+from typing import List, Optional, Union
 
 import questionary
 from rich.console import Console
 from rich.syntax import Syntax
 
+import nf_core.components
 import nf_core.modules.modules_utils
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
@@ -22,26 +24,26 @@
 class ComponentInstall(ComponentCommand):
     def __init__(
         self,
-        pipeline_dir,
-        component_type,
-        force=False,
-        prompt=False,
-        sha=None,
-        remote_url=None,
-        branch=None,
-        no_pull=False,
-        installed_by=False,
+        pipeline_dir: Union[str, Path],
+        component_type: str,
+        force: bool = False,
+        prompt: bool = False,
+        sha: Optional[str] = None,
+        remote_url: Optional[str] = None,
+        branch: Optional[str] = None,
+        no_pull: bool = False,
+        installed_by: Optional[List[str]] = None,
     ):
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
         self.force = force
         self.prompt = prompt
         self.sha = sha
-        if installed_by:
+        if installed_by is not None:
             self.installed_by = installed_by
         else:
-            self.installed_by = self.component_type
+            self.installed_by = [self.component_type]
 
-    def install(self, component, silent=False):
+    def install(self, component: str, silent: bool = False) -> bool:
         if self.repo_type == "modules":
             log.error(f"You cannot install a {component} in a clone of nf-core/modules")
             return False
@@ -67,8 +69,11 @@ def install(self, component, silent=False):
         # Verify SHA
         if not self.modules_repo.verify_sha(self.prompt, self.sha):
             return False
+        if self.modules_repo is None:
+            return False
 
         # Check and verify component name
+
         component = self.collect_and_verify_name(component, self.modules_repo)
         if not component:
             return False
@@ -156,19 +161,21 @@ def install_included_components(self, subworkflow_dir):
         modules_to_install, subworkflows_to_install = get_components_to_install(subworkflow_dir)
         for s_install in subworkflows_to_install:
             original_installed = self.installed_by
-            self.installed_by = Path(subworkflow_dir).parts[-1]
+            self.installed_by = [Path(subworkflow_dir).parts[-1]]
             self.install(s_install, silent=True)
             self.installed_by = original_installed
         for m_install in modules_to_install:
             original_component_type = self.component_type
             self.component_type = "modules"
             original_installed = self.installed_by
-            self.installed_by = Path(subworkflow_dir).parts[-1]
+            self.installed_by = [Path(subworkflow_dir).parts[-1]]
             self.install(m_install, silent=True)
             self.component_type = original_component_type
             self.installed_by = original_installed
 
-    def collect_and_verify_name(self, component, modules_repo):
+    def collect_and_verify_name(
+        self, component: Optional[str], modules_repo: nf_core.modules.modules_repo.ModulesRepo
+    ) -> str:
         """
         Collect component name.
         Check that the supplied name is an available module/subworkflow.
@@ -180,18 +187,19 @@ def collect_and_verify_name(self, component, modules_repo):
                 style=nf_core.utils.nfcore_question_style,
             ).unsafe_ask()
 
+        if component is None:
+            return ""
+
         # Check that the supplied name is an available module/subworkflow
         if component and component not in modules_repo.get_avail_components(self.component_type, commit=self.sha):
             log.error(
                 f"{self.component_type[:-1].title()} '{component}' not found in list of available {self.component_type}."
             )
             log.info(f"Use the command 'nf-core {self.component_type} list' to view available software")
-            return False
 
         if not modules_repo.component_exists(component, self.component_type, commit=self.sha):
             warn_msg = f"{self.component_type[:-1].title()} '{component}' not found in remote '{modules_repo.remote_url}' ({modules_repo.branch})"
             log.warning(warn_msg)
-            return False
 
         return component
 
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index 7dd39bd904..2cd59dc489 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -7,7 +7,7 @@
 import operator
 import os
 from pathlib import Path
-from typing import List, Optional, Union
+from typing import List, Optional, Tuple, Union
 
 import rich.box
 import rich.console
@@ -37,12 +37,12 @@ class LintExceptionError(Exception):
 class LintResult:
     """An object to hold the results of a lint test"""
 
-    def __init__(self, component, lint_test, message, file_path):
+    def __init__(self, component: NFCoreComponent, lint_test: str, message: str, file_path: Path):
         self.component = component
         self.lint_test = lint_test
         self.message = message
         self.file_path = file_path
-        self.component_name = component.component_name
+        self.component_name: str = component.component_name
 
 
 @rich.repr.auto
@@ -73,9 +73,9 @@ def __init__(
         )
 
         self.fail_warned = fail_warned
-        self.passed: List[str] = []
-        self.warned: List[str] = []
-        self.failed: List[str] = []
+        self.passed: List[LintResult] = []
+        self.warned: List[LintResult] = []
+        self.failed: List[LintResult] = []
         if self.component_type == "modules":
             self.lint_tests = self.get_all_module_lint_tests(self.repo_type == "pipeline")
         else:
@@ -88,17 +88,21 @@ def __init__(
             for repo_url, components in modules_json.get_all_components(self.component_type).items():
                 if remote_url is not None and remote_url != repo_url:
                     continue
-                for org, comp in components:
-                    self.all_remote_components.append(
-                        NFCoreComponent(
-                            comp,
-                            repo_url,
-                            Path(self.directory, self.component_type, org, comp),
-                            self.repo_type,
-                            Path(self.directory),
-                            self.component_type,
-                        )
+                if isinstance(components, str):
+                    raise LookupError(
+                        f"Error parsing modules.json: {components}. " f"Please check the file for errors or try again."
                     )
+                org, comp = components
+                self.all_remote_components.append(
+                    NFCoreComponent(
+                        comp,
+                        repo_url,
+                        Path(self.directory, self.component_type, org, comp),
+                        self.repo_type,
+                        Path(self.directory),
+                        self.component_type,
+                    )
+                )
             if not self.all_remote_components:
                 raise LookupError(
                     f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline."
@@ -119,7 +123,7 @@ def __init__(
                     for comp in self.get_local_components()
                 ]
             self.config = nf_core.utils.fetch_wf_config(Path(self.directory), cache_config=True)
-        else:
+        elif self.repo_type == "modules":
             component_dir = Path(
                 self.directory,
                 self.default_modules_path if self.component_type == "modules" else self.default_subworkflows_path,
diff --git a/nf_core/components/list.py b/nf_core/components/list.py
index f5f2744e17..b24732e5c3 100644
--- a/nf_core/components/list.py
+++ b/nf_core/components/list.py
@@ -1,6 +1,6 @@
 import json
 import logging
-from typing import Dict, List, Optional, Tuple, Union, cast
+from typing import Dict, List, Optional, Union, cast
 
 import rich.table
 
@@ -87,18 +87,18 @@ def pattern_msg(keywords: List[str]) -> str:
                 return ""
 
             # Verify that 'modules.json' is consistent with the installed modules
-            modules_json: ModulesJson = ModulesJson(self.dir)
+            modules_json: ModulesJson = ModulesJson(self.directory)
             modules_json.check_up_to_date()
 
             # Filter by keywords
-            repos_with_comps: Dict[str, List[Tuple[str, str]]] = {
+            repos_with_comps = {
                 repo_url: [comp for comp in components if all(k in comp[1] for k in keywords)]
                 for repo_url, components in modules_json.get_all_components(self.component_type).items()
             }
 
             # Nothing found
             if sum(map(len, repos_with_comps)) == 0:
-                log.info(f"No nf-core {self.component_type} found in '{self.dir}'{pattern_msg(keywords)}")
+                log.info(f"No nf-core {self.component_type} found in '{self.directory}'{pattern_msg(keywords)}")
                 return ""
 
             table.add_column("Repository")
@@ -160,5 +160,5 @@ def pattern_msg(keywords: List[str]) -> str:
                 f"{pattern_msg(keywords)}:\n"
             )
         else:
-            log.info(f"{self.component_type.capitalize()} installed in '{self.dir}'{pattern_msg(keywords)}:\n")
+            log.info(f"{self.component_type.capitalize()} installed in '{self.directory}'{pattern_msg(keywords)}:\n")
         return table
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 5d0baf63dd..1433122225 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -5,7 +5,7 @@
 import logging
 import re
 from pathlib import Path
-from typing import Union
+from typing import List, Optional, Tuple, Union
 
 log = logging.getLogger(__name__)
 
@@ -18,13 +18,13 @@ class NFCoreComponent:
 
     def __init__(
         self,
-        component_name,
-        repo_url,
-        component_dir,
-        repo_type,
-        base_dir,
-        component_type,
-        remote_component=True,
+        component_name: str,
+        repo_url: Optional[str],
+        component_dir: Path,
+        repo_type: str,
+        base_dir: Path,
+        component_type: str,
+        remote_component: bool = True,
     ):
         """
         Initialize the object
@@ -46,21 +46,21 @@ def __init__(
         self.component_dir = component_dir
         self.repo_type = repo_type
         self.base_dir = base_dir
-        self.passed = []
-        self.warned = []
-        self.failed = []
-        self.inputs = []
-        self.outputs = []
-        self.has_meta = False
-        self.git_sha = None
-        self.is_patched = False
+        self.passed: List[Tuple[str, str, Path]] = []
+        self.warned: List[Tuple[str, str, Path]] = []
+        self.failed: List[Tuple[str, str, Path]] = []
+        self.inputs: List[str] = []
+        self.outputs: List[str] = []
+        self.has_meta: bool = False
+        self.git_sha: Optional[str] = None
+        self.is_patched: bool = False
 
         if remote_component:
             # Initialize the important files
-            self.main_nf = Path(self.component_dir, "main.nf")
-            self.meta_yml = Path(self.component_dir, "meta.yml")
+            self.main_nf: Path = Path(self.component_dir, "main.nf")
+            self.meta_yml: Optional[Path] = Path(self.component_dir, "meta.yml")
             self.process_name = ""
-            self.environment_yml = Path(self.component_dir, "environment.yml")
+            self.environment_yml: Optional[Path] = Path(self.component_dir, "environment.yml")
 
             repo_dir = self.component_dir.parts[: self.component_dir.parts.index(self.component_name.split("/")[0])][-1]
             self.org = repo_dir
@@ -79,8 +79,8 @@ def __init__(
             self.component_name = self.component_dir.stem
             # These attributes are only used by nf-core modules
             # so just initialize them to None
-            self.meta_yml = ""
-            self.environment_yml = ""
+            self.meta_yml = None
+            self.environment_yml = None
             self.test_dir = None
             self.test_yml = None
             self.test_main_nf = None
@@ -155,10 +155,10 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st
                         included_components.append(component)
         return included_components
 
-    def get_inputs_from_main_nf(self):
+    def get_inputs_from_main_nf(self) -> None:
         """Collect all inputs from the main.nf file."""
-        inputs = []
-        with open(self.main_nf) as f:
+        inputs: List[str] = []
+        with open(str(self.main_nf)) as f:
             data = f.read()
         # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo
         # regex matches:
@@ -171,7 +171,6 @@ def get_inputs_from_main_nf(self):
         # don't match anything inside comments or after "output:"
         if "input:" not in data:
             log.debug(f"Could not find any inputs in {self.main_nf}")
-            return inputs
         input_data = data.split("input:")[1].split("output:")[0]
         regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
         matches = re.finditer(regex, input_data, re.MULTILINE)
@@ -187,7 +186,7 @@ def get_inputs_from_main_nf(self):
 
     def get_outputs_from_main_nf(self):
         outputs = []
-        with open(self.main_nf) as f:
+        with open(str(self.main_nf)) as f:
             data = f.read()
         # get output values from main.nf after "output:". the names are always after "emit:"
         if "output:" not in data:
diff --git a/nf_core/components/patch.py b/nf_core/components/patch.py
index 55d5747451..5b29c152d8 100644
--- a/nf_core/components/patch.py
+++ b/nf_core/components/patch.py
@@ -30,6 +30,10 @@ def _parameter_checks(self, component):
             raise UserWarning("The command was not run in a valid pipeline directory.")
 
         components = self.modules_json.get_all_components(self.component_type).get(self.modules_repo.remote_url)
+        if components is None:
+            raise UserWarning(
+                f"No {self.component_type[:-1]}s found in the 'modules.json' file for the remote '{self.modules_repo.remote_url}'"
+            )
         component_names = [component for _, component in components]
 
         if component is not None and component not in component_names:
diff --git a/nf_core/components/remove.py b/nf_core/components/remove.py
index 8d884db6c4..c2c5843918 100644
--- a/nf_core/components/remove.py
+++ b/nf_core/components/remove.py
@@ -58,10 +58,10 @@ def remove(self, component, removed_by=None, removed_components=None, force=Fals
             removed_components = []
 
         # Get the module/subworkflow directory
-        component_dir = Path(self.dir, self.component_type, repo_path, component)
+        component_dir = Path(self.directory, self.component_type, repo_path, component)
 
         # Load the modules.json file
-        modules_json = ModulesJson(self.dir)
+        modules_json = ModulesJson(self.directory)
         modules_json.load()
 
         # Verify that the module/subworkflow is actually installed
@@ -98,9 +98,16 @@ def remove(self, component, removed_by=None, removed_components=None, force=Fals
                 for file, stmts in include_stmts.items():
                     renderables = []
                     for stmt in stmts:
+                        # check that the line number is integer
+                        if not isinstance(stmt["line_number"], int):
+                            log.error(
+                                f"Could not parse line number '{stmt['line_number']}' in '{file}'. Please report this issue."
+                            )
+                            continue
+
                         renderables.append(
                             Syntax(
-                                stmt["line"],
+                                str(stmt["line"]),
                                 "groovy",
                                 theme="ansi_dark",
                                 line_numbers=True,
@@ -123,7 +130,7 @@ def remove(self, component, removed_by=None, removed_components=None, force=Fals
                         style=nf_core.utils.nfcore_question_style,
                     ).unsafe_ask():
                         # add the component back to modules.json
-                        if not ComponentInstall(self.dir, self.component_type, force=True).install(
+                        if not ComponentInstall(self.directory, self.component_type, force=True).install(
                             component, silent=True
                         ):
                             log.warning(
@@ -133,7 +140,9 @@ def remove(self, component, removed_by=None, removed_components=None, force=Fals
                         return removed
             # Remove the component files of all entries removed from modules.json
             removed = (
-                True if self.clear_component_dir(component, Path(self.dir, removed_component_dir)) or removed else False
+                True
+                if self.clear_component_dir(component, Path(self.directory, removed_component_dir)) or removed
+                else False
             )
             removed_components.append(component)
 
diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
index 1b94d5910c..fb0dc7d50d 100644
--- a/nf_core/modules/bump_versions.py
+++ b/nf_core/modules/bump_versions.py
@@ -76,10 +76,10 @@ def bump_versions(
             )
 
         # Get list of all modules
-        _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.dir)
+        _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.directory)
 
         # Load the .nf-core.yml config
-        _, self.tools_config = nf_core.utils.load_tools_config(self.dir)
+        _, self.tools_config = nf_core.utils.load_tools_config(self.directory)
 
         # Prompt for module or all
         if module is None and not all_modules:
@@ -179,7 +179,7 @@ def bump_module_version(self, module: NFCoreComponent) -> bool:
             except (LookupError, ValueError):
                 self.failed.append(
                     (
-                        f"Conda version not specified correctly: {module.main_nf.relative_to(self.dir)}",
+                        f"Conda version not specified correctly: {Path(module.main_nf).relative_to(self.directory)}",
                         module.component_name,
                     )
                 )
@@ -245,12 +245,12 @@ def bump_module_version(self, module: NFCoreComponent) -> bool:
                 fh.write(content)
 
             # change version in environment.yml
-            with open(module.environment_yml) as fh:
+            with open(str(module.environment_yml)) as fh:
                 env_yml = yaml.safe_load(fh)
             env_yml["dependencies"][0] = re.sub(
                 bioconda_packages[0], f"bioconda::{bioconda_tool_name}={last_ver}", env_yml["dependencies"][0]
             )
-            with open(module.environment_yml, "w") as fh:
+            with open(str(module.environment_yml), "w") as fh:
                 yaml.dump(env_yml, fh, default_flow_style=False, Dumper=custom_yaml_dumper())
 
             self.updated.append(
@@ -272,7 +272,7 @@ def get_bioconda_version(self, module: NFCoreComponent) -> List[str]:
         # Check whether file exists and load it
         bioconda_packages = []
         try:
-            with open(module.environment_yml) as fh:
+            with open(str(module.environment_yml)) as fh:
                 env_yml = yaml.safe_load(fh)
             bioconda_packages = env_yml.get("dependencies", [])
         except FileNotFoundError:
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index 90d39104d2..2b10b4df5a 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -8,18 +8,33 @@
 
 import logging
 import os
+from pathlib import Path
+from typing import List, Optional, Union
 
 import questionary
 import rich
 import rich.progress
 
+import nf_core.components
+import nf_core.components.nfcore_component
 import nf_core.modules.modules_utils
 import nf_core.utils
 from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult
+from nf_core.components.nfcore_component import NFCoreComponent
 from nf_core.pipelines.lint_utils import console
 
 log = logging.getLogger(__name__)
 
+from .environment_yml import environment_yml
+from .main_nf import main_nf
+from .meta_yml import meta_yml
+from .module_changes import module_changes
+from .module_deprecations import module_deprecations
+from .module_patch import module_patch
+from .module_tests import module_tests
+from .module_todos import module_todos
+from .module_version import module_version
+
 
 class ModuleLint(ComponentLint):
     """
@@ -28,25 +43,25 @@ class ModuleLint(ComponentLint):
     """
 
     # Import lint functions
-    from .environment_yml import environment_yml  # type: ignore[misc]
-    from .main_nf import main_nf  # type: ignore[misc]
-    from .meta_yml import meta_yml  # type: ignore[misc]
-    from .module_changes import module_changes  # type: ignore[misc]
-    from .module_deprecations import module_deprecations  # type: ignore[misc]
-    from .module_patch import module_patch  # type: ignore[misc]
-    from .module_tests import module_tests  # type: ignore[misc]
-    from .module_todos import module_todos  # type: ignore[misc]
-    from .module_version import module_version  # type: ignore[misc]
+    environment_yml = environment_yml
+    main_nf = main_nf
+    meta_yml = meta_yml
+    module_changes = module_changes
+    module_deprecations = module_deprecations
+    module_patch = module_patch
+    module_tests = module_tests
+    module_todos = module_todos
+    module_version = module_version
 
     def __init__(
         self,
-        directory,
-        fail_warned=False,
-        remote_url=None,
-        branch=None,
-        no_pull=False,
-        registry=None,
-        hide_progress=False,
+        directory: Union[str, Path],
+        fail_warned: bool = False,
+        remote_url: Optional[str] = None,
+        branch: Optional[str] = None,
+        no_pull: bool = False,
+        registry: Optional[str] = None,
+        hide_progress: bool = False,
     ):
         super().__init__(
             component_type="modules",
@@ -155,7 +170,9 @@ def lint(
             self._print_results(show_passed=show_passed, sort_by=sort_by)
             self.print_summary()
 
-    def lint_modules(self, modules, registry="quay.io", local=False, fix_version=False):
+    def lint_modules(
+        self, modules: List[NFCoreComponent], registry: str = "quay.io", local: bool = False, fix_version: bool = False
+    ) -> None:
         """
         Lint a list of modules
 
@@ -185,7 +202,14 @@ def lint_modules(self, modules, registry="quay.io", local=False, fix_version=Fal
                 progress_bar.update(lint_progress, advance=1, test_name=mod.component_name)
                 self.lint_module(mod, progress_bar, registry=registry, local=local, fix_version=fix_version)
 
-    def lint_module(self, mod, progress_bar, registry, local=False, fix_version=False):
+    def lint_module(
+        self,
+        mod: NFCoreComponent,
+        progress_bar: rich.progress.Progress,
+        registry: str,
+        local: bool = False,
+        fix_version: bool = False,
+    ):
         """
         Perform linting on one module
 
diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py
index e10ef1761d..e34b9d5856 100644
--- a/nf_core/modules/lint/environment_yml.py
+++ b/nf_core/modules/lint/environment_yml.py
@@ -5,7 +5,7 @@
 import yaml
 from jsonschema import exceptions, validators
 
-from nf_core.components.lint import ComponentLint
+from nf_core.components.lint import ComponentLint, LintExceptionError
 from nf_core.components.nfcore_component import NFCoreComponent
 from nf_core.utils import custom_yaml_dumper
 
@@ -22,8 +22,10 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
     """
     env_yml = None
     #  load the environment.yml file
+    if module.environment_yml is None:
+        raise LintExceptionError("Module does not have an `environment.yml` file")
     try:
-        with open(Path(module.component_dir, "environment.yml")) as fh:
+        with open(str(module.environment_yml)) as fh:
             env_yml = yaml.safe_load(fh)
 
         module.passed.append(("environment_yml_exists", "Module's `environment.yml` exists", module.environment_yml))
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 81308ba5c5..985a92fa1f 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -6,19 +6,24 @@
 import re
 import sqlite3
 from pathlib import Path
+from typing import List, Tuple
 from urllib.parse import urlparse, urlunparse
 
 import requests
 import yaml
+from rich.progress import Progress
 
 import nf_core
 import nf_core.modules.modules_utils
+from nf_core.components.nfcore_component import NFCoreComponent
 from nf_core.modules.modules_differ import ModulesDiffer
 
 log = logging.getLogger(__name__)
 
 
-def main_nf(module_lint_object, module, fix_version, registry, progress_bar):
+def main_nf(
+    module_lint_object, module: NFCoreComponent, fix_version: bool, registry: str, progress_bar: Progress
+) -> Tuple[List[str], List[str]]:
     """
     Lint a ``main.nf`` module file
 
@@ -43,7 +48,7 @@ def main_nf(module_lint_object, module, fix_version, registry, progress_bar):
 
     # Check if we have a patch file affecting the 'main.nf' file
     # otherwise read the lines directly from the module
-    lines = None
+    lines: List[str] = []
     if module.is_patched:
         lines = ModulesDiffer.try_apply_patch(
             module.component_name,
@@ -51,8 +56,9 @@ def main_nf(module_lint_object, module, fix_version, registry, progress_bar):
             module.patch_path,
             Path(module.component_dir).relative_to(module.base_dir),
             reverse=True,
-        ).get("main.nf")
-    if lines is None:
+        ).get("main.nf", [""])
+
+    if not lines:
         try:
             # Check whether file exists and load it
             with open(module.main_nf) as fh:
@@ -60,10 +66,13 @@ def main_nf(module_lint_object, module, fix_version, registry, progress_bar):
             module.passed.append(("main_nf_exists", "Module file exists", module.main_nf))
         except FileNotFoundError:
             module.failed.append(("main_nf_exists", "Module file does not exist", module.main_nf))
-            return
 
     deprecated_i = ["initOptions", "saveFiles", "getSoftwareName", "getProcessName", "publishDir"]
-    lines_j = "\n".join(lines)
+    if lines is not None:
+        lines_j = "\n".join(lines)
+    else:
+        lines_j = ""
+
     for i in deprecated_i:
         if i in lines_j:
             module.failed.append(
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 4c036713c8..32110b7131 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -4,7 +4,7 @@
 import yaml
 from jsonschema import exceptions, validators
 
-from nf_core.components.lint import ComponentLint
+from nf_core.components.lint import ComponentLint, LintExceptionError
 from nf_core.components.nfcore_component import NFCoreComponent
 from nf_core.modules.modules_differ import ModulesDiffer
 
@@ -53,9 +53,11 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
         ).get("meta.yml")
         if lines is not None:
             meta_yaml = yaml.safe_load("".join(lines))
+    if module.meta_yml is None:
+        raise LintExceptionError("Module does not have a `meta.yml` file")
     if meta_yaml is None:
         try:
-            with open(module.meta_yml) as fh:
+            with open(str(module.meta_yml)) as fh:
                 meta_yaml = yaml.safe_load(fh)
             module.passed.append(("meta_yml_exists", "Module `meta.yml` exists", module.meta_yml))
         except FileNotFoundError:
diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py
index e79554f2b6..36d927f084 100644
--- a/nf_core/modules/modules_differ.py
+++ b/nf_core/modules/modules_differ.py
@@ -4,6 +4,7 @@
 import logging
 import os
 from pathlib import Path
+from typing import List, Union
 
 from rich.console import Console
 from rich.syntax import Syntax
@@ -295,7 +296,7 @@ def print_diff(
                 console.print(Syntax("".join(diff), "diff", theme="ansi_dark", padding=1))
 
     @staticmethod
-    def per_file_patch(patch_fn):
+    def per_file_patch(patch_fn: Union[str, Path]) -> dict[str, List[str]]:
         """
         Splits a patch file for several files into one patch per file.
 
@@ -306,12 +307,12 @@ def per_file_patch(patch_fn):
             dict[str, str]: A dictionary indexed by the filenames with the
                             file patches as values
         """
-        with open(patch_fn) as fh:
+        with open(str(patch_fn)) as fh:
             lines = fh.readlines()
 
         patches = {}
         i = 0
-        patch_lines = []
+        patch_lines: list[str] = []
         key = "preamble"
         while i < len(lines):
             line = lines[i]
@@ -391,12 +392,12 @@ def try_apply_single_patch(file_lines, patch, reverse=False):
         """
         Tries to apply a patch to a modified file. Since the line numbers in
         the patch does not agree if the file is modified, the old and new
-        lines in the patch are reconstructed and then we look for the old lines
+        lines inpatch are reconstructed and then we look for the old lines
         in the modified file. If all hunk in the patch are found in the new file
         it is updated with the new lines from the patch file.
 
         Args:
-            new_fn (str | Path): Path to the modified file
+            file_lines ([str]): The lines of the file to be patched
             patch (str | Path): (Outdated) patch for the file
             reverse (bool): Apply the patch in reverse
 
@@ -450,7 +451,9 @@ def try_apply_single_patch(file_lines, patch, reverse=False):
         return patched_new_lines
 
     @staticmethod
-    def try_apply_patch(module, repo_path, patch_path, module_dir, reverse=False):
+    def try_apply_patch(
+        module: str, repo_path: Union[str, Path], patch_path: Union[str, Path], module_dir: Path, reverse: bool = False
+    ) -> dict[str, List[str]]:
         """
         Try applying a full patch file to a module
 
@@ -459,6 +462,7 @@ def try_apply_patch(module, repo_path, patch_path, module_dir, reverse=False):
             repo_path (str): Name of the repository where the module resides
             patch_path (str): The absolute path to the patch file to be applied
             module_dir (Path): The directory containing the module
+            reverse (bool): Apply the patch in reverse
 
         Returns:
             dict[str, str]: A dictionary with file paths (relative to the pipeline dir)
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 63c356a79a..faeb84fc35 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -6,7 +6,7 @@
 import shutil
 import tempfile
 from pathlib import Path
-from typing import Union
+from typing import Any, List, Optional, Tuple, Union
 
 import git
 import questionary
@@ -153,7 +153,7 @@ def get_pipeline_module_repositories(self, component_type, directory, repos=None
         # The function might rename some directories, keep track of them
         renamed_dirs = {}
         # Check if there are any untracked repositories
-        dirs_not_covered = self.directory_tree_uncovered(directory, [Path(ModulesRepo(url).repo_path) for url in repos])
+        dirs_not_covered = self.dir_tree_uncovered(directory, [Path(ModulesRepo(url).repo_path) for url in repos])
         if len(dirs_not_covered) > 0:
             log.info(f"Found custom {component_type[:-1]} repositories when creating 'modules.json'")
             # Loop until all directories in the base directory are covered by a remote
@@ -203,7 +203,7 @@ def get_pipeline_module_repositories(self, component_type, directory, repos=None
                 if component_type not in repos[nrepo_remote]:
                     repos[nrepo_remote][component_type] = {}
                 repos[nrepo_remote][component_type][nrepo_name] = {}
-                dirs_not_covered = self.directory_tree_uncovered(
+                dirs_not_covered = self.dir_tree_uncovered(
                     directory, [Path(name) for url in repos for name in repos[url][component_type]]
                 )
 
@@ -244,7 +244,9 @@ def dir_tree_uncovered(self, components_directory, repos):
             depth += 1
         return dirs_not_covered
 
-    def determine_branches_and_shas(self, component_type, install_dir, remote_url, components):
+    def determine_branches_and_shas(
+        self, component_type: str, install_dir: Union[str, Path], remote_url: str, components: List[Path]
+    ) -> dict[Path, dict[str, Any]]:
         """
         Determines what branch and commit sha each module/subworkflow in the pipeline belongs to
 
@@ -265,6 +267,8 @@ def determine_branches_and_shas(self, component_type, install_dir, remote_url, c
             repo_path = self.modules_dir / install_dir
         elif component_type == "subworkflows":
             repo_path = self.subworkflows_dir / install_dir
+        else:
+            raise ValueError(f"Unknown component type '{component_type}'")
         # Get the branches present in the repository, as well as the default branch
         available_branches = ModulesRepo.get_remote_branches(remote_url)
         sb_local = []
@@ -282,16 +286,16 @@ def determine_branches_and_shas(self, component_type, install_dir, remote_url, c
                 if patch_file.is_file():
                     temp_module_dir = self.try_apply_patch_reverse(component, install_dir, patch_file, component_path)
                     correct_commit_sha = self.find_correct_commit_sha(
-                        component_type, component, temp_module_dir, modules_repo
+                        component_type, str(component), temp_module_dir, modules_repo
                     )
                 else:
                     correct_commit_sha = self.find_correct_commit_sha(
-                        component_type, component, component_path, modules_repo
+                        component_type, str(component), component_path, modules_repo
                     )
                     if correct_commit_sha is None:
                         # Check in the old path
                         correct_commit_sha = self.find_correct_commit_sha(
-                            component_type, component, repo_path / component_type / component, modules_repo
+                            component_type, str(component), repo_path / component_type / component, modules_repo
                         )
                 if correct_commit_sha is None:
                     log.info(
@@ -334,7 +338,7 @@ def determine_branches_and_shas(self, component_type, install_dir, remote_url, c
         # Clean up the modules/subworkflows we were unable to find the sha for
         for component in sb_local:
             log.debug(f"Moving {component_type[:-1]} '{Path(install_dir, component)}' to 'local' directory")
-            self.move_component_to_local(component_type, component, install_dir)
+            self.move_component_to_local(component_type, component, str(install_dir))
 
         for component in dead_components:
             log.debug(f"Removing {component_type[:-1]} {Path(install_dir, component)}'")
@@ -342,7 +346,13 @@ def determine_branches_and_shas(self, component_type, install_dir, remote_url, c
 
         return repo_entry
 
-    def find_correct_commit_sha(self, component_type, component_name, component_path, modules_repo):
+    def find_correct_commit_sha(
+        self,
+        component_type: str,
+        component_name: Union[str, Path],
+        component_path: Union[str, Path],
+        modules_repo: ModulesRepo,
+    ) -> Optional[str]:
         """
         Returns the SHA for the latest commit where the local files are identical to the remote files
         Args:
@@ -370,24 +380,27 @@ def find_correct_commit_sha(self, component_type, component_name, component_path
                 return commit_sha
         return None
 
-    def move_component_to_local(self, component_type, component, repo_name):
+    def move_component_to_local(self, component_type: str, component: Union[str, Path], repo_name: str):
         """
         Move a module/subworkflow to the 'local' directory
 
         Args:
-            component (str): The name of the module/subworkflow
+            component_type (str): The type of component, either 'modules' or 'subworkflows'
+            component (Union[str,Path]): The name of the module/subworkflow
             repo_name (str): The name of the repository the module resides in
         """
         if component_type == "modules":
             directory = self.modules_dir
         elif component_type == "subworkflows":
             directory = self.subworkflows_dir
+        else:
+            raise ValueError(f"Unknown component type '{component_type}'")
         current_path = directory / repo_name / component
         local_dir = directory / "local"
         if not local_dir.exists():
             local_dir.mkdir()
 
-        to_name = component
+        to_name = str(component)
         # Check if there is already a subdirectory with the name
         while (local_dir / to_name).exists():
             # Add a time suffix to the path to make it unique
@@ -395,7 +408,7 @@ def move_component_to_local(self, component_type, component, repo_name):
             to_name += f"-{datetime.datetime.now().strftime('%y%m%d%H%M%S')}"
         shutil.move(current_path, local_dir / to_name)
 
-    def unsynced_components(self):
+    def unsynced_components(self) -> Tuple[List[Path], List[Path], dict]:
         """
         Compute the difference between the modules/subworkflows in the directory and the
         modules/subworkflows in the 'modules.json' file. This is done by looking at all
@@ -406,6 +419,7 @@ def unsynced_components(self):
             by the modules.json file, and modules/subworkflows in the modules.json where
             the installation directory is missing
         """
+        assert self.modules_json is not None  # mypy
         # Add all modules from modules.json to missing_installation
         missing_installation = copy.deepcopy(self.modules_json["repos"])
         # Obtain the path of all installed modules
@@ -429,14 +443,27 @@ def unsynced_components(self):
 
         return untracked_dirs_modules, untracked_dirs_subworkflows, missing_installation
 
-    def parse_dirs(self, dirs, missing_installation, component_type):
+    def parse_dirs(self, dirs: List[Path], missing_installation: dict, component_type: str) -> Tuple[List[Path], dict]:
+        """
+        Parse directories and check if they are tracked in the modules.json file
+
+        Args:
+            dirs ([ Path ]): List of directories to check
+            missing_installation (dict): Dictionary with the modules.json entries
+            component_type (str): The type of component, either 'modules' or 'subworkflows'
+
+        Returns:
+            (untracked_dirs ([ Path ]), missing_installation (dict)): List of directories that are not tracked
+            by the modules.json file, and the updated missing_installation dictionary
+        """
+
         untracked_dirs = []
         for dir_ in dirs:
             # Check if the module/subworkflows directory exists in modules.json
             install_dir = dir_.parts[0]
-            component = str(Path(*dir_.parts[1:]))
+            component = Path(*dir_.parts[1:])
             component_in_file = False
-            git_url = None
+            git_url = ""
             for repo in missing_installation:
                 if component_type in missing_installation[repo]:
                     if install_dir in missing_installation[repo][component_type]:
@@ -453,9 +480,7 @@ def parse_dirs(self, dirs, missing_installation, component_type):
                 # Check if the entry has a git sha and branch before removing
                 components_dict = module_repo[component_type][install_dir]
                 if "git_sha" not in components_dict[component] or "branch" not in components_dict[component]:
-                    self.determine_branches_and_shas(
-                        component_type, component, git_url, module_repo["base_path"], [component]
-                    )
+                    self.determine_branches_and_shas(component_type, component, git_url, [component])
                 # Remove the module/subworkflow from modules/subworkflows without installation
                 module_repo[component_type][install_dir].pop(component)
                 if len(module_repo[component_type][install_dir]) == 0:
@@ -470,13 +495,14 @@ def parse_dirs(self, dirs, missing_installation, component_type):
 
         return untracked_dirs, missing_installation
 
-    def has_git_url_and_modules(self):
+    def has_git_url_and_modules(self) -> bool:
         """
         Check that all repo entries in the modules.json
         has a git url and a modules dict entry
         Returns:
             (bool): True if they are found for all repos, False otherwise
         """
+        assert self.modules_json is not None  # mypy
         for repo_url, repo_entry in self.modules_json.get("repos", {}).items():
             if "modules" not in repo_entry:
                 if "subworkflows" in repo_entry:
@@ -538,7 +564,7 @@ def reinstall_repo(self, install_dir, remote_url, module_entries):
                     failed_to_install.append(module)
         return failed_to_install
 
-    def check_up_to_date(self):
+    def check_up_to_date(self) -> bool:
         """
         Checks whether the modules and subworkflows installed in the directory
         are consistent with the entries in the 'modules.json' file and vice versa.
@@ -558,6 +584,8 @@ def check_up_to_date(self):
             self.load()
             if not self.has_git_url_and_modules():
                 raise UserWarning
+
+            assert self.modules_json is not None  # mypy
             # check that all "installed_by" entries are lists and not strings
             # [these strings come from an older dev version, so this check can probably be removed in a future release]
             for _, repo_entry in self.modules_json.get("repos", {}).items():
@@ -601,7 +629,7 @@ def check_up_to_date(self):
         if len(subworkflows_missing_from_modules_json) > 0:
             dump_modules_json = True
             self.resolve_missing_from_modules_json(subworkflows_missing_from_modules_json, "subworkflows")
-
+        assert self.modules_json is not None  # mypy
         # If the "installed_by" value is not present for modules/subworkflows, add it.
         for repo, repo_content in self.modules_json["repos"].items():
             for component_type, dir_content in repo_content.items():
@@ -626,8 +654,9 @@ def check_up_to_date(self):
 
         if dump_modules_json:
             self.dump(run_prettier=True)
+        return True
 
-    def load(self):
+    def load(self) -> None:
         """
         Loads the modules.json file into the variable 'modules_json'
 
@@ -648,14 +677,14 @@ def load(self):
 
     def update(
         self,
-        component_type,
-        modules_repo,
-        component_name,
-        component_version,
-        installed_by,
-        installed_by_log=None,
-        write_file=True,
-    ):
+        component_type: str,
+        modules_repo: ModulesRepo,
+        component_name: str,
+        component_version: str,
+        installed_by: Optional[List[str]],
+        installed_by_log: Optional[List[str]] = None,
+        write_file: bool = True,
+    ) -> bool:
         """
         Updates the 'module.json' file with new module/subworkflow info
 
@@ -675,9 +704,11 @@ def update(
 
         if self.modules_json is None:
             self.load()
+            assert self.modules_json is not None  # mypy
         repo_name = modules_repo.repo_path
         remote_url = modules_repo.remote_url
         branch = modules_repo.branch
+
         if remote_url not in self.modules_json["repos"]:
             self.modules_json["repos"][remote_url] = {component_type: {repo_name: {}}}
         if component_type not in self.modules_json["repos"][remote_url]:
@@ -757,6 +788,8 @@ def add_patch_entry(self, module_name, repo_url, install_dir, patch_filename, wr
         """
         if self.modules_json is None:
             self.load()
+            assert self.modules_json is not None  # mypy
+
         if repo_url not in self.modules_json["repos"]:
             raise LookupError(f"Repo '{repo_url}' not present in 'modules.json'")
         if module_name not in self.modules_json["repos"][repo_url]["modules"][install_dir]:
@@ -768,6 +801,8 @@ def add_patch_entry(self, module_name, repo_url, install_dir, patch_filename, wr
     def remove_patch_entry(self, module_name, repo_url, install_dir, write_file=True):
         if self.modules_json is None:
             self.load()
+            assert self.modules_json is not None  # mypy
+
         try:
             del self.modules_json["repos"][repo_url]["modules"][install_dir][module_name]["patch"]
         except KeyError:
@@ -789,6 +824,7 @@ def get_patch_fn(self, module_name, repo_url, install_dir):
         """
         if self.modules_json is None:
             self.load()
+            assert self.modules_json is not None  # mypy
         path = (
             self.modules_json["repos"]
             .get(repo_url, {})
@@ -845,6 +881,8 @@ def repo_present(self, repo_name):
         """
         if self.modules_json is None:
             self.load()
+            assert self.modules_json is not None  # mypy
+
         return repo_name in self.modules_json.get("repos", {})
 
     def module_present(self, module_name, repo_url, install_dir):
@@ -859,6 +897,7 @@ def module_present(self, module_name, repo_url, install_dir):
         """
         if self.modules_json is None:
             self.load()
+            assert self.modules_json is not None  # mypy
         return module_name in self.modules_json.get("repos", {}).get(repo_url, {}).get("modules", {}).get(
             install_dir, {}
         )
@@ -872,8 +911,8 @@ def get_modules_json(self) -> dict:
         """
         if self.modules_json is None:
             self.load()
-
-        return copy.deepcopy(self.modules_json)  # type: ignore
+            assert self.modules_json is not None  # mypy
+        return copy.deepcopy(self.modules_json)
 
     def get_component_version(self, component_type, component_name, repo_url, install_dir):
         """
@@ -889,6 +928,7 @@ def get_component_version(self, component_type, component_name, repo_url, instal
         """
         if self.modules_json is None:
             self.load()
+            assert self.modules_json is not None  # mypy
         return (
             self.modules_json.get("repos", {})
             .get(repo_url, {})
@@ -912,6 +952,7 @@ def get_module_version(self, module_name, repo_url, install_dir):
         """
         if self.modules_json is None:
             self.load()
+            assert self.modules_json is not None  # mypy
         return (
             self.modules_json.get("repos", {})
             .get(repo_url, {})
@@ -935,6 +976,7 @@ def get_subworkflow_version(self, subworkflow_name, repo_url, install_dir):
         """
         if self.modules_json is None:
             self.load()
+            assert self.modules_json is not None  # mypy
         return (
             self.modules_json.get("repos", {})
             .get(repo_url, {})
@@ -944,7 +986,7 @@ def get_subworkflow_version(self, subworkflow_name, repo_url, install_dir):
             .get("git_sha", None)
         )
 
-    def get_all_components(self, component_type):
+    def get_all_components(self, component_type: str) -> dict[str, Tuple[(str, str)]]:
         """
         Retrieves all pipeline modules/subworkflows that are reported in the modules.json
 
@@ -954,6 +996,8 @@ def get_all_components(self, component_type):
         """
         if self.modules_json is None:
             self.load()
+            assert self.modules_json is not None  # mypy
+
         if self.pipeline_components is None:
             self.pipeline_components = {}
             for repo, repo_entry in self.modules_json.get("repos", {}).items():
@@ -987,6 +1031,7 @@ def get_dependent_components(
 
         if self.modules_json is None:
             self.load()
+            assert self.modules_json is not None  # mypy
         component_types = ["modules"] if component_type == "modules" else ["modules", "subworkflows"]
         # Find all components that have an entry of install by of  a given component, recursively call this function for subworkflows
         for type in component_types:
@@ -1016,10 +1061,11 @@ def get_installed_by_entries(self, component_type, name):
         """
         if self.modules_json is None:
             self.load()
+            assert self.modules_json is not None  # mypy
         installed_by_entries = {}
-        for repo_url, repo_entry in self.modules_json.get("repos", {}).items():
+        for _, repo_entry in self.modules_json.get("repos", {}).items():
             if component_type in repo_entry:
-                for install_dir, components in repo_entry[component_type].items():
+                for _, components in repo_entry[component_type].items():
                     if name in components:
                         installed_by_entries = components[name]["installed_by"]
                         break
@@ -1037,6 +1083,7 @@ def get_component_branch(self, component_type, component, repo_url, install_dir)
         """
         if self.modules_json is None:
             self.load()
+            assert self.modules_json is not None  # mypy
         branch = (
             self.modules_json["repos"]
             .get(repo_url, {})
@@ -1096,7 +1143,8 @@ def resolve_missing_installation(self, missing_installation, component_type):
                 log.info(
                     f"Was unable to reinstall some {component_type}. Removing 'modules.json' entries: {', '.join(uninstallable_components)}"
                 )
-
+            if self.modules_json is None:
+                raise UserWarning("No modules.json file found")
             for (repo_url, install_dir), component_entries in remove_from_mod_json.items():
                 for component in component_entries:
                     self.modules_json["repos"][repo_url][component_type][install_dir].pop(component)
@@ -1113,7 +1161,7 @@ def resolve_missing_from_modules_json(self, missing_from_modules_json, component
             log.info(
                 f"Recomputing commit SHAs for {component_type} which were missing from 'modules.json': {', '.join(format_missing)}"
             )
-
+        assert self.modules_json is not None  # mypy
         # Get the remotes we are missing
         tracked_repos = {repo_url: (repo_entry) for repo_url, repo_entry in self.modules_json["repos"].items()}
         repos, _ = self.get_pipeline_module_repositories(component_type, self.modules_dir, tracked_repos)
@@ -1186,7 +1234,7 @@ def recreate_dependencies(self, repo, org, subworkflow):
 
         sw_path = Path(self.subworkflows_dir, org, subworkflow)
         dep_mods, dep_subwfs = get_components_to_install(sw_path)
-
+        assert self.modules_json is not None  # mypy
         for dep_mod in dep_mods:
             installed_by = self.modules_json["repos"][repo]["modules"][org][dep_mod]["installed_by"]
             if installed_by == ["modules"]:
diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py
index 9694920274..b345dfe8b4 100644
--- a/nf_core/modules/modules_repo.py
+++ b/nf_core/modules/modules_repo.py
@@ -1,6 +1,7 @@
 import logging
 import os
 import shutil
+from typing import Optional
 
 import git
 import rich
@@ -35,7 +36,13 @@ class ModulesRepo(SyncedRepo):
     local_repo_statuses = {}
     no_pull_global = False
 
-    def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=False):
+    def __init__(
+        self,
+        remote_url: Optional[str] = None,
+        branch: Optional[str] = None,
+        no_pull: bool = False,
+        hide_progress: bool = False,
+    ):
         """
         Initializes the object and clones the git repository if it is not already present
         """
diff --git a/nf_core/modules/modules_utils.py b/nf_core/modules/modules_utils.py
index 6796de41ec..ecfe5f24ee 100644
--- a/nf_core/modules/modules_utils.py
+++ b/nf_core/modules/modules_utils.py
@@ -36,7 +36,7 @@ def repo_full_name_from_remote(remote_url: str) -> str:
     return path
 
 
-def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], List[NFCoreComponent]]:
+def get_installed_modules(directory: Path, repo_type="modules") -> Tuple[List[str], List[NFCoreComponent]]:
     """
     Make a list of all modules installed in this repository
 
@@ -52,15 +52,15 @@ def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], Lis
     # initialize lists
     local_modules: List[str] = []
     nfcore_modules_names: List[str] = []
-    local_modules_dir: Optional[str] = None
-    nfcore_modules_dir = os.path.join(dir, "modules", "nf-core")
+    local_modules_dir: Optional[Path] = None
+    nfcore_modules_dir = Path(directory, "modules", "nf-core")
 
     # Get local modules
     if repo_type == "pipeline":
-        local_modules_dir = os.path.join(dir, "modules", "local")
+        local_modules_dir = Path(directory, "modules", "local")
 
         # Filter local modules
-        if os.path.exists(local_modules_dir):
+        if local_modules_dir.exists():
             local_modules = os.listdir(local_modules_dir)
             local_modules = sorted([x for x in local_modules if x.endswith(".nf")])
 
@@ -89,7 +89,7 @@ def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], Lis
             "nf-core/modules",
             Path(nfcore_modules_dir, m),
             repo_type=repo_type,
-            base_dir=Path(dir),
+            base_dir=directory,
             component_type="modules",
         )
         for m in nfcore_modules_names
diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py
index 601f351fda..af39334744 100644
--- a/nf_core/subworkflows/lint/subworkflow_tests.py
+++ b/nf_core/subworkflows/lint/subworkflow_tests.py
@@ -202,9 +202,12 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
                 f"subworkflows_{org_alphabet}",
             ]
             included_components = []
-            if subworkflow.main_nf.is_file():
+            if subworkflow.main_nf is not None and Path(subworkflow.main_nf).is_file():
                 included_components = subworkflow._get_included_components(subworkflow.main_nf)
-            chained_components_tags = subworkflow._get_included_components_in_chained_tests(subworkflow.nftest_main_nf)
+            if subworkflow.nftest_main_nf is not None and subworkflow.nftest_main_nf.is_file():
+                chained_components_tags = subworkflow._get_included_components_in_chained_tests(
+                    subworkflow.nftest_main_nf
+                )
             log.debug(f"Included components: {included_components}")
             log.debug(f"Required tags: {required_tags}")
             log.debug(f"Included components for chained nf-tests: {chained_components_tags}")
diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py
index 4d6a3f6a4e..4b69d4af87 100644
--- a/nf_core/synced_repo.py
+++ b/nf_core/synced_repo.py
@@ -4,7 +4,7 @@
 import shutil
 from configparser import NoOptionError, NoSectionError
 from pathlib import Path
-from typing import Dict
+from typing import Dict, Optional, Union
 
 import git
 from git.exc import GitCommandError
@@ -51,9 +51,14 @@ def update(self, op_code, cur_count, max_count=None, message=""):
         """
         if not self.progress_bar.tasks[self.tid].started:
             self.progress_bar.start_task(self.tid)
-        self.progress_bar.update(
-            self.tid, total=max_count, completed=cur_count, state=f"{cur_count / max_count * 100:.1f}%"
-        )
+        if cur_count is not None and max_count is not None:
+            cur_count = float(cur_count)
+            max_count = float(max_count)
+            state = f"{cur_count / max_count * 100:.1f}%"
+        else:
+            state = "Unknown"
+
+        self.progress_bar.update(self.tid, total=max_count, completed=cur_count, state=state)
 
 
 class SyncedRepo:
@@ -139,6 +144,9 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa
 
         self.avail_module_names = None
 
+    def setup_local_repo(self, remote_url, branch, hide_progress):
+        pass
+
     def verify_sha(self, prompt, sha):
         """
         Verify that 'sha' and 'prompt' arguments are not provided together.
@@ -258,7 +266,7 @@ def component_exists(self, component_name, component_type, checkout=True, commit
         """
         return component_name in self.get_avail_components(component_type, checkout=checkout, commit=commit)
 
-    def get_component_dir(self, component_name, component_type):
+    def get_component_dir(self, component_name: str, component_type: str) -> Path:
         """
         Returns the file path of a module/subworkflow directory in the repo.
         Does not verify that the path exists.
@@ -269,11 +277,15 @@ def get_component_dir(self, component_name, component_type):
             component_path (str): The path of the module/subworkflow in the local copy of the repository
         """
         if component_type == "modules":
-            return os.path.join(self.modules_dir, component_name)
+            return Path(self.modules_dir, component_name)
         elif component_type == "subworkflows":
-            return os.path.join(self.subworkflows_dir, component_name)
+            return Path(self.subworkflows_dir, component_name)
+        else:
+            raise ValueError(f"Invalid component type: {component_type}")
 
-    def install_component(self, component_name, install_dir, commit, component_type):
+    def install_component(
+        self, component_name: str, install_dir: Union[str, Path], commit: str, component_type: str
+    ) -> bool:
         """
         Install the module/subworkflow files into a pipeline at the given commit
 
@@ -281,6 +293,7 @@ def install_component(self, component_name, install_dir, commit, component_type)
             component_name (str): The name of the module/subworkflow
             install_dir (str): The path where the module/subworkflow should be installed
             commit (str): The git SHA for the version of the module/subworkflow to be installed
+            component_type (str): Either 'modules' or 'subworkflows'
 
         Returns:
             (bool): Whether the operation was successful or not
@@ -332,6 +345,8 @@ def component_files_identical(self, component_name, base_path, commit, component
         return files_identical
 
     def ensure_git_user_config(self, default_name: str, default_email: str) -> None:
+        if self.repo is None:
+            raise ValueError("Repository not initialized")
         try:
             with self.repo.config_reader() as git_config:
                 user_name = git_config.get_value("user", "name", default=None)
@@ -346,7 +361,7 @@ def ensure_git_user_config(self, default_name: str, default_email: str) -> None:
                 if not user_email:
                     git_config.set_value("user", "email", default_email)
 
-    def get_component_git_log(self, component_name, component_type, depth=None):
+    def get_component_git_log(self, component_name: Union[str, Path], component_type: str, depth: Optional[int] = None):
         """
         Fetches the commit history the of requested module/subworkflow since a given date. The default value is
         not arbitrary - it is the last time the structure of the nf-core/modules repository was had an
@@ -358,19 +373,26 @@ def get_component_git_log(self, component_name, component_type, depth=None):
         Returns:
             ( dict ): Iterator of commit SHAs and associated (truncated) message
         """
+
+        if self.repo is None:
+            raise ValueError("Repository not initialized")
         self.checkout_branch()
-        component_path = os.path.join(component_type, self.repo_path, component_name)
+        component_path = Path(component_type, self.repo_path, component_name)
+
         commits_new = self.repo.iter_commits(max_count=depth, paths=component_path)
-        commits_new = [
-            {"git_sha": commit.hexsha, "trunc_message": commit.message.partition("\n")[0]} for commit in commits_new
-        ]
+        if not commits_new:
+            raise ValueError(f"Could not find any commits for '{component_name}' in '{self.remote_url}'")
+        else:
+            commits_new = [
+                {"git_sha": commit.hexsha, "trunc_message": commit.message.splitlines()[0]} for commit in commits_new
+            ]
         commits_old = []
         if component_type == "modules":
             # Grab commits also from previous modules structure
-            component_path = os.path.join("modules", component_name)
+            component_path = Path("modules", component_name)
             commits_old = self.repo.iter_commits(max_count=depth, paths=component_path)
             commits_old = [
-                {"git_sha": commit.hexsha, "trunc_message": commit.message.partition("\n")[0]} for commit in commits_old
+                {"git_sha": commit.hexsha, "trunc_message": commit.message.splitlines()[0]} for commit in commits_old
             ]
         commits = iter(commits_new + commits_old)
         return commits
@@ -385,6 +407,8 @@ def sha_exists_on_branch(self, sha):
         """
         Verifies that a given commit sha exists on the branch
         """
+        if self.repo is None:
+            raise ValueError("Repository not initialized")
         self.checkout_branch()
         return sha in (commit.hexsha for commit in self.repo.iter_commits())
 
@@ -399,10 +423,12 @@ def get_commit_info(self, sha):
         Raises:
             LookupError: If the search for the commit fails
         """
+        if self.repo is None:
+            raise ValueError("Repository not initialized")
         self.checkout_branch()
         for commit in self.repo.iter_commits():
             if commit.hexsha == sha:
-                message = commit.message.partition("\n")[0]
+                message = commit.message.splitlines()[0]
                 date_obj = commit.committed_datetime
                 date = str(date_obj.date())
                 return message, date
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 0cd812cb04..d1e9ccfe95 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -22,11 +22,12 @@
 from typing import Dict, Generator, List, Optional, Tuple, Union
 
 import git
-import prompt_toolkit
+import prompt_toolkit.styles
 import questionary
-import requests
+import requests.auth
 import requests_cache
 import rich
+import rich.markup
 import yaml
 from packaging.version import Version
 from rich.live import Live
@@ -524,8 +525,9 @@ def __call__(self, r):
                     self.auth_mode = f"gh CLI config: {gh_cli_config['github.com']['user']}"
             except Exception:
                 ex_type, ex_value, _ = sys.exc_info()
-                output = rich.markup.escape(f"{ex_type.__name__}: {ex_value}")
-                log.debug(f"Couldn't auto-auth with GitHub CLI auth from '{gh_cli_config_fn}': [red]{output}")
+                if ex_type is not None:
+                    output = rich.markup.escape(f"{ex_type.__name__}: {ex_value}")
+                    log.debug(f"Couldn't auto-auth with GitHub CLI auth from '{gh_cli_config_fn}': [red]{output}")
 
         # Default auth if we have a GitHub Token (eg. GitHub Actions CI)
         if os.environ.get("GITHUB_TOKEN") is not None and self.auth is None:
@@ -804,6 +806,8 @@ def get_tag_date(tag_date):
                         singularity_image = all_singularity[k]["image"]
                         current_date = date
                         docker_image_name = docker_image["image_name"].lstrip("quay.io/")
+                if singularity_image is None:
+                    raise LookupError(f"Could not find singularity container for {package}")
                 return docker_image_name, singularity_image["image_name"]
             except TypeError:
                 raise LookupError(f"Could not find docker or singularity container for {package}")
@@ -1072,7 +1076,7 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, dict]:
     return config_fn, tools_config
 
 
-def determine_base_dir(directory="."):
+def determine_base_dir(directory: Union[Path, str] = ".") -> Path:
     base_dir = start_dir = Path(directory).absolute()
     # Only iterate up the tree if the start dir doesn't have a config
     while not get_first_available_path(base_dir, CONFIG_PATHS) and base_dir != base_dir.parent:
@@ -1080,7 +1084,7 @@ def determine_base_dir(directory="."):
         config_fn = get_first_available_path(base_dir, CONFIG_PATHS)
         if config_fn:
             break
-    return directory if (base_dir == start_dir or str(base_dir) == base_dir.root) else base_dir
+    return Path(directory) if (base_dir == start_dir or str(base_dir) == base_dir.root) else base_dir
 
 
 def get_first_available_path(directory: Union[Path, str], paths: List[str]) -> Union[Path, None]:

From 69d59a81c3b23a583857c1f2d03db04cdd3f0da9 Mon Sep 17 00:00:00 2001
From: LaurenceKuhl <laurence.kuhlburger@gmail.com>
Date: Fri, 19 Jul 2024 08:44:03 +0200
Subject: [PATCH 099/414] Update nf_core/__main__.py
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 nf_core/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index cb99bdedcc..3da153ee1f 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -2188,7 +2188,7 @@ def command_create(ctx, name, description, author, version, force, outdir, templ
     log.warning(
         "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead."
     )
-    pipelines_create(ctx, name, description, author, force, outdir, template_yaml, organisation)
+    pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation)
 
 
 # Main script is being run - launch the CLI

From 6a4ff6133f7efbe74f321c20436635d778166d14 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?=
 <mashehu@users.noreply.github.com>
Date: Mon, 22 Jul 2024 09:40:06 +0200
Subject: [PATCH 100/414] Update .pre-commit-config.yaml

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 872bd61e0a..fc2011cb99 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.2
+    rev: v0.5.4
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

From 61898dc14663fa3e81f78fdd5a62756217de7dc5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 22 Jul 2024 11:11:55 +0200
Subject: [PATCH 101/414] fix rich imports, remove boolean type for
 `installed_by`, fix more occurences of `dir`

---
 nf_core/components/create.py                  |  1 +
 nf_core/components/patch.py                   | 10 +--
 nf_core/modules/install.py                    |  2 +-
 nf_core/modules/modules_repo.py               |  1 +
 nf_core/modules/patch.py                      |  2 +-
 nf_core/pipelines/create/create.py            |  6 +-
 nf_core/subworkflows/install.py               |  2 +-
 nf_core/subworkflows/lint/__init__.py         |  8 +--
 .../subworkflows/lint/subworkflow_version.py  |  2 +-
 tests/modules/test_install.py                 |  8 +--
 tests/modules/test_lint.py                    | 62 +++++++++----------
 tests/modules/test_remove.py                  |  8 +--
 tests/subworkflows/test_install.py            | 45 ++++++--------
 tests/subworkflows/test_lint.py               | 40 ++++++------
 tests/subworkflows/test_remove.py             | 20 +++---
 15 files changed, 109 insertions(+), 108 deletions(-)

diff --git a/nf_core/components/create.py b/nf_core/components/create.py
index 532c2a46d6..413790099d 100644
--- a/nf_core/components/create.py
+++ b/nf_core/components/create.py
@@ -14,6 +14,7 @@
 import jinja2
 import questionary
 import rich
+import rich.prompt
 import yaml
 from packaging.version import parse as parse_version
 
diff --git a/nf_core/components/patch.py b/nf_core/components/patch.py
index 5b29c152d8..0332a1fe42 100644
--- a/nf_core/components/patch.py
+++ b/nf_core/components/patch.py
@@ -15,7 +15,7 @@
 
 
 class ComponentPatch(ComponentCommand):
-    def __init__(self, pipeline_dir, component_type, remote_url=None, branch=None, no_pull=False, installed_by=False):
+    def __init__(self, pipeline_dir, component_type, remote_url=None, branch=None, no_pull=False, installed_by=None):
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
 
         self.modules_json = ModulesJson(pipeline_dir)
@@ -88,8 +88,8 @@ def patch(self, component=None):
         patch_filename = f"{component.replace('/', '-')}.diff"
         component_relpath = Path(self.component_type, component_dir, component)
         patch_relpath = Path(component_relpath, patch_filename)
-        component_current_dir = Path(self.dir, component_relpath)
-        patch_path = Path(self.dir, patch_relpath)
+        component_current_dir = Path(self.directory, component_relpath)
+        patch_path = Path(self.directory, patch_relpath)
 
         if patch_path.exists():
             remove = questionary.confirm(
@@ -189,8 +189,8 @@ def remove(self, component):
         patch_filename = f"{component.replace('/', '-')}.diff"
         component_relpath = Path(self.component_type, component_dir, component)
         patch_relpath = Path(component_relpath, patch_filename)
-        patch_path = Path(self.dir, patch_relpath)
-        component_path = Path(self.dir, component_relpath)
+        patch_path = Path(self.directory, patch_relpath)
+        component_path = Path(self.directory, component_relpath)
 
         if patch_path.exists():
             remove = questionary.confirm(
diff --git a/nf_core/modules/install.py b/nf_core/modules/install.py
index e1755cee98..7055abe49a 100644
--- a/nf_core/modules/install.py
+++ b/nf_core/modules/install.py
@@ -11,7 +11,7 @@ def __init__(
         remote_url=None,
         branch=None,
         no_pull=False,
-        installed_by=False,
+        installed_by=None,
     ):
         super().__init__(
             pipeline_dir,
diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py
index b345dfe8b4..a979ae45b8 100644
--- a/nf_core/modules/modules_repo.py
+++ b/nf_core/modules/modules_repo.py
@@ -6,6 +6,7 @@
 import git
 import rich
 import rich.progress
+import rich.prompt
 from git.exc import GitCommandError, InvalidGitRepositoryError
 
 import nf_core.modules.modules_json
diff --git a/nf_core/modules/patch.py b/nf_core/modules/patch.py
index b4e86f2d19..bbad0d428e 100644
--- a/nf_core/modules/patch.py
+++ b/nf_core/modules/patch.py
@@ -6,5 +6,5 @@
 
 
 class ModulePatch(ComponentPatch):
-    def __init__(self, pipeline_dir, remote_url=None, branch=None, no_pull=False, installed_by=False):
+    def __init__(self, pipeline_dir, remote_url=None, branch=None, no_pull=False, installed_by=None):
         super().__init__(pipeline_dir, "modules", remote_url, branch, no_pull, installed_by)
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index c5af956690..aecba94236 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -512,12 +512,14 @@ def fix_linting(self):
     def make_pipeline_logo(self):
         """Fetch a logo for the new pipeline from the nf-core website"""
         email_logo_path = Path(self.outdir) / "assets"
-        create_logo(text=self.jinja_params["short_name"], dir=email_logo_path, theme="light", force=bool(self.force))
+        create_logo(
+            text=self.jinja_params["short_name"], directory=email_logo_path, theme="light", force=bool(self.force)
+        )
         for theme in ["dark", "light"]:
             readme_logo_path = Path(self.outdir) / "docs" / "images"
             create_logo(
                 text=self.jinja_params["short_name"],
-                dir=readme_logo_path,
+                directory=readme_logo_path,
                 width=600,
                 theme=theme,
                 force=bool(self.force),
diff --git a/nf_core/subworkflows/install.py b/nf_core/subworkflows/install.py
index 6c5cfb12b2..70a6b0afa5 100644
--- a/nf_core/subworkflows/install.py
+++ b/nf_core/subworkflows/install.py
@@ -11,7 +11,7 @@ def __init__(
         remote_url=None,
         branch=None,
         no_pull=False,
-        installed_by=False,
+        installed_by=None,
     ):
         super().__init__(
             pipeline_dir,
diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py
index a3cacf2952..a073710884 100644
--- a/nf_core/subworkflows/lint/__init__.py
+++ b/nf_core/subworkflows/lint/__init__.py
@@ -36,7 +36,7 @@ class SubworkflowLint(ComponentLint):
 
     def __init__(
         self,
-        dir,
+        directory,
         fail_warned=False,
         remote_url=None,
         branch=None,
@@ -46,7 +46,7 @@ def __init__(
     ):
         super().__init__(
             component_type="subworkflows",
-            dir=dir,
+            directory=directory,
             fail_warned=fail_warned,
             remote_url=remote_url,
             branch=branch,
@@ -122,9 +122,9 @@ def lint(
             remote_subworkflows = self.all_remote_components
 
         if self.repo_type == "modules":
-            log.info(f"Linting modules repo: [magenta]'{self.dir}'")
+            log.info(f"Linting modules repo: [magenta]'{self.directory}'")
         else:
-            log.info(f"Linting pipeline: [magenta]'{self.dir}'")
+            log.info(f"Linting pipeline: [magenta]'{self.directory}'")
         if subworkflow:
             log.info(f"Linting subworkflow: [magenta]'{subworkflow}'")
 
diff --git a/nf_core/subworkflows/lint/subworkflow_version.py b/nf_core/subworkflows/lint/subworkflow_version.py
index 5801abd885..1acb95e779 100644
--- a/nf_core/subworkflows/lint/subworkflow_version.py
+++ b/nf_core/subworkflows/lint/subworkflow_version.py
@@ -21,7 +21,7 @@ def subworkflow_version(subworkflow_lint_object, subworkflow):
     newer version of the subworkflow available.
     """
 
-    modules_json_path = Path(subworkflow_lint_object.dir, "modules.json")
+    modules_json_path = Path(subworkflow_lint_object.directory, "modules.json")
     # Verify that a git_sha exists in the `modules.json` file for this module
     version = subworkflow_lint_object.modules_json.get_subworkflow_version(
         subworkflow.component_name, subworkflow.repo_url, subworkflow.org
diff --git a/tests/modules/test_install.py b/tests/modules/test_install.py
index b90f01ee61..cfdaac47ed 100644
--- a/tests/modules/test_install.py
+++ b/tests/modules/test_install.py
@@ -19,14 +19,14 @@
 class TestModulesCreate(TestModules):
     def test_modules_install_nopipeline(self):
         """Test installing a module - no pipeline given"""
-        self.mods_install.dir = None
+        self.mods_install.directory = None
         assert self.mods_install.install("foo") is False
 
     @with_temporary_folder
     def test_modules_install_emptypipeline(self, tmpdir):
         """Test installing a module - empty dir given"""
         os.mkdir(os.path.join(tmpdir, "nf-core-pipe"))
-        self.mods_install.dir = os.path.join(tmpdir, "nf-core-pipe")
+        self.mods_install.directory = os.path.join(tmpdir, "nf-core-pipe")
         with pytest.raises(UserWarning) as excinfo:
             self.mods_install.install("foo")
         assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
@@ -38,8 +38,8 @@ def test_modules_install_nomodule(self):
     def test_modules_install_trimgalore(self):
         """Test installing a module - TrimGalore!"""
         assert self.mods_install.install("trimgalore") is not False
-        assert self.mods_install.dir is not None
-        module_path = Path(self.mods_install.dir, "modules", "nf-core", "trimgalore")
+        assert self.mods_install.directory is not None
+        module_path = Path(self.mods_install.directory, "modules", "nf-core", "trimgalore")
         assert os.path.exists(module_path)
 
     def test_modules_install_trimgalore_twice(self):
diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py
index 6448916acf..fc9871db2e 100644
--- a/tests/modules/test_lint.py
+++ b/tests/modules/test_lint.py
@@ -180,7 +180,7 @@ def _setup_patch(self, pipeline_dir: Union[str, Path], modify_module: bool):
     def test_modules_lint_trimgalore(self):
         """Test linting the TrimGalore! module"""
         self.mods_install.install("trimgalore")
-        module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
+        module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir)
         module_lint.lint(print_results=False, module="trimgalore")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -191,11 +191,11 @@ def test_modules_lint_empty(self):
         self.mods_remove.remove("fastqc", force=True)
         self.mods_remove.remove("multiqc", force=True)
         with pytest.raises(LookupError):
-            nf_core.modules.ModuleLint(dir=self.pipeline_dir)
+            nf_core.modules.ModuleLint(directory=self.pipeline_dir)
 
     def test_modules_lint_new_modules(self):
         """lint a new module"""
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, all_modules=True)
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -206,13 +206,13 @@ def test_modules_lint_no_gitlab(self):
         self.mods_remove.remove("fastqc", force=True)
         self.mods_remove.remove("multiqc", force=True)
         with pytest.raises(LookupError):
-            nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+            nf_core.modules.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
 
     def test_modules_lint_gitlab_modules(self):
         """Lint modules from a different remote"""
         self.mods_install_gitlab.install("fastqc")
         self.mods_install_gitlab.install("multiqc")
-        module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+        module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
         module_lint.lint(print_results=False, all_modules=True)
         assert len(module_lint.failed) == 2
         assert len(module_lint.passed) > 0
@@ -221,7 +221,7 @@ def test_modules_lint_gitlab_modules(self):
     def test_modules_lint_multiple_remotes(self):
         """Lint modules from a different remote"""
         self.mods_install_gitlab.install("multiqc")
-        module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+        module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
         module_lint.lint(print_results=False, all_modules=True)
         assert len(module_lint.failed) == 1
         assert len(module_lint.passed) > 0
@@ -229,14 +229,14 @@ def test_modules_lint_multiple_remotes(self):
 
     def test_modules_lint_registry(self):
         """Test linting the samtools module and alternative registry"""
-        self.mods_install.install("samtools")
-        module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, registry="public.ecr.aws")
-        module_lint.lint(print_results=False, module="samtools")
+        assert self.mods_install.install("samtools/sort")
+        module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir, registry="public.ecr.aws")
+        module_lint.lint(print_results=False, module="samtools/sort")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
-        module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
-        module_lint.lint(print_results=False, module="samtools")
+        module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir)
+        module_lint.lint(print_results=False, module="samtools/sort")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
@@ -255,7 +255,7 @@ def test_modules_lint_patched_modules(self):
         # to avoid error from try_apply_patch() during linting
         with set_wd(self.pipeline_dir):
             module_lint = nf_core.modules.ModuleLint(
-                dir=self.pipeline_dir,
+                directory=self.pipeline_dir,
                 remote_url=GITLAB_URL,
                 branch=PATCH_BRANCH,
                 hide_progress=True,
@@ -298,7 +298,7 @@ def test_modules_lint_check_url(self):
 
     def test_modules_lint_snapshot_file(self):
         """Test linting a module with a snapshot file"""
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -315,7 +315,7 @@ def test_modules_lint_snapshot_file_missing_fail(self):
             "tests",
             "main.nf.test.snap",
         ).unlink()
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         Path(
             self.nfcore_modules,
@@ -359,7 +359,7 @@ def test_modules_lint_snapshot_file_not_needed(self):
             "w",
         ) as fh:
             fh.write(new_content)
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -377,7 +377,7 @@ def test_modules_environment_yml_file_doesnt_exists(self):
                 "environment.yml.bak",
             )
         )
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         Path(
             self.nfcore_modules,
@@ -403,7 +403,7 @@ def test_modules_environment_yml_file_doesnt_exists(self):
 
     def test_modules_environment_yml_file_sorted_correctly(self):
         """Test linting a module with a correctly sorted environment.yml file"""
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -438,7 +438,7 @@ def test_modules_environment_yml_file_sorted_incorrectly(self):
             "w",
         ) as fh:
             fh.write(yaml_content)
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         # we fix the sorting on the fly, so this should pass
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
@@ -471,7 +471,7 @@ def test_modules_environment_yml_file_not_array(self):
             "w",
         ) as fh:
             fh.write(yaml.dump(yaml_content))
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -504,7 +504,7 @@ def test_modules_environment_yml_file_name_mismatch(self):
             "w",
         ) as fh:
             fh.write(yaml.dump(yaml_content))
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         # reset changes
         yaml_content["name"] = "bpipe_test"
@@ -536,7 +536,7 @@ def test_modules_meta_yml_incorrect_licence_field(self):
             "w",
         ) as fh:
             fh.write(yaml.dump(meta_yml))
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
 
         # reset changes
@@ -559,7 +559,7 @@ def test_modules_meta_yml_input_mismatch(self):
         main_nf_new = main_nf.replace("path bam", "path bai")
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
             fh.write(main_nf_new)
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
             fh.write(main_nf)
@@ -578,7 +578,7 @@ def test_modules_meta_yml_output_mismatch(self):
         main_nf_new = main_nf.replace("emit: bam", "emit: bai")
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
             fh.write(main_nf_new)
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
             fh.write(main_nf)
@@ -625,7 +625,7 @@ def test_modules_meta_yml_incorrect_name(self):
             "w",
         ) as fh:
             fh.write(yaml.dump(environment_yml))
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
 
         # reset changes
@@ -659,7 +659,7 @@ def test_modules_missing_test_dir(self):
         Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests").rename(
             Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak")
         )
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak").rename(
             Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests")
@@ -690,7 +690,7 @@ def test_modules_missing_test_main_nf(self):
                 "main.nf.test.bak",
             )
         )
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         Path(
             self.nfcore_modules,
@@ -719,7 +719,7 @@ def test_modules_missing_test_main_nf(self):
     def test_modules_unused_pytest_files(self):
         """Test linting a nf-test module with files still present in `tests/modules/`"""
         Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").mkdir(parents=True, exist_ok=True)
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").rmdir()
         assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
@@ -735,7 +735,7 @@ def test_nftest_failing_linting(self):
         self.nfcore_modules = Path(tmp_dir, "modules-test")
         Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_NFTEST_BRANCH)
 
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="kallisto/quant")
 
         assert len(module_lint.failed) == 3, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
@@ -774,7 +774,7 @@ def test_modules_absent_version(self):
             "w",
         ) as fh:
             fh.write(new_content)
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         with open(
             Path(
@@ -812,7 +812,7 @@ def test_modules_empty_file_in_snapshot(self):
         with open(snap_file, "w") as fh:
             json.dump(snap, fh)
 
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -841,7 +841,7 @@ def test_modules_empty_file_in_stub_snapshot(self):
         with open(snap_file, "w") as fh:
             json.dump(snap, fh)
 
-        module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
diff --git a/tests/modules/test_remove.py b/tests/modules/test_remove.py
index a80c8b0986..2caece7ce5 100644
--- a/tests/modules/test_remove.py
+++ b/tests/modules/test_remove.py
@@ -8,8 +8,8 @@ class TestModulesRemove(TestModules):
     def test_modules_remove_trimgalore(self):
         """Test removing TrimGalore! module after installing it"""
         self.mods_install.install("trimgalore")
-        assert self.mods_install.dir is not None
-        module_path = Path(self.mods_install.dir, "modules", "nf-core", "modules", "trimgalore")
+        assert self.mods_install.directory is not None
+        module_path = Path(self.mods_install.directory, "modules", "nf-core", "modules", "trimgalore")
         assert self.mods_remove.remove("trimgalore")
         assert os.path.exists(module_path) is False
 
@@ -20,7 +20,7 @@ def test_modules_remove_trimgalore_uninstalled(self):
     def test_modules_remove_multiqc_from_gitlab(self):
         """Test removing multiqc module after installing it from an alternative source"""
         self.mods_install_gitlab.install("multiqc")
-        assert self.mods_install.dir is not None
-        module_path = Path(self.mods_install_gitlab.dir, "modules", "nf-core-test", "multiqc")
+        assert self.mods_install.directory is not None
+        module_path = Path(self.mods_install_gitlab.directory, "modules", "nf-core-test", "multiqc")
         assert self.mods_remove_gitlab.remove("multiqc", force=True)
         assert os.path.exists(module_path) is False
diff --git a/tests/subworkflows/test_install.py b/tests/subworkflows/test_install.py
index e0b2fc1ab6..af1ad92415 100644
--- a/tests/subworkflows/test_install.py
+++ b/tests/subworkflows/test_install.py
@@ -1,4 +1,3 @@
-import os
 from pathlib import Path
 
 import pytest
@@ -20,8 +19,8 @@
 class TestSubworkflowsInstall(TestSubworkflows):
     def test_subworkflow_install_nopipeline(self):
         """Test installing a subworkflow - no pipeline given"""
-        assert self.subworkflow_install.dir is not None
-        self.subworkflow_install.dir = ""
+        assert self.subworkflow_install.directory is not None
+        self.subworkflow_install.directory = Path("non_existent_dir")
         assert self.subworkflow_install.install("foo") is False
 
     @with_temporary_folder
@@ -29,7 +28,7 @@ def test_subworkflows_install_emptypipeline(self, tmpdir):
         """Test installing a subworkflow - empty dir given"""
 
         Path(tmpdir, "nf-core-pipe").mkdir(exist_ok=True)
-        self.subworkflow_install.dir = os.path.join(tmpdir, "nf-core-pipe")
+        self.subworkflow_install.directory = Path(tmpdir, "nf-core-pipe")
         with pytest.raises(UserWarning) as excinfo:
             self.subworkflow_install.install("foo")
         assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
@@ -41,28 +40,22 @@ def test_subworkflows_install_nosubworkflow(self):
     def test_subworkflows_install_bam_sort_stats_samtools(self):
         """Test installing a subworkflow - bam_sort_stats_samtools"""
         assert self.subworkflow_install.install("bam_sort_stats_samtools") is not False
-        subworkflow_path = os.path.join(
-            self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_sort_stats_samtools"
+        subworkflow_path = Path(
+            self.subworkflow_install.directory, "subworkflows", "nf-core", "bam_sort_stats_samtools"
         )
-        sub_subworkflow_path = os.path.join(
-            self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_stats_samtools"
-        )
-        samtools_index_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
-        samtools_sort_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "sort")
-        samtools_stats_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats")
-        samtools_idxstats_path = os.path.join(
-            self.subworkflow_install.dir, "modules", "nf-core", "samtools", "idxstats"
-        )
-        samtools_flagstat_path = os.path.join(
-            self.subworkflow_install.dir, "modules", "nf-core", "samtools", "flagstat"
-        )
-        assert os.path.exists(subworkflow_path)
-        assert os.path.exists(sub_subworkflow_path)
-        assert os.path.exists(samtools_index_path)
-        assert os.path.exists(samtools_sort_path)
-        assert os.path.exists(samtools_stats_path)
-        assert os.path.exists(samtools_idxstats_path)
-        assert os.path.exists(samtools_flagstat_path)
+        sub_subworkflow_path = Path(self.subworkflow_install.directory, "subworkflows", "nf-core", "bam_stats_samtools")
+        samtools_index_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "index")
+        samtools_sort_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "sort")
+        samtools_stats_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "stats")
+        samtools_idxstats_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "idxstats")
+        samtools_flagstat_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "flagstat")
+        assert subworkflow_path.exists()
+        assert sub_subworkflow_path.exists()
+        assert samtools_index_path.exists()
+        assert samtools_sort_path.exists()
+        assert samtools_stats_path.exists()
+        assert samtools_idxstats_path.exists()
+        assert samtools_flagstat_path.exists()
 
     def test_subworkflows_install_bam_sort_stats_samtools_twice(self):
         """Test installing a subworkflow - bam_sort_stats_samtools already there"""
@@ -87,7 +80,7 @@ def test_subworkflows_install_different_branch_fail(self):
 
     def test_subworkflows_install_tracking(self):
         """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json"""
-        self.subworkflow_install.install("bam_sort_stats_samtools")
+        assert self.subworkflow_install.install("bam_sort_stats_samtools")
 
         # Verify that the installed_by entry was added correctly
         modules_json = ModulesJson(self.pipeline_dir)
diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py
index f8c9bedbf3..38bcc2b2c0 100644
--- a/tests/subworkflows/test_lint.py
+++ b/tests/subworkflows/test_lint.py
@@ -14,7 +14,7 @@ class TestSubworkflowsLint(TestSubworkflows):
     def test_subworkflows_lint(self):
         """Test linting the fastq_align_bowtie2 subworkflow"""
         self.subworkflow_install.install("fastq_align_bowtie2")
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
         subworkflow_lint.lint(print_results=False, subworkflow="fastq_align_bowtie2")
         assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
         assert len(subworkflow_lint.passed) > 0
@@ -26,11 +26,11 @@ def test_subworkflows_lint_empty(self):
         self.subworkflow_remove.remove("utils_nfcore_pipeline", force=True)
         self.subworkflow_remove.remove("utils_nfvalidation_plugin", force=True)
         with pytest.raises(LookupError):
-            nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
+            nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
 
     def test_subworkflows_lint_new_subworkflow(self):
         """lint a new subworkflow"""
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
         subworkflow_lint.lint(print_results=True, all_subworkflows=True)
         assert len(subworkflow_lint.failed) == 0
 
@@ -40,13 +40,13 @@ def test_subworkflows_lint_new_subworkflow(self):
     def test_subworkflows_lint_no_gitlab(self):
         """Test linting a pipeline with no subworkflows installed"""
         with pytest.raises(LookupError):
-            nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+            nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
 
     def test_subworkflows_lint_gitlab_subworkflows(self):
         """Lint subworkflows from a different remote"""
         self.subworkflow_install_gitlab.install("bam_stats_samtools")
         subworkflow_lint = nf_core.subworkflows.SubworkflowLint(
-            dir=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
+            directory=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
         )
         subworkflow_lint.lint(print_results=False, all_subworkflows=True)
         assert len(subworkflow_lint.failed) == 0
@@ -58,7 +58,7 @@ def test_subworkflows_lint_multiple_remotes(self):
         self.subworkflow_install_gitlab.install("bam_stats_samtools")
         self.subworkflow_install.install("fastq_align_bowtie2")
         subworkflow_lint = nf_core.subworkflows.SubworkflowLint(
-            dir=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
+            directory=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
         )
         subworkflow_lint.lint(print_results=False, all_subworkflows=True)
         assert len(subworkflow_lint.failed) == 0
@@ -67,7 +67,7 @@ def test_subworkflows_lint_multiple_remotes(self):
 
     def test_subworkflows_lint_snapshot_file(self):
         """Test linting a subworkflow with a snapshot file"""
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
         subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
         assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
         assert len(subworkflow_lint.passed) > 0
@@ -83,7 +83,7 @@ def test_subworkflows_lint_snapshot_file_missing_fail(self):
             "tests",
             "main.nf.test.snap",
         ).unlink()
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
         subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
         Path(
             self.nfcore_modules,
@@ -132,7 +132,7 @@ def test_subworkflows_lint_snapshot_file_not_needed(self):
             "tests",
             "main.nf.test.snap",
         ).unlink()
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
         subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
         Path(
             self.nfcore_modules,
@@ -179,7 +179,7 @@ def test_subworkflows_lint_less_than_two_modules_warning(self):
             "w",
         ) as fh:
             fh.write(new_content)
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
         subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools")
         assert len(subworkflow_lint.failed) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
         assert len(subworkflow_lint.passed) > 0
@@ -218,7 +218,7 @@ def test_subworkflows_lint_include_multiple_alias(self):
         ) as fh:
             fh.write(new_content)
 
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
         subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools")
         assert len(subworkflow_lint.failed) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
         assert len(subworkflow_lint.passed) > 0
@@ -265,7 +265,7 @@ def test_subworkflows_lint_capitalization_fail(self):
             "w",
         ) as fh:
             fh.write(new_content)
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
         subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools")
         assert len(subworkflow_lint.failed) >= 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
         assert len(subworkflow_lint.passed) > 0
@@ -276,7 +276,7 @@ def test_subworkflows_lint_capitalization_fail(self):
         self.subworkflow_remove.remove("bam_stats_samtools", force=True)
 
     def test_subworkflows_absent_version(self):
-        """Test linting a nf-test module if the versions is absent in the snapshot file `"""
+        """Test linting a nf-test subworkflow if the versions is absent in the snapshot file `"""
         snap_file = Path(
             self.nfcore_modules,
             "subworkflows",
@@ -291,7 +291,11 @@ def test_subworkflows_absent_version(self):
         with open(snap_file, "w") as fh:
             fh.write(new_content)
 
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        import ipdb
+
+        ipdb.set_trace()
+
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
         subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
         assert len(subworkflow_lint.failed) == 0
         assert len(subworkflow_lint.passed) > 0
@@ -308,7 +312,7 @@ def test_subworkflows_missing_test_dir(self):
         test_dir_copy = shutil.copytree(test_dir, test_dir.parent / "tests_copy")
         shutil.rmtree(test_dir)
 
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
         subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
         assert len(subworkflow_lint.failed) == 0
         assert len(subworkflow_lint.passed) > 0
@@ -324,7 +328,7 @@ def test_subworkflows_missing_main_nf(self):
         main_nf_copy = shutil.copy(main_nf, main_nf.parent / "main_nf_copy")
         main_nf.unlink()
 
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
         subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
         assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
         assert len(subworkflow_lint.passed) > 0
@@ -351,7 +355,7 @@ def test_subworkflows_empty_file_in_snapshot(self):
         with open(snap_file, "w") as fh:
             json.dump(snap, fh)
 
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
         subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
         assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
         assert len(subworkflow_lint.passed) > 0
@@ -379,7 +383,7 @@ def test_subworkflows_empty_file_in_stub_snapshot(self):
         with open(snap_file, "w") as fh:
             json.dump(snap, fh)
 
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
         subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
         assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
         assert len(subworkflow_lint.passed) > 0
diff --git a/tests/subworkflows/test_remove.py b/tests/subworkflows/test_remove.py
index 61c016b232..bad5a2ddbb 100644
--- a/tests/subworkflows/test_remove.py
+++ b/tests/subworkflows/test_remove.py
@@ -14,10 +14,10 @@ def test_subworkflows_remove_subworkflow(self):
         """Test removing subworkflow and all it's dependencies after installing it"""
         self.subworkflow_install.install("bam_sort_stats_samtools")
 
-        subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
+        subworkflow_path = Path(self.subworkflow_install.directory, "subworkflows", "nf-core")
         bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
         bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
-        samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
+        samtools_index_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "index")
         ModulesJson(self.pipeline_dir)
         mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json()
         assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
@@ -40,10 +40,10 @@ def test_subworkflows_remove_subworkflow_keep_installed_module(self):
         self.subworkflow_install.install("bam_sort_stats_samtools")
         self.mods_install.install("samtools/index")
 
-        subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
+        subworkflow_path = Path(self.subworkflow_install.directory, "subworkflows", "nf-core")
         bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
         bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
-        samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
+        samtools_index_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "index")
 
         mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json()
         assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
@@ -67,11 +67,11 @@ def test_subworkflows_remove_one_of_two_subworkflow(self):
         """Test removing subworkflow and all it's dependencies after installing it"""
         self.subworkflow_install.install("bam_sort_stats_samtools")
         self.subworkflow_install.install("bam_stats_samtools")
-        subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
+        subworkflow_path = Path(self.subworkflow_install.directory, "subworkflows", "nf-core")
         bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
         bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
-        samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
-        samtools_stats_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats")
+        samtools_index_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "index")
+        samtools_stats_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "stats")
 
         assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
 
@@ -85,11 +85,11 @@ def test_subworkflows_remove_one_of_two_subworkflow(self):
     def test_subworkflows_remove_included_subworkflow(self):
         """Test removing subworkflow which is installed by another subworkflow and all it's dependencies."""
         self.subworkflow_install.install("bam_sort_stats_samtools")
-        subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
+        subworkflow_path = Path(self.subworkflow_install.directory, "subworkflows", "nf-core")
         bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
         bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
-        samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
-        samtools_stats_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats")
+        samtools_index_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "index")
+        samtools_stats_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "stats")
 
         assert self.subworkflow_remove.remove("bam_stats_samtools") is False
 

From 47229ff0bc9a30f8b5ee95e7b308d5445ad7339a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 22 Jul 2024 12:15:33 +0200
Subject: [PATCH 102/414] fix types and tests

---
 nf_core/components/components_command.py |   1 +
 nf_core/components/components_utils.py   |   4 +-
 nf_core/components/info.py               |   8 +-
 nf_core/components/install.py            |   9 +-
 nf_core/components/lint/__init__.py      |  32 +++---
 nf_core/components/list.py               |   4 +-
 nf_core/components/nfcore_component.py   |   6 +-
 nf_core/modules/lint/module_version.py   |   8 +-
 nf_core/modules/modules_json.py          | 123 +++++++++++++----------
 nf_core/modules/modules_repo.py          |   5 +-
 nf_core/synced_repo.py                   |  63 ++++++------
 nf_core/utils.py                         |  52 +++++++---
 12 files changed, 185 insertions(+), 130 deletions(-)

diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 13a6fed338..8d200021c2 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -38,6 +38,7 @@ def __init__(
         self.hide_progress = hide_progress
         self.no_prompts = no_prompts
         self._configure_repo_and_paths()
+        self.repo_type: Optional[str] = None
 
     def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
         """
diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py
index 32f6c0fc11..743efd386d 100644
--- a/nf_core/components/components_utils.py
+++ b/nf_core/components/components_utils.py
@@ -27,7 +27,7 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P
 
     # Figure out the repository type from the .nf-core.yml config file if we can
     config_fn, tools_config = nf_core.utils.load_tools_config(base_dir)
-    repo_type: Optional[str] = tools_config.get("repository_type", None)
+    repo_type = tools_config.get("repository_type", None)
 
     # If not set, prompt the user
     if not repo_type and use_prompt:
@@ -101,7 +101,7 @@ def prompt_component_version_sha(
     git_sha = ""
     page_nbr = 1
 
-    all_commits = modules_repo.get_component_git_log(component_name, component_type)
+    all_commits = iter(modules_repo.get_component_git_log(component_name, component_type))
     next_page_commits = [next(all_commits, None) for _ in range(10)]
     next_page_commits = [commit for commit in next_page_commits if commit is not None]
 
diff --git a/nf_core/components/info.py b/nf_core/components/info.py
index 8597875af4..d07486f638 100644
--- a/nf_core/components/info.py
+++ b/nf_core/components/info.py
@@ -97,7 +97,6 @@ def init_mod_name(self, component):
         Args:
             module: str: Module name to check
         """
-        assert self.modules_json is not None  # mypy
         if component is None:
             self.local = questionary.confirm(
                 f"Is the {self.component_type[:-1]} locally installed?", style=nf_core.utils.nfcore_question_style
@@ -105,7 +104,8 @@ def init_mod_name(self, component):
             if self.local:
                 if self.repo_type == "modules":
                     components = self.get_components_clone_modules()
-                else:
+                elif self.repo_type == "pipeline":
+                    assert self.modules_json is not None  # mypy
                     all_components = self.modules_json.get_all_components(self.component_type).get(
                         self.modules_repo.remote_url, []
                     )
@@ -117,6 +117,8 @@ def init_mod_name(self, component):
                         raise UserWarning(
                             f"No {self.component_type[:-1]} installed from '{self.modules_repo.remote_url}'"
                         )
+                else:
+                    raise UserWarning("Unknown repository type")
             else:
                 components = self.modules_repo.get_avail_components(self.component_type)
             components.sort()
@@ -174,8 +176,8 @@ def get_local_yaml(self):
             Optional[dict]: Parsed meta.yml if found, None otherwise
         """
 
-        assert self.modules_json is not None  # mypy
         if self.repo_type == "pipeline":
+            assert self.modules_json is not None  # mypy
             # Try to find and load the meta.yml file
             component_base_path = Path(self.directory, self.component_type)
             # Check that we have any modules/subworkflows installed from this repo
diff --git a/nf_core/components/install.py b/nf_core/components/install.py
index e6c31b3cbb..aa8aac81e6 100644
--- a/nf_core/components/install.py
+++ b/nf_core/components/install.py
@@ -100,8 +100,11 @@ def install(self, component: str, silent: bool = False) -> bool:
             modules_json.load()
             modules_json.update(self.component_type, self.modules_repo, component, current_version, self.installed_by)
             return False
-
-        version = self.get_version(component, self.sha, self.prompt, current_version, self.modules_repo)
+        try:
+            version = self.get_version(component, self.sha, self.prompt, current_version, self.modules_repo)
+        except UserWarning as e:
+            log.error(e)
+            return False
         if not version:
             return False
 
@@ -174,7 +177,7 @@ def install_included_components(self, subworkflow_dir):
             self.installed_by = original_installed
 
     def collect_and_verify_name(
-        self, component: Optional[str], modules_repo: nf_core.modules.modules_repo.ModulesRepo
+        self, component: Optional[str], modules_repo: "nf_core.modules.modules_repo.ModulesRepo"
     ) -> str:
         """
         Collect component name.
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index 2cd59dc489..ada3ee30c2 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -92,17 +92,17 @@ def __init__(
                     raise LookupError(
                         f"Error parsing modules.json: {components}. " f"Please check the file for errors or try again."
                     )
-                org, comp = components
-                self.all_remote_components.append(
-                    NFCoreComponent(
-                        comp,
-                        repo_url,
-                        Path(self.directory, self.component_type, org, comp),
-                        self.repo_type,
-                        Path(self.directory),
-                        self.component_type,
+                for org, comp in components:
+                    self.all_remote_components.append(
+                        NFCoreComponent(
+                            comp,
+                            repo_url,
+                            Path(self.directory, self.component_type, org, comp),
+                            self.repo_type,
+                            Path(self.directory),
+                            self.component_type,
+                        )
                     )
-                )
             if not self.all_remote_components:
                 raise LookupError(
                     f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline."
@@ -123,7 +123,7 @@ def __init__(
                     for comp in self.get_local_components()
                 ]
             self.config = nf_core.utils.fetch_wf_config(Path(self.directory), cache_config=True)
-        elif self.repo_type == "modules":
+        else:
             component_dir = Path(
                 self.directory,
                 self.default_modules_path if self.component_type == "modules" else self.default_subworkflows_path,
@@ -141,11 +141,11 @@ def __init__(
                 Path(self.directory).joinpath("tests", "config"), cache_config=True
             )
 
-        if registry is None:
-            self.registry = self.config.get("docker.registry", "quay.io")
-        else:
-            self.registry = registry
-        log.debug(f"Registry set to {self.registry}")
+            if registry is None:
+                self.registry = self.config.get("docker.registry", "quay.io")
+            else:
+                self.registry = registry
+            log.debug(f"Registry set to {self.registry}")
 
         self.lint_config = None
         self.modules_json = None
diff --git a/nf_core/components/list.py b/nf_core/components/list.py
index b24732e5c3..67468b4a5a 100644
--- a/nf_core/components/list.py
+++ b/nf_core/components/list.py
@@ -5,7 +5,7 @@
 import rich.table
 
 from nf_core.components.components_command import ComponentCommand
-from nf_core.modules.modules_json import ModulesJson
+from nf_core.modules.modules_json import ModulesJson, ModulesJsonModuleEntry
 from nf_core.modules.modules_repo import ModulesRepo
 
 log = logging.getLogger(__name__)
@@ -110,7 +110,7 @@ def pattern_msg(keywords: List[str]) -> str:
             modules_json_file = modules_json.modules_json
 
             for repo_url, component_with_dir in sorted(repos_with_comps.items()):
-                repo_entry: Dict[str, Dict[str, Dict[str, Dict[str, Union[str, List[str]]]]]]
+                repo_entry: Dict[str, Dict[str, Dict[str, ModulesJsonModuleEntry]]]
                 if modules_json_file is None:
                     log.warning(f"Modules JSON file '{modules_json.modules_json_path}' is missing. ")
                     continue
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 1433122225..0c63141c73 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -21,7 +21,7 @@ def __init__(
         component_name: str,
         repo_url: Optional[str],
         component_dir: Path,
-        repo_type: str,
+        repo_type: Optional[str],
         base_dir: Path,
         component_type: str,
         remote_component: bool = True,
@@ -54,6 +54,7 @@ def __init__(
         self.has_meta: bool = False
         self.git_sha: Optional[str] = None
         self.is_patched: bool = False
+        self.branch: Optional[str] = None
 
         if remote_component:
             # Initialize the important files
@@ -85,6 +86,9 @@ def __init__(
             self.test_yml = None
             self.test_main_nf = None
 
+    def __repr__(self) -> str:
+        return f"<NFCoreComponent {self.component_name} {self.component_dir} {self.repo_url}>"
+
     def _get_main_nf_tags(self, test_main_nf: Union[Path, str]):
         """Collect all tags from the main.nf.test file."""
         tags = []
diff --git a/nf_core/modules/lint/module_version.py b/nf_core/modules/lint/module_version.py
index d08658f5da..d0ef17a44d 100644
--- a/nf_core/modules/lint/module_version.py
+++ b/nf_core/modules/lint/module_version.py
@@ -8,11 +8,12 @@
 import nf_core
 import nf_core.modules.modules_repo
 import nf_core.modules.modules_utils
+from nf_core.modules.modules_utils import NFCoreComponent
 
 log = logging.getLogger(__name__)
 
 
-def module_version(module_lint_object, module):
+def module_version(module_lint_object: "nf_core.modules.lint.ModuleLint", module: "NFCoreComponent"):
     """
     Verifies that the module has a version specified in the ``modules.json`` file
 
@@ -20,8 +21,9 @@ def module_version(module_lint_object, module):
     containing a commit SHA. If that is true, it verifies that there are no
     newer version of the module available.
     """
-
-    modules_json_path = Path(module_lint_object.dir, "modules.json")
+    assert module_lint_object.modules_json is not None  # mypy
+    assert module.repo_url is not None  # mypy
+    modules_json_path = Path(module_lint_object.directory, "modules.json")
     # Verify that a git_sha exists in the `modules.json` file for this module
     version = module_lint_object.modules_json.get_module_version(module.component_name, module.repo_url, module.org)
     if version is None:
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index faeb84fc35..c0e41d1b42 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -6,7 +6,7 @@
 import shutil
 import tempfile
 from pathlib import Path
-from typing import Any, List, Optional, Tuple, Union
+from typing import Dict, List, NotRequired, Optional, Tuple, TypedDict, Union
 
 import git
 import questionary
@@ -27,6 +27,19 @@
 log = logging.getLogger(__name__)
 
 
+class ModulesJsonModuleEntry(TypedDict):
+    branch: str
+    git_sha: str
+    installed_by: List[str]
+    patch: NotRequired[str]
+
+
+class ModulesJsonType(TypedDict):
+    name: str
+    homePage: str
+    repos: Dict[str, Dict[str, Dict[str, Dict[str, ModulesJsonModuleEntry]]]]
+
+
 class ModulesJson:
     """
     An object for handling a 'modules.json' file in a pipeline
@@ -43,10 +56,10 @@ def __init__(self, pipeline_dir: Union[str, Path]):
         self.modules_dir = self.directory / "modules"
         self.subworkflows_dir = self.directory / "subworkflows"
         self.modules_json_path = self.directory / "modules.json"
-        self.modules_json = None
+        self.modules_json: Optional[ModulesJsonType] = None
         self.pipeline_modules = None
         self.pipeline_subworkflows = None
-        self.pipeline_components = None
+        self.pipeline_components: Optional[Dict[str, List[Tuple[str, str]]]] = None
 
     def __str__(self):
         if self.modules_json is None:
@@ -56,7 +69,7 @@ def __str__(self):
     def __repr__(self):
         return self.__str__()
 
-    def create(self):
+    def create(self) -> None:
         """
         Creates the modules.json file from the modules and subworkflows installed in the pipeline directory
 
@@ -66,7 +79,7 @@ def create(self):
         pipeline_config = nf_core.utils.fetch_wf_config(self.directory)
         pipeline_name = pipeline_config.get("manifest.name", "")
         pipeline_url = pipeline_config.get("manifest.homePage", "")
-        new_modules_json = {"name": pipeline_name.strip("'"), "homePage": pipeline_url.strip("'"), "repos": {}}
+        new_modules_json = ModulesJsonType(name=pipeline_name, homePage=pipeline_url, repos={})
 
         if not self.modules_dir.exists():
             if rich.prompt.Confirm.ask(
@@ -79,7 +92,6 @@ def create(self):
 
         # Get repositories
         repos, _ = self.get_pipeline_module_repositories("modules", self.modules_dir)
-
         # Get all module/subworkflow names in the repos
         repo_module_names = self.get_component_names_from_repo(repos, self.modules_dir)
         repo_subworkflow_names = self.get_component_names_from_repo(repos, self.subworkflows_dir)
@@ -105,7 +117,9 @@ def create(self):
         self.modules_json = new_modules_json
         self.dump()
 
-    def get_component_names_from_repo(self, repos, directory):
+    def get_component_names_from_repo(
+        self, repos: Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, str | List[str]]]]]], directory: Path
+    ) -> List[Tuple[str, List[str], str]]:
         """
         Get component names from repositories in a pipeline.
 
@@ -122,8 +136,8 @@ def get_component_names_from_repo(self, repos, directory):
             components = (
                 repo_url,
                 [
-                    str(Path(component_name).relative_to(directory / modules_repo.repo_path))
-                    for component_name, _, file_names in os.walk(directory / modules_repo.repo_path)
+                    str(component_name.relative_to(directory / modules_repo.repo_path))
+                    for component_name, _, file_names in Path.walk(directory / modules_repo.repo_path)
                     if "main.nf" in file_names
                 ],
                 modules_repo.repo_path,
@@ -131,7 +145,9 @@ def get_component_names_from_repo(self, repos, directory):
             names.append(components)
         return names
 
-    def get_pipeline_module_repositories(self, component_type, directory, repos=None):
+    def get_pipeline_module_repositories(
+        self, component_type: str, directory: Path, repos: Optional[Dict] = None
+    ) -> Tuple[Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, Union[str, List[str]]]]]]], Dict[Path, Path]]:
         """
         Finds all module repositories in the modules and subworkflows directory.
         Ignores the local modules/subworkflows.
@@ -153,6 +169,7 @@ def get_pipeline_module_repositories(self, component_type, directory, repos=None
         # The function might rename some directories, keep track of them
         renamed_dirs = {}
         # Check if there are any untracked repositories
+
         dirs_not_covered = self.dir_tree_uncovered(directory, [Path(ModulesRepo(url).repo_path) for url in repos])
         if len(dirs_not_covered) > 0:
             log.info(f"Found custom {component_type[:-1]} repositories when creating 'modules.json'")
@@ -245,8 +262,12 @@ def dir_tree_uncovered(self, components_directory, repos):
         return dirs_not_covered
 
     def determine_branches_and_shas(
-        self, component_type: str, install_dir: Union[str, Path], remote_url: str, components: List[Path]
-    ) -> dict[Path, dict[str, Any]]:
+        self,
+        component_type: str,
+        install_dir: Union[str, Path],
+        remote_url: str,
+        components: List[str],
+    ) -> Dict[str, ModulesJsonModuleEntry]:
         """
         Determines what branch and commit sha each module/subworkflow in the pipeline belongs to
 
@@ -273,10 +294,10 @@ def determine_branches_and_shas(
         available_branches = ModulesRepo.get_remote_branches(remote_url)
         sb_local = []
         dead_components = []
-        repo_entry = {}
+        repo_entry: Dict[str, ModulesJsonModuleEntry] = {}
         for component in sorted(components):
             modules_repo = default_modules_repo
-            component_path = repo_path / component
+            component_path = Path(repo_path, component)
             correct_commit_sha = None
             tried_branches = {default_modules_repo.branch}
             found_sha = False
@@ -286,16 +307,16 @@ def determine_branches_and_shas(
                 if patch_file.is_file():
                     temp_module_dir = self.try_apply_patch_reverse(component, install_dir, patch_file, component_path)
                     correct_commit_sha = self.find_correct_commit_sha(
-                        component_type, str(component), temp_module_dir, modules_repo
+                        component_type, component, temp_module_dir, modules_repo
                     )
                 else:
                     correct_commit_sha = self.find_correct_commit_sha(
-                        component_type, str(component), component_path, modules_repo
+                        component_type, component, component_path, modules_repo
                     )
                     if correct_commit_sha is None:
                         # Check in the old path
                         correct_commit_sha = self.find_correct_commit_sha(
-                            component_type, str(component), repo_path / component_type / component, modules_repo
+                            component_type, component, repo_path / component_type / component, modules_repo
                         )
                 if correct_commit_sha is None:
                     log.info(
@@ -328,7 +349,7 @@ def determine_branches_and_shas(
                 else:
                     found_sha = True
                     break
-            if found_sha:
+            if found_sha and correct_commit_sha is not None:
                 repo_entry[component] = {
                     "branch": modules_repo.branch,
                     "git_sha": correct_commit_sha,
@@ -337,7 +358,7 @@ def determine_branches_and_shas(
 
         # Clean up the modules/subworkflows we were unable to find the sha for
         for component in sb_local:
-            log.debug(f"Moving {component_type[:-1]} '{Path(install_dir, component)}' to 'local' directory")
+            log.debug(f"Moving {component_type[:-1]} '{Path(install_dir, str(component))}' to 'local' directory")
             self.move_component_to_local(component_type, component, str(install_dir))
 
         for component in dead_components:
@@ -408,14 +429,14 @@ def move_component_to_local(self, component_type: str, component: Union[str, Pat
             to_name += f"-{datetime.datetime.now().strftime('%y%m%d%H%M%S')}"
         shutil.move(current_path, local_dir / to_name)
 
-    def unsynced_components(self) -> Tuple[List[Path], List[Path], dict]:
+    def unsynced_components(self) -> Tuple[List[str], List[str], dict]:
         """
         Compute the difference between the modules/subworkflows in the directory and the
         modules/subworkflows in the 'modules.json' file. This is done by looking at all
         directories containing a 'main.nf' file
 
         Returns:
-            (untrack_dirs ([ Path ]), missing_installation (dict)): Directories that are not tracked
+            (untrack_dirs ([ str ]), missing_installation (dict)): Directories that are not tracked
             by the modules.json file, and modules/subworkflows in the modules.json where
             the installation directory is missing
         """
@@ -443,7 +464,7 @@ def unsynced_components(self) -> Tuple[List[Path], List[Path], dict]:
 
         return untracked_dirs_modules, untracked_dirs_subworkflows, missing_installation
 
-    def parse_dirs(self, dirs: List[Path], missing_installation: dict, component_type: str) -> Tuple[List[Path], dict]:
+    def parse_dirs(self, dirs: List[Path], missing_installation: Dict, component_type: str) -> Tuple[List[str], Dict]:
         """
         Parse directories and check if they are tracked in the modules.json file
 
@@ -461,9 +482,10 @@ def parse_dirs(self, dirs: List[Path], missing_installation: dict, component_typ
         for dir_ in dirs:
             # Check if the module/subworkflows directory exists in modules.json
             install_dir = dir_.parts[0]
-            component = Path(*dir_.parts[1:])
+            component = "/".join(dir_.parts[1:])
             component_in_file = False
             git_url = ""
+
             for repo in missing_installation:
                 if component_type in missing_installation[repo]:
                     if install_dir in missing_installation[repo][component_type]:
@@ -564,7 +586,7 @@ def reinstall_repo(self, install_dir, remote_url, module_entries):
                     failed_to_install.append(module)
         return failed_to_install
 
-    def check_up_to_date(self) -> bool:
+    def check_up_to_date(self):
         """
         Checks whether the modules and subworkflows installed in the directory
         are consistent with the entries in the 'modules.json' file and vice versa.
@@ -715,14 +737,12 @@ def update(
             self.modules_json["repos"][remote_url][component_type] = {repo_name: {}}
         repo_component_entry = self.modules_json["repos"][remote_url][component_type][repo_name]
         if component_name not in repo_component_entry:
-            repo_component_entry[component_name] = {}
+            repo_component_entry[component_name] = {"branch": "", "git_sha": "", "installed_by": []}
         repo_component_entry[component_name]["git_sha"] = component_version
         repo_component_entry[component_name]["branch"] = branch
         try:
             if installed_by not in repo_component_entry[component_name]["installed_by"] and installed_by is not None:
-                repo_component_entry[component_name]["installed_by"].append(installed_by)
-        except KeyError:
-            repo_component_entry[component_name]["installed_by"] = [installed_by]
+                repo_component_entry[component_name]["installed_by"] += installed_by
         finally:
             new_installed_by = repo_component_entry[component_name]["installed_by"] + list(installed_by_log)
             repo_component_entry[component_name]["installed_by"] = sorted([*set(new_installed_by)])
@@ -912,7 +932,7 @@ def get_modules_json(self) -> dict:
         if self.modules_json is None:
             self.load()
             assert self.modules_json is not None  # mypy
-        return copy.deepcopy(self.modules_json)
+        return copy.deepcopy(self.modules_json)  # type: ignore
 
     def get_component_version(self, component_type, component_name, repo_url, install_dir):
         """
@@ -938,7 +958,7 @@ def get_component_version(self, component_type, component_name, repo_url, instal
             .get("git_sha", None)
         )
 
-    def get_module_version(self, module_name, repo_url, install_dir):
+    def get_module_version(self, module_name: str, repo_url: str, install_dir: str) -> Optional[str]:
         """
         Returns the version of a module
 
@@ -953,14 +973,11 @@ def get_module_version(self, module_name, repo_url, install_dir):
         if self.modules_json is None:
             self.load()
             assert self.modules_json is not None  # mypy
-        return (
-            self.modules_json.get("repos", {})
-            .get(repo_url, {})
-            .get("modules", {})
-            .get(install_dir, {})
-            .get(module_name, {})
-            .get("git_sha", None)
-        )
+        try:
+            sha = self.modules_json["repos"][repo_url]["modules"][install_dir][module_name]["git_sha"]
+        except KeyError:
+            sha = None
+        return sha
 
     def get_subworkflow_version(self, subworkflow_name, repo_url, install_dir):
         """
@@ -986,7 +1003,7 @@ def get_subworkflow_version(self, subworkflow_name, repo_url, install_dir):
             .get("git_sha", None)
         )
 
-    def get_all_components(self, component_type: str) -> dict[str, Tuple[(str, str)]]:
+    def get_all_components(self, component_type: str) -> dict[str, List[Tuple[(str, str)]]]:
         """
         Retrieves all pipeline modules/subworkflows that are reported in the modules.json
 
@@ -1002,8 +1019,8 @@ def get_all_components(self, component_type: str) -> dict[str, Tuple[(str, str)]
             self.pipeline_components = {}
             for repo, repo_entry in self.modules_json.get("repos", {}).items():
                 if component_type in repo_entry:
-                    for dir, components in repo_entry[component_type].items():
-                        self.pipeline_components[repo] = [(dir, m) for m in components]
+                    for directory, components in repo_entry[component_type].items():
+                        self.pipeline_components[repo] = [(directory, m) for m in components]
 
         return self.pipeline_components
 
@@ -1072,7 +1089,9 @@ def get_installed_by_entries(self, component_type, name):
 
         return installed_by_entries
 
-    def get_component_branch(self, component_type, component, repo_url, install_dir):
+    def get_component_branch(
+        self, component_type: str, component: Union[str, Path], repo_url: str, install_dir: str
+    ) -> str:
         """
         Gets the branch from which the module/subworkflow was installed
 
@@ -1084,14 +1103,10 @@ def get_component_branch(self, component_type, component, repo_url, install_dir)
         if self.modules_json is None:
             self.load()
             assert self.modules_json is not None  # mypy
-        branch = (
-            self.modules_json["repos"]
-            .get(repo_url, {})
-            .get(component_type, {})
-            .get(install_dir, {})
-            .get(component, {})
-            .get("branch")
-        )
+        try:
+            branch = self.modules_json["repos"][repo_url][component_type][install_dir][str(component)]["branch"]
+        except (KeyError, TypeError):
+            branch = None
         if branch is None:
             raise LookupError(
                 f"Could not find branch information for component '{Path(install_dir, component)}'."
@@ -1112,7 +1127,7 @@ def dump(self, run_prettier: bool = False) -> None:
                 with open(self.modules_json_path, "w") as fh:
                     json.dump(self.modules_json, fh, indent=4)
 
-    def resolve_missing_installation(self, missing_installation, component_type):
+    def resolve_missing_installation(self, missing_installation: Dict, component_type: str) -> None:
         missing_but_in_mod_json = [
             f"'{component_type}/{install_dir}/{component}'"
             for repo_url, contents in missing_installation.items()
@@ -1168,7 +1183,7 @@ def resolve_missing_from_modules_json(self, missing_from_modules_json, component
 
         # Get tuples of components that miss installation and their install directory
         def components_with_repos():
-            for dir in missing_from_modules_json:
+            for directory in missing_from_modules_json:
                 for repo_url in repos:
                     modules_repo = ModulesRepo(repo_url)
                     paths_in_directory = []
@@ -1178,12 +1193,12 @@ def components_with_repos():
                     )
                     for dir_name, _, _ in os.walk(repo_url_path):
                         if component_type == "modules":
-                            if len(Path(dir).parts) > 1:  # The module name is TOOL/SUBTOOL
+                            if len(Path(directory).parts) > 1:  # The module name is TOOL/SUBTOOL
                                 paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:])))
                                 pass
                         paths_in_directory.append(Path(dir_name).parts[-1])
                     if dir in paths_in_directory:
-                        yield (modules_repo.repo_path, dir)
+                        yield (modules_repo.repo_path, directory)
 
         # Add all components into a dictionary with install directories
         repos_with_components = {}
diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py
index a979ae45b8..daa7b59811 100644
--- a/nf_core/modules/modules_repo.py
+++ b/nf_core/modules/modules_repo.py
@@ -1,6 +1,7 @@
 import logging
 import os
 import shutil
+from pathlib import Path
 from typing import Optional
 
 import git
@@ -72,8 +73,8 @@ def __init__(
             self.verify_branch()
 
         # Convenience variable
-        self.modules_dir = os.path.join(self.local_repo_dir, "modules", self.repo_path)
-        self.subworkflows_dir = os.path.join(self.local_repo_dir, "subworkflows", self.repo_path)
+        self.modules_dir = Path(self.local_repo_dir, "modules", self.repo_path)
+        self.subworkflows_dir = Path(self.local_repo_dir, "subworkflows", self.repo_path)
 
         self.avail_module_names = None
 
diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py
index 4b69d4af87..33e7f0a54a 100644
--- a/nf_core/synced_repo.py
+++ b/nf_core/synced_repo.py
@@ -4,7 +4,7 @@
 import shutil
 from configparser import NoOptionError, NoSectionError
 from pathlib import Path
-from typing import Dict, Optional, Union
+from typing import Dict, Iterable, Optional, Union
 
 import git
 from git.exc import GitCommandError
@@ -121,28 +121,32 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa
             remote_url = NF_CORE_MODULES_REMOTE
 
         self.remote_url = remote_url
+        self.fullname = None
+        self.local_repo_dir = None
 
         self.repo = None
         # TODO: SyncedRepo doesn't have this method and both the ModulesRepo and
         # the WorkflowRepo define their own including custom init methods. This needs
         # fixing.
         self.setup_local_repo(remote_url, branch, hide_progress)
+        if self.local_repo_dir is None:
+            raise ValueError("Repository not initialized")
+        else:
+            config_fn, repo_config = load_tools_config(self.local_repo_dir)
+            try:
+                self.repo_path = repo_config["org_path"]
+            except KeyError:
+                raise UserWarning(f"'org_path' key not present in {config_fn.name}")
 
-        config_fn, repo_config = load_tools_config(self.local_repo_dir)
-        try:
-            self.repo_path = repo_config["org_path"]
-        except KeyError:
-            raise UserWarning(f"'org_path' key not present in {config_fn.name}")
-
-        # Verify that the repo seems to be correctly configured
-        if self.repo_path != NF_CORE_MODULES_NAME or self.branch:
-            self.verify_branch()
+            # Verify that the repo seems to be correctly configured
+            if self.repo_path != NF_CORE_MODULES_NAME or self.branch:
+                self.verify_branch()
 
-        # Convenience variable
-        self.modules_dir = os.path.join(self.local_repo_dir, "modules", self.repo_path)
-        self.subworkflows_dir = os.path.join(self.local_repo_dir, "subworkflows", self.repo_path)
+            # Convenience variable
+            self.modules_dir = Path(self.local_repo_dir, "modules", self.repo_path)
+            self.subworkflows_dir = Path(self.local_repo_dir, "subworkflows", self.repo_path)
 
-        self.avail_module_names = None
+            self.avail_module_names = None
 
     def setup_local_repo(self, remote_url, branch, hide_progress):
         pass
@@ -361,7 +365,9 @@ def ensure_git_user_config(self, default_name: str, default_email: str) -> None:
                 if not user_email:
                     git_config.set_value("user", "email", default_email)
 
-    def get_component_git_log(self, component_name: Union[str, Path], component_type: str, depth: Optional[int] = None):
+    def get_component_git_log(
+        self, component_name: Union[str, Path], component_type: str, depth: Optional[int] = None
+    ) -> Iterable[Dict[str, str]]:
         """
         Fetches the commit history the of requested module/subworkflow since a given date. The default value is
         not arbitrary - it is the last time the structure of the nf-core/modules repository was had an
@@ -373,35 +379,32 @@ def get_component_git_log(self, component_name: Union[str, Path], component_type
         Returns:
             ( dict ): Iterator of commit SHAs and associated (truncated) message
         """
-
         if self.repo is None:
             raise ValueError("Repository not initialized")
         self.checkout_branch()
         component_path = Path(component_type, self.repo_path, component_name)
 
-        commits_new = self.repo.iter_commits(max_count=depth, paths=component_path)
-        if not commits_new:
-            raise ValueError(f"Could not find any commits for '{component_name}' in '{self.remote_url}'")
-        else:
-            commits_new = [
-                {"git_sha": commit.hexsha, "trunc_message": commit.message.splitlines()[0]} for commit in commits_new
-            ]
-        commits_old = []
+        commits_new_iter = self.repo.iter_commits(max_count=depth, paths=component_path)
+        commits_old_iter = []
         if component_type == "modules":
             # Grab commits also from previous modules structure
-            component_path = Path("modules", component_name)
-            commits_old = self.repo.iter_commits(max_count=depth, paths=component_path)
-            commits_old = [
-                {"git_sha": commit.hexsha, "trunc_message": commit.message.splitlines()[0]} for commit in commits_old
-            ]
+            old_component_path = Path("modules", component_name)
+            commits_old_iter = self.repo.iter_commits(max_count=depth, paths=old_component_path)
+
+        commits_old = [{"git_sha": commit.hexsha, "trunc_message": commit.message} for commit in commits_old_iter]
+        commits_new = [{"git_sha": commit.hexsha, "trunc_message": commit.message} for commit in commits_new_iter]
         commits = iter(commits_new + commits_old)
+
         return commits
 
     def get_latest_component_version(self, component_name, component_type):
         """
         Returns the latest commit in the repository
         """
-        return list(self.get_component_git_log(component_name, component_type, depth=1))[0]["git_sha"]
+        try:
+            return list(self.get_component_git_log(component_name, component_type, depth=1))[0]["git_sha"]
+        except UserWarning:
+            return None
 
     def sha_exists_on_branch(self, sha):
         """
diff --git a/nf_core/utils.py b/nf_core/utils.py
index d1e9ccfe95..4d0566b1af 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -30,6 +30,7 @@
 import rich.markup
 import yaml
 from packaging.version import Version
+from pydantic import BaseModel, ValidationError
 from rich.live import Live
 from rich.spinner import Spinner
 
@@ -175,9 +176,9 @@ def _load_conda_environment(self) -> bool:
             log.debug("No conda `environment.yml` file found.")
             return False
 
-    def _fp(self, fn):
+    def _fp(self, fn: Union[str, Path]) -> Path:
         """Convenience function to get full path to a file in the pipeline"""
-        return os.path.join(self.wf_path, fn)
+        return Path(self.wf_path, fn)
 
     def list_files(self) -> List[Path]:
         """Get a list of all files in the pipeline"""
@@ -191,9 +192,8 @@ def list_files(self) -> List[Path]:
                     files.append(full_fn)
                 else:
                     log.debug(f"`git ls-files` returned '{full_fn}' but could not open it!")
-        except subprocess.CalledProcessError as e:
+        except subprocess.CalledProcessError:
             # Failed, so probably not initialised as a git repository - just a list of all files
-            log.debug(f"Couldn't call 'git ls-files': {e}")
             files = []
             for file_path in self.wf_path.rglob("*"):
                 if file_path.is_file():
@@ -1041,7 +1041,26 @@ def get_repo_releases_branches(pipeline, wfs):
 DEPRECATED_CONFIG_PATHS = [".nf-core-lint.yml", ".nf-core-lint.yaml"]
 
 
-def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, dict]:
+class NFCoreTemplateConfig(BaseModel):
+    org: str
+    name: str
+    description: str
+    author: str
+    version: Optional[str]
+    force: Optional[bool]
+    outdir: Optional[str]
+    skip_features: Optional[list]
+    is_nfcore: Optional[bool]
+
+
+class NFCoreYamlConfig(BaseModel):
+    nf_core_version: str
+    repository_type: str
+    org_path: str
+    template: NFCoreTemplateConfig
+
+
+def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, NFCoreYamlConfig]:
     """
     Parse the nf-core.yml configuration file
 
@@ -1059,21 +1078,26 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, dict]:
     if config_fn is None:
         depr_path = get_first_available_path(directory, DEPRECATED_CONFIG_PATHS)
         if depr_path:
-            log.error(
-                f"Deprecated `{depr_path.name}` file found! The file will not be loaded. "
-                f"Please rename the file to `{CONFIG_PATHS[0]}`."
+            raise AssertionError(
+                f"Deprecated `{depr_path.name}` file found! Please rename the file to `{CONFIG_PATHS[0]}`."
             )
         else:
-            log.debug(f"No tools config file found: {CONFIG_PATHS[0]}")
-        return Path(directory, CONFIG_PATHS[0]), {}
-
-    with open(config_fn) as fh:
+            raise AssertionError(f"Could not find a config file in the directory '{directory}'")
+    with open(str(config_fn)) as fh:
         tools_config = yaml.safe_load(fh)
+
     # If the file is empty
-    tools_config = tools_config or {}
+    if tools_config is None:
+        raise AssertionError(f"Config file '{config_fn}' is empty")
+
+    # Check for required fields
+    try:
+        nf_core_yaml_config = NFCoreYamlConfig(**tools_config)
+    except ValidationError as e:
+        raise AssertionError(f"Config file '{config_fn}' is invalid: {e}")
 
     log.debug("Using config file: %s", config_fn)
-    return config_fn, tools_config
+    return config_fn, nf_core_yaml_config
 
 
 def determine_base_dir(directory: Union[Path, str] = ".") -> Path:

From b2336adaf288e3c64d02c28fb7e3e58cd22bd4cc Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 23 Jul 2024 14:24:21 +0200
Subject: [PATCH 103/414] remove remaining mention to 'defaults'

---
 nf_core/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/utils.py b/nf_core/utils.py
index 48d1c3ca3d..d5bf328b59 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -635,7 +635,7 @@ def anaconda_package(dep, dep_channels=None):
     """
 
     if dep_channels is None:
-        dep_channels = ["conda-forge", "bioconda", "defaults"]
+        dep_channels = ["conda-forge", "bioconda"]
 
     # Check if each dependency is the latest available version
     if "=" in dep:

From ff1a49520f69d228acead56fc232760ded321fe3 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 24 Jul 2024 14:21:12 +0200
Subject: [PATCH 104/414] avoid circular import due to modules_json being
 importetd

---
 nf_core/modules/__init__.py            | 12 -----
 nf_core/modules/lint/module_version.py |  5 +-
 tests/modules/test_bump_versions.py    | 10 ++--
 tests/modules/test_create.py           | 16 +++---
 tests/modules/test_info.py             | 10 ++--
 tests/modules/test_install.py          |  6 +--
 tests/modules/test_lint.py             | 69 +++++++++++++-------------
 tests/modules/test_list.py             | 26 +++++-----
 tests/modules/test_modules_json.py     |  4 +-
 tests/modules/test_patch.py            | 29 ++++++-----
 tests/modules/test_update.py           | 20 +++++---
 tests/test_subworkflows.py             | 43 +---------------
 12 files changed, 105 insertions(+), 145 deletions(-)

diff --git a/nf_core/modules/__init__.py b/nf_core/modules/__init__.py
index 6be871ece8..e69de29bb2 100644
--- a/nf_core/modules/__init__.py
+++ b/nf_core/modules/__init__.py
@@ -1,12 +0,0 @@
-from .bump_versions import ModuleVersionBumper
-from .create import ModuleCreate
-from .info import ModuleInfo
-from .install import ModuleInstall
-from .lint import ModuleLint
-from .list import ModuleList
-from .modules_json import ModulesJson
-from .modules_repo import ModulesRepo
-from .modules_utils import ModuleExceptionError
-from .patch import ModulePatch
-from .remove import ModuleRemove
-from .update import ModuleUpdate
diff --git a/nf_core/modules/lint/module_version.py b/nf_core/modules/lint/module_version.py
index d0ef17a44d..207d5e9418 100644
--- a/nf_core/modules/lint/module_version.py
+++ b/nf_core/modules/lint/module_version.py
@@ -6,6 +6,7 @@
 from pathlib import Path
 
 import nf_core
+import nf_core.modules.lint
 import nf_core.modules.modules_repo
 import nf_core.modules.modules_utils
 from nf_core.modules.modules_utils import NFCoreComponent
@@ -40,8 +41,8 @@ def module_version(module_lint_object: "nf_core.modules.lint.ModuleLint", module
         )
         modules_repo = nf_core.modules.modules_repo.ModulesRepo(remote_url=module.repo_url, branch=module.branch)
 
-        module_git_log = modules_repo.get_component_git_log(module.component_name, "modules")
-        if version == next(module_git_log)["git_sha"]:
+        module_git_log = list(modules_repo.get_component_git_log(module.component_name, "modules"))
+        if version == module_git_log[0]["git_sha"]:
             module.passed.append(("module_version", "Module is the latest version", module.component_dir))
         else:
             module.warned.append(("module_version", "New version available", module.component_dir))
diff --git a/tests/modules/test_bump_versions.py b/tests/modules/test_bump_versions.py
index 29e030668d..d46b8747c8 100644
--- a/tests/modules/test_bump_versions.py
+++ b/tests/modules/test_bump_versions.py
@@ -3,7 +3,7 @@
 
 import pytest
 
-import nf_core.modules
+import nf_core.modules.bump_versions
 from nf_core.modules.modules_utils import ModuleExceptionError
 
 from ..test_modules import TestModules
@@ -19,19 +19,19 @@ def test_modules_bump_versions_single_module(self):
         new_content = re.sub(r"bioconda::star=\d.\d.\d\D?", r"bioconda::star=2.6.1d", content)
         with open(env_yml_path, "w") as fh:
             fh.write(new_content)
-        version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+        version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
         version_bumper.bump_versions(module="bpipe/test")
         assert len(version_bumper.failed) == 0
 
     def test_modules_bump_versions_all_modules(self):
         """Test updating all modules"""
-        version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+        version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
         version_bumper.bump_versions(all_modules=True)
         assert len(version_bumper.failed) == 0
 
     def test_modules_bump_versions_fail(self):
         """Fail updating a module with wrong name"""
-        version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+        version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
         with pytest.raises(ModuleExceptionError) as excinfo:
             version_bumper.bump_versions(module="no/module")
         assert "Could not find the specified module:" in str(excinfo.value)
@@ -45,6 +45,6 @@ def test_modules_bump_versions_fail_unknown_version(self):
         new_content = re.sub(r"bioconda::bpipe=\d.\d.\d\D?", r"bioconda::bpipe=xxx", content)
         with open(env_yml_path, "w") as fh:
             fh.write(new_content)
-        version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+        version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
         version_bumper.bump_versions(module="bpipe/test")
         assert "Conda package had unknown version" in version_bumper.failed[0][0]
diff --git a/tests/modules/test_create.py b/tests/modules/test_create.py
index c847501830..219f869997 100644
--- a/tests/modules/test_create.py
+++ b/tests/modules/test_create.py
@@ -9,7 +9,7 @@
 import yaml
 from git.repo import Repo
 
-import nf_core.modules
+import nf_core.modules.create
 from tests.utils import (
     GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH,
     GITLAB_URL,
@@ -26,7 +26,7 @@ def test_modules_create_succeed(self):
         with responses.RequestsMock() as rsps:
             mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7")
             mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7")
-            module_create = nf_core.modules.ModuleCreate(
+            module_create = nf_core.modules.create.ModuleCreate(
                 self.pipeline_dir, "trimgalore", "@author", "process_single", True, True, conda_name="trim-galore"
             )
             with requests_cache.disabled():
@@ -38,7 +38,7 @@ def test_modules_create_fail_exists(self):
         with responses.RequestsMock() as rsps:
             mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7")
             mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7")
-            module_create = nf_core.modules.ModuleCreate(
+            module_create = nf_core.modules.create.ModuleCreate(
                 self.pipeline_dir, "trimgalore", "@author", "process_single", False, False, conda_name="trim-galore"
             )
             with requests_cache.disabled():
@@ -53,7 +53,7 @@ def test_modules_create_nfcore_modules(self):
         with responses.RequestsMock() as rsps:
             mock_anaconda_api_calls(rsps, "fastqc", "0.11.9")
             mock_biocontainers_api_calls(rsps, "fastqc", "0.11.9")
-            module_create = nf_core.modules.ModuleCreate(
+            module_create = nf_core.modules.create.ModuleCreate(
                 self.nfcore_modules, "fastqc", "@author", "process_low", False, False
             )
             with requests_cache.disabled():
@@ -68,7 +68,7 @@ def test_modules_create_nfcore_modules_subtool(self):
         with responses.RequestsMock() as rsps:
             mock_anaconda_api_calls(rsps, "star", "2.8.10a")
             mock_biocontainers_api_calls(rsps, "star", "2.8.10a")
-            module_create = nf_core.modules.ModuleCreate(
+            module_create = nf_core.modules.create.ModuleCreate(
                 self.nfcore_modules, "star/index", "@author", "process_medium", False, False
             )
             with requests_cache.disabled():
@@ -94,7 +94,7 @@ def test_modules_migrate(self, mock_rich_ask):
 
         # Create a module with --migrate-pytest
         mock_rich_ask.return_value = True
-        module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
+        module_create = nf_core.modules.create.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
         module_create.create()
 
         with open(module_dir / "main.nf") as fh:
@@ -128,7 +128,7 @@ def test_modules_migrate_no_delete(self, mock_rich_ask):
 
         # Create a module with --migrate-pytest
         mock_rich_ask.return_value = False
-        module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
+        module_create = nf_core.modules.create.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
         module_create.create()
 
         # Check that pytest folder is not deleted
@@ -157,7 +157,7 @@ def test_modules_migrate_symlink(self, mock_rich_ask):
 
         # Create a module with --migrate-pytest
         mock_rich_ask.return_value = True
-        module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
+        module_create = nf_core.modules.create.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
         module_create.create()
 
         # Check that symlink is deleted
diff --git a/tests/modules/test_info.py b/tests/modules/test_info.py
index 8906854044..8e60bed316 100644
--- a/tests/modules/test_info.py
+++ b/tests/modules/test_info.py
@@ -1,6 +1,6 @@
 from rich.console import Console
 
-import nf_core.modules
+import nf_core.modules.info
 
 from ..test_modules import TestModules
 from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL
@@ -9,7 +9,7 @@
 class TestModulesCreate(TestModules):
     def test_modules_info_remote(self):
         """Test getting info about a remote module"""
-        mods_info = nf_core.modules.ModuleInfo(self.pipeline_dir, "fastqc")
+        mods_info = nf_core.modules.info.ModuleInfo(self.pipeline_dir, "fastqc")
         mods_info_output = mods_info.get_component_info()
         console = Console(record=True)
         console.print(mods_info_output)
@@ -21,7 +21,7 @@ def test_modules_info_remote(self):
 
     def test_modules_info_remote_gitlab(self):
         """Test getting info about a module in the remote gitlab repo"""
-        mods_info = nf_core.modules.ModuleInfo(
+        mods_info = nf_core.modules.info.ModuleInfo(
             self.pipeline_dir, "fastqc", remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH
         )
         mods_info_output = mods_info.get_component_info()
@@ -37,7 +37,7 @@ def test_modules_info_remote_gitlab(self):
     def test_modules_info_local(self):
         """Test getting info about a locally installed module"""
         self.mods_install.install("trimgalore")
-        mods_info = nf_core.modules.ModuleInfo(self.pipeline_dir, "trimgalore")
+        mods_info = nf_core.modules.info.ModuleInfo(self.pipeline_dir, "trimgalore")
         mods_info_output = mods_info.get_component_info()
         console = Console(record=True)
         console.print(mods_info_output)
@@ -50,7 +50,7 @@ def test_modules_info_local(self):
 
     def test_modules_info_in_modules_repo(self):
         """Test getting info about a module in the modules repo"""
-        mods_info = nf_core.modules.ModuleInfo(self.nfcore_modules, "fastqc")
+        mods_info = nf_core.modules.info.ModuleInfo(self.nfcore_modules, "fastqc")
         mods_info.local = True
         mods_info_output = mods_info.get_component_info()
         console = Console(record=True)
diff --git a/tests/modules/test_install.py b/tests/modules/test_install.py
index cfdaac47ed..8f7ac0a1dc 100644
--- a/tests/modules/test_install.py
+++ b/tests/modules/test_install.py
@@ -19,14 +19,14 @@
 class TestModulesCreate(TestModules):
     def test_modules_install_nopipeline(self):
         """Test installing a module - no pipeline given"""
-        self.mods_install.directory = None
+        self.pipeline_dir = None
         assert self.mods_install.install("foo") is False
 
     @with_temporary_folder
     def test_modules_install_emptypipeline(self, tmpdir):
         """Test installing a module - empty dir given"""
-        os.mkdir(os.path.join(tmpdir, "nf-core-pipe"))
-        self.mods_install.directory = os.path.join(tmpdir, "nf-core-pipe")
+        Path(tmpdir, "nf-core-pipe").mkdir()
+        self.mods_install.directory = Path(tmpdir, "nf-core-pipe")
         with pytest.raises(UserWarning) as excinfo:
             self.mods_install.install("foo")
         assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py
index fc9871db2e..dfe288a6ee 100644
--- a/tests/modules/test_lint.py
+++ b/tests/modules/test_lint.py
@@ -6,8 +6,9 @@
 import yaml
 from git.repo import Repo
 
-import nf_core.modules
-from nf_core.modules.lint import main_nf
+import nf_core.modules.lint
+import nf_core.modules.patch
+from nf_core.modules.lint.main_nf import check_container_link_line, check_process_labels
 from nf_core.utils import set_wd
 
 from ..test_modules import TestModules
@@ -160,7 +161,7 @@
 
 class TestModulesCreate(TestModules):
     def _setup_patch(self, pipeline_dir: Union[str, Path], modify_module: bool):
-        install_obj = nf_core.modules.ModuleInstall(
+        install_obj = nf_core.modules.install.ModuleInstall(
             pipeline_dir,
             prompt=False,
             force=False,
@@ -180,7 +181,7 @@ def _setup_patch(self, pipeline_dir: Union[str, Path], modify_module: bool):
     def test_modules_lint_trimgalore(self):
         """Test linting the TrimGalore! module"""
         self.mods_install.install("trimgalore")
-        module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
         module_lint.lint(print_results=False, module="trimgalore")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -191,11 +192,11 @@ def test_modules_lint_empty(self):
         self.mods_remove.remove("fastqc", force=True)
         self.mods_remove.remove("multiqc", force=True)
         with pytest.raises(LookupError):
-            nf_core.modules.ModuleLint(directory=self.pipeline_dir)
+            nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
 
     def test_modules_lint_new_modules(self):
         """lint a new module"""
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, all_modules=True)
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -206,13 +207,13 @@ def test_modules_lint_no_gitlab(self):
         self.mods_remove.remove("fastqc", force=True)
         self.mods_remove.remove("multiqc", force=True)
         with pytest.raises(LookupError):
-            nf_core.modules.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
+            nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
 
     def test_modules_lint_gitlab_modules(self):
         """Lint modules from a different remote"""
         self.mods_install_gitlab.install("fastqc")
         self.mods_install_gitlab.install("multiqc")
-        module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
         module_lint.lint(print_results=False, all_modules=True)
         assert len(module_lint.failed) == 2
         assert len(module_lint.passed) > 0
@@ -221,7 +222,7 @@ def test_modules_lint_gitlab_modules(self):
     def test_modules_lint_multiple_remotes(self):
         """Lint modules from a different remote"""
         self.mods_install_gitlab.install("multiqc")
-        module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
         module_lint.lint(print_results=False, all_modules=True)
         assert len(module_lint.failed) == 1
         assert len(module_lint.passed) > 0
@@ -230,12 +231,12 @@ def test_modules_lint_multiple_remotes(self):
     def test_modules_lint_registry(self):
         """Test linting the samtools module and alternative registry"""
         assert self.mods_install.install("samtools/sort")
-        module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir, registry="public.ecr.aws")
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, registry="public.ecr.aws")
         module_lint.lint(print_results=False, module="samtools/sort")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
-        module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
         module_lint.lint(print_results=False, module="samtools/sort")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -248,13 +249,13 @@ def test_modules_lint_patched_modules(self):
         self._setup_patch(str(self.pipeline_dir), True)
 
         # Create a patch file
-        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
         patch_obj.patch(BISMARK_ALIGN)
 
         # change temporarily working directory to the pipeline directory
         # to avoid error from try_apply_patch() during linting
         with set_wd(self.pipeline_dir):
-            module_lint = nf_core.modules.ModuleLint(
+            module_lint = nf_core.modules.lint.ModuleLint(
                 directory=self.pipeline_dir,
                 remote_url=GITLAB_URL,
                 branch=PATCH_BRANCH,
@@ -273,7 +274,7 @@ def test_modules_lint_check_process_labels(self):
         for test_case in PROCESS_LABEL_TEST_CASES:
             process, passed, warned, failed = test_case
             mocked_ModuleLint = MockModuleLint()
-            main_nf.check_process_labels(mocked_ModuleLint, process.splitlines())
+            check_process_labels(mocked_ModuleLint, process.splitlines())
             assert len(mocked_ModuleLint.passed) == passed
             assert len(mocked_ModuleLint.warned) == warned
             assert len(mocked_ModuleLint.failed) == failed
@@ -284,7 +285,7 @@ def test_modules_lint_check_url(self):
             mocked_ModuleLint = MockModuleLint()
             for line in process.splitlines():
                 if line.strip():
-                    main_nf.check_container_link_line(mocked_ModuleLint, line, registry="quay.io")
+                    check_container_link_line(mocked_ModuleLint, line, registry="quay.io")
 
             assert (
                 len(mocked_ModuleLint.passed) == passed
@@ -298,7 +299,7 @@ def test_modules_lint_check_url(self):
 
     def test_modules_lint_snapshot_file(self):
         """Test linting a module with a snapshot file"""
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -315,7 +316,7 @@ def test_modules_lint_snapshot_file_missing_fail(self):
             "tests",
             "main.nf.test.snap",
         ).unlink()
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         Path(
             self.nfcore_modules,
@@ -359,7 +360,7 @@ def test_modules_lint_snapshot_file_not_needed(self):
             "w",
         ) as fh:
             fh.write(new_content)
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -377,7 +378,7 @@ def test_modules_environment_yml_file_doesnt_exists(self):
                 "environment.yml.bak",
             )
         )
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         Path(
             self.nfcore_modules,
@@ -403,7 +404,7 @@ def test_modules_environment_yml_file_doesnt_exists(self):
 
     def test_modules_environment_yml_file_sorted_correctly(self):
         """Test linting a module with a correctly sorted environment.yml file"""
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -438,7 +439,7 @@ def test_modules_environment_yml_file_sorted_incorrectly(self):
             "w",
         ) as fh:
             fh.write(yaml_content)
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         # we fix the sorting on the fly, so this should pass
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
@@ -471,7 +472,7 @@ def test_modules_environment_yml_file_not_array(self):
             "w",
         ) as fh:
             fh.write(yaml.dump(yaml_content))
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -504,7 +505,7 @@ def test_modules_environment_yml_file_name_mismatch(self):
             "w",
         ) as fh:
             fh.write(yaml.dump(yaml_content))
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         # reset changes
         yaml_content["name"] = "bpipe_test"
@@ -536,7 +537,7 @@ def test_modules_meta_yml_incorrect_licence_field(self):
             "w",
         ) as fh:
             fh.write(yaml.dump(meta_yml))
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
 
         # reset changes
@@ -559,7 +560,7 @@ def test_modules_meta_yml_input_mismatch(self):
         main_nf_new = main_nf.replace("path bam", "path bai")
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
             fh.write(main_nf_new)
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
             fh.write(main_nf)
@@ -578,7 +579,7 @@ def test_modules_meta_yml_output_mismatch(self):
         main_nf_new = main_nf.replace("emit: bam", "emit: bai")
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
             fh.write(main_nf_new)
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
             fh.write(main_nf)
@@ -625,7 +626,7 @@ def test_modules_meta_yml_incorrect_name(self):
             "w",
         ) as fh:
             fh.write(yaml.dump(environment_yml))
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
 
         # reset changes
@@ -659,7 +660,7 @@ def test_modules_missing_test_dir(self):
         Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests").rename(
             Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak")
         )
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak").rename(
             Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests")
@@ -690,7 +691,7 @@ def test_modules_missing_test_main_nf(self):
                 "main.nf.test.bak",
             )
         )
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         Path(
             self.nfcore_modules,
@@ -719,7 +720,7 @@ def test_modules_missing_test_main_nf(self):
     def test_modules_unused_pytest_files(self):
         """Test linting a nf-test module with files still present in `tests/modules/`"""
         Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").mkdir(parents=True, exist_ok=True)
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").rmdir()
         assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
@@ -735,7 +736,7 @@ def test_nftest_failing_linting(self):
         self.nfcore_modules = Path(tmp_dir, "modules-test")
         Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_NFTEST_BRANCH)
 
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="kallisto/quant")
 
         assert len(module_lint.failed) == 3, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
@@ -774,7 +775,7 @@ def test_modules_absent_version(self):
             "w",
         ) as fh:
             fh.write(new_content)
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         with open(
             Path(
@@ -812,7 +813,7 @@ def test_modules_empty_file_in_snapshot(self):
         with open(snap_file, "w") as fh:
             json.dump(snap, fh)
 
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
@@ -841,7 +842,7 @@ def test_modules_empty_file_in_stub_snapshot(self):
         with open(snap_file, "w") as fh:
             json.dump(snap, fh)
 
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules)
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
diff --git a/tests/modules/test_list.py b/tests/modules/test_list.py
index 81484cc8f0..fdbb61f69e 100644
--- a/tests/modules/test_list.py
+++ b/tests/modules/test_list.py
@@ -4,7 +4,7 @@
 import yaml
 from rich.console import Console
 
-import nf_core.modules
+import nf_core.modules.list
 
 from ..test_modules import TestModules
 from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL
@@ -13,7 +13,7 @@
 class TestModulesCreate(TestModules):
     def test_modules_list_remote(self):
         """Test listing available modules"""
-        mods_list = nf_core.modules.ModuleList(None, remote=True)
+        mods_list = nf_core.modules.list.ModuleList(None, remote=True)
         listed_mods = mods_list.list_components()
         console = Console(record=True)
         console.print(listed_mods)
@@ -22,7 +22,9 @@ def test_modules_list_remote(self):
 
     def test_modules_list_remote_gitlab(self):
         """Test listing the modules in the remote gitlab repo"""
-        mods_list = nf_core.modules.ModuleList(None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH)
+        mods_list = nf_core.modules.list.ModuleList(
+            None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH
+        )
         listed_mods = mods_list.list_components()
         console = Console(record=True)
         console.print(listed_mods)
@@ -31,7 +33,7 @@ def test_modules_list_remote_gitlab(self):
 
     def test_modules_list_pipeline(self):
         """Test listing locally installed modules"""
-        mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
+        mods_list = nf_core.modules.list.ModuleList(self.pipeline_dir, remote=False)
         listed_mods = mods_list.list_components()
         console = Console(record=True)
         console.print(listed_mods)
@@ -42,7 +44,7 @@ def test_modules_list_pipeline(self):
     def test_modules_install_and_list_pipeline(self):
         """Test listing locally installed modules"""
         self.mods_install.install("trimgalore")
-        mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
+        mods_list = nf_core.modules.list.ModuleList(self.pipeline_dir, remote=False)
         listed_mods = mods_list.list_components()
         console = Console(record=True)
         console.print(listed_mods)
@@ -52,7 +54,7 @@ def test_modules_install_and_list_pipeline(self):
     def test_modules_install_gitlab_and_list_pipeline(self):
         """Test listing locally installed modules"""
         self.mods_install_gitlab.install("fastqc")
-        mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
+        mods_list = nf_core.modules.list.ModuleList(self.pipeline_dir, remote=False)
         listed_mods = mods_list.list_components()
         console = Console(record=True)
         console.print(listed_mods)
@@ -61,7 +63,7 @@ def test_modules_install_gitlab_and_list_pipeline(self):
 
     def test_modules_list_local_json(self):
         """Test listing locally installed modules as JSON"""
-        mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
+        mods_list = nf_core.modules.list.ModuleList(self.pipeline_dir, remote=False)
         listed_mods = mods_list.list_components(print_json=True)
         listed_mods = json.loads(listed_mods)
         assert "fastqc" in listed_mods
@@ -69,7 +71,7 @@ def test_modules_list_local_json(self):
 
     def test_modules_list_remote_json(self):
         """Test listing available modules as JSON"""
-        mods_list = nf_core.modules.ModuleList(None, remote=True)
+        mods_list = nf_core.modules.list.ModuleList(None, remote=True)
         listed_mods = mods_list.list_components(print_json=True)
         listed_mods = json.loads(listed_mods)
         assert "fastqc" in listed_mods
@@ -77,7 +79,7 @@ def test_modules_list_remote_json(self):
 
     def test_modules_list_with_one_keyword(self):
         """Test listing available modules with one keyword"""
-        mods_list = nf_core.modules.ModuleList(None, remote=True)
+        mods_list = nf_core.modules.list.ModuleList(None, remote=True)
         listed_mods = mods_list.list_components(keywords=["qc"])
         console = Console(record=True)
         console.print(listed_mods)
@@ -86,7 +88,7 @@ def test_modules_list_with_one_keyword(self):
 
     def test_modules_list_with_keywords(self):
         """Test listing available modules with multiple keywords"""
-        mods_list = nf_core.modules.ModuleList(None, remote=True)
+        mods_list = nf_core.modules.list.ModuleList(None, remote=True)
         listed_mods = mods_list.list_components(keywords=["fastq", "qc"])
         console = Console(record=True)
         console.print(listed_mods)
@@ -95,7 +97,7 @@ def test_modules_list_with_keywords(self):
 
     def test_modules_list_with_unused_keyword(self):
         """Test listing available modules with an unused keyword"""
-        mods_list = nf_core.modules.ModuleList(None, remote=True)
+        mods_list = nf_core.modules.list.ModuleList(None, remote=True)
         with self.assertLogs(level="INFO") as log:
             listed_mods = mods_list.list_components(keywords=["you_will_never_find_me"])
             self.assertIn("No available", log.output[0])
@@ -116,7 +118,7 @@ def test_modules_list_in_wrong_repo_fail(self):
             yaml.safe_dump(nf_core_yml, fh)
         # expect error logged
         with self.assertLogs(level="ERROR") as log:
-            mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
+            mods_list = nf_core.modules.list.ModuleList(self.pipeline_dir, remote=False)
             listed_mods = mods_list.list_components()
             self.assertIn("must be run from a pipeline directory", log.output[0])
             # expect empty list
diff --git a/tests/modules/test_modules_json.py b/tests/modules/test_modules_json.py
index 319b5ad657..2ab058fa70 100644
--- a/tests/modules/test_modules_json.py
+++ b/tests/modules/test_modules_json.py
@@ -36,7 +36,7 @@ def test_mod_json_update(self):
         mod_json_obj = ModulesJson(self.pipeline_dir)
         # Update the modules.json file
         mod_repo_obj = ModulesRepo()
-        mod_json_obj.update("modules", mod_repo_obj, "MODULE_NAME", "GIT_SHA", "modules", write_file=False)
+        mod_json_obj.update("modules", mod_repo_obj, "MODULE_NAME", "GIT_SHA", ["modules"], write_file=False)
         mod_json = mod_json_obj.get_modules_json()
         assert "MODULE_NAME" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]
         assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]
@@ -155,7 +155,7 @@ def test_mod_json_up_to_date_reinstall_fails(self):
         mod_json_obj = ModulesJson(self.pipeline_dir)
 
         # Update the fastqc module entry to an invalid git_sha
-        mod_json_obj.update("modules", ModulesRepo(), "fastqc", "INVALID_GIT_SHA", "modules", write_file=True)
+        mod_json_obj.update("modules", ModulesRepo(), "fastqc", "INVALID_GIT_SHA", ["modules"], write_file=True)
 
         # Remove the fastqc module
         fastqc_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "fastqc")
diff --git a/tests/modules/test_patch.py b/tests/modules/test_patch.py
index 230bb1ce8f..c3eb94d374 100644
--- a/tests/modules/test_patch.py
+++ b/tests/modules/test_patch.py
@@ -6,7 +6,10 @@
 import pytest
 
 import nf_core.components.components_command
-import nf_core.modules
+import nf_core.components.patch
+import nf_core.modules.modules_json
+import nf_core.modules.patch
+import nf_core.modules.update
 
 from ..test_modules import TestModules
 from ..utils import GITLAB_URL
@@ -29,7 +32,7 @@
 
 
 def setup_patch(pipeline_dir, modify_module):
-    install_obj = nf_core.modules.ModuleInstall(
+    install_obj = nf_core.modules.install.ModuleInstall(
         pipeline_dir, prompt=False, force=False, remote_url=GITLAB_URL, branch=PATCH_BRANCH, sha=ORG_SHA
     )
 
@@ -66,7 +69,7 @@ def test_create_patch_no_change(self):
         setup_patch(self.pipeline_dir, False)
 
         # Try creating a patch file
-        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
         with pytest.raises(UserWarning):
             patch_obj.patch(BISMARK_ALIGN)
 
@@ -84,7 +87,7 @@ def test_create_patch_change(self):
         setup_patch(self.pipeline_dir, True)
 
         # Try creating a patch file
-        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
         patch_obj.patch(BISMARK_ALIGN)
 
         module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
@@ -119,7 +122,7 @@ def test_create_patch_try_apply_successful(self):
         module_path = Path(self.pipeline_dir, module_relpath)
 
         # Try creating a patch file
-        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
         patch_obj.patch(BISMARK_ALIGN)
 
         patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
@@ -132,7 +135,7 @@ def test_create_patch_try_apply_successful(self):
             "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
         )
 
-        update_obj = nf_core.modules.ModuleUpdate(
+        update_obj = nf_core.modules.update.ModuleUpdate(
             self.pipeline_dir, sha=SUCCEED_SHA, remote_url=GITLAB_URL, branch=PATCH_BRANCH
         )
         # Install the new files
@@ -187,7 +190,7 @@ def test_create_patch_try_apply_failed(self):
         module_path = Path(self.pipeline_dir, module_relpath)
 
         # Try creating a patch file
-        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
         patch_obj.patch(BISMARK_ALIGN)
 
         patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
@@ -200,7 +203,7 @@ def test_create_patch_try_apply_failed(self):
             "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
         )
 
-        update_obj = nf_core.modules.ModuleUpdate(
+        update_obj = nf_core.modules.update.ModuleUpdate(
             self.pipeline_dir, sha=FAIL_SHA, remote_url=GITLAB_URL, branch=PATCH_BRANCH
         )
         # Install the new files
@@ -226,7 +229,7 @@ def test_create_patch_update_success(self):
         module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
 
         # Try creating a patch file
-        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
         patch_obj.patch(BISMARK_ALIGN)
 
         patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
@@ -240,7 +243,7 @@ def test_create_patch_update_success(self):
         )
 
         # Update the module
-        update_obj = nf_core.modules.ModuleUpdate(
+        update_obj = nf_core.modules.update.ModuleUpdate(
             self.pipeline_dir,
             sha=SUCCEED_SHA,
             show_diff=False,
@@ -287,7 +290,7 @@ def test_create_patch_update_fail(self):
         module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
 
         # Try creating a patch file
-        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
         patch_obj.patch(BISMARK_ALIGN)
 
         patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
@@ -304,7 +307,7 @@ def test_create_patch_update_fail(self):
         with open(module_path / patch_fn) as fh:
             patch_contents = fh.read()
 
-        update_obj = nf_core.modules.ModuleUpdate(
+        update_obj = nf_core.modules.update.ModuleUpdate(
             self.pipeline_dir,
             sha=FAIL_SHA,
             show_diff=False,
@@ -339,7 +342,7 @@ def test_remove_patch(self):
         setup_patch(self.pipeline_dir, True)
 
         # Try creating a patch file
-        patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+        patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
         patch_obj.patch(BISMARK_ALIGN)
 
         module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
diff --git a/tests/modules/test_update.py b/tests/modules/test_update.py
index a33aac3775..1f81eab487 100644
--- a/tests/modules/test_update.py
+++ b/tests/modules/test_update.py
@@ -167,9 +167,10 @@ def test_update_with_config_fixed_version(self):
         # Fix the trimgalore version in the .nf-core.yml to an old version
         update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": OLD_TRIMGALORE_SHA}}}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        tools_config["update"] = update_config
+        setattr(tools_config, "update", update_config)
+        assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
-            yaml.dump(tools_config, f)
+            yaml.dump(tools_config.model_dump(), f)
 
         # Update all modules in the pipeline
         update_obj = ModuleUpdate(
@@ -191,9 +192,10 @@ def test_update_with_config_dont_update(self):
         # Set the trimgalore field to no update in the .nf-core.yml
         update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": False}}}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        tools_config["update"] = update_config
+        setattr(tools_config, "update", update_config)
+        assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
-            yaml.dump(tools_config, f)
+            yaml.dump(tools_config.model_dump(), f)
 
         # Update all modules in the pipeline
         update_obj = ModuleUpdate(
@@ -219,9 +221,10 @@ def test_update_with_config_fix_all(self):
         # Fix the version of all nf-core modules in the .nf-core.yml to an old version
         update_config = {GITLAB_URL: OLD_TRIMGALORE_SHA}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        tools_config["update"] = update_config
+        setattr(tools_config, "update", update_config)
+        assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
-            yaml.dump(tools_config, f)
+            yaml.dump(tools_config.model_dump(), f)
 
         # Update all modules in the pipeline
         update_obj = ModuleUpdate(
@@ -242,9 +245,10 @@ def test_update_with_config_no_updates(self):
         # Fix the version of all nf-core modules in the .nf-core.yml to an old version
         update_config = {GITLAB_URL: False}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        tools_config["update"] = update_config
+        setattr(tools_config, "update", update_config)
+        assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
-            yaml.dump(tools_config, f)
+            yaml.dump(tools_config.model_dump(), f)
 
         # Update all modules in the pipeline
         update_obj = ModuleUpdate(
diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py
index af581fc9ab..7c18ab0a2d 100644
--- a/tests/test_subworkflows.py
+++ b/tests/test_subworkflows.py
@@ -1,14 +1,13 @@
 """Tests covering the subworkflows commands"""
 
 import json
-import os
-import shutil
 import unittest
 from pathlib import Path
 
 import pytest
 
 import nf_core.modules
+import nf_core.modules.install
 import nf_core.pipelines.create.create
 import nf_core.subworkflows
 
@@ -104,49 +103,11 @@ def setUp(self):
             force=False,
             sha="8c343b3c8a0925949783dc547666007c245c235b",
         )
-        self.mods_install = nf_core.modules.ModuleInstall(self.pipeline_dir, prompt=False, force=True)
+        self.mods_install = nf_core.modules.install.ModuleInstall(self.pipeline_dir, prompt=False, force=True)
 
         # Set up remove objects
         self.subworkflow_remove = nf_core.subworkflows.SubworkflowRemove(self.pipeline_dir)
 
-    def tearDown(self):
-        """Clean up temporary files and folders"""
-
-        if os.path.exists(self.tmp_dir):
-            shutil.rmtree(self.tmp_dir)
-
     @pytest.fixture(autouse=True)
     def _use_caplog(self, caplog):
         self.caplog = caplog
-
-    # ################################################
-    # # Test of the individual subworkflow commands. #
-    # ################################################
-
-    # from .subworkflows.list import (  # type: ignore[misc]
-    #     test_subworkflows_install_and_list_subworkflows,
-    #     test_subworkflows_install_gitlab_and_list_subworkflows,
-    #     test_subworkflows_list_remote,
-    #     test_subworkflows_list_remote_gitlab,
-    # )
-    # from .subworkflows.remove import (  # type: ignore[misc]
-    #     test_subworkflows_remove_included_subworkflow,
-    #     test_subworkflows_remove_one_of_two_subworkflow,
-    #     test_subworkflows_remove_subworkflow,
-    #     test_subworkflows_remove_subworkflow_keep_installed_module,
-    # )
-    # from .subworkflows.update import (  # type: ignore[misc]
-    #     test_install_and_update,
-    #     test_install_at_hash_and_update,
-    #     test_install_at_hash_and_update_and_save_diff_limit_output,
-    #     test_install_at_hash_and_update_and_save_diff_to_file,
-    #     test_install_at_hash_and_update_limit_output,
-    #     test_update_all,
-    #     test_update_all_linked_components_from_subworkflow,
-    #     test_update_all_subworkflows_from_module,
-    #     test_update_change_of_included_modules,
-    #     test_update_with_config_dont_update,
-    #     test_update_with_config_fix_all,
-    #     test_update_with_config_fixed_version,
-    #     test_update_with_config_no_updates,
-    # )

From 0cf5f8b2f6f36d7904d95368c2ae2964bcbc09af Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 09:08:04 +0200
Subject: [PATCH 105/414] remove broken _repr_ (breaks because not all
 parameters are intilaized)

---
 nf_core/components/lint/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index ada3ee30c2..f5ce3ddb7f 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -45,7 +45,6 @@ def __init__(self, component: NFCoreComponent, lint_test: str, message: str, fil
         self.component_name: str = component.component_name
 
 
-@rich.repr.auto
 class ComponentLint(ComponentCommand):
     """
     An object for linting modules and subworkflows either in a clone of the 'nf-core/modules'

From 879e808b37f5bf7ed4e15aaef111ba025779a08f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 13:27:14 +0200
Subject: [PATCH 106/414] add types

---
 nf_core/components/components_command.py |   1 -
 nf_core/components/components_utils.py   |  16 +-
 nf_core/components/create.py             |  21 +--
 nf_core/components/info.py               |  14 +-
 nf_core/components/install.py            |   4 +
 nf_core/components/lint/__init__.py      |  12 +-
 nf_core/components/nfcore_component.py   |   1 +
 nf_core/modules/bump_versions.py         |  10 +-
 nf_core/modules/modules_json.py          |   7 +-
 nf_core/pipelines/create/create.py       |  50 +++---
 nf_core/pipelines/create/utils.py        |  20 +--
 nf_core/pipelines/lint/__init__.py       |  24 +--
 nf_core/pipelines/lint/modules_json.py   |   9 +-
 nf_core/subworkflows/lint/main_nf.py     |  14 +-
 nf_core/synced_repo.py                   |  33 ++--
 tests/pipelines/test_sync.py             | 186 ++++++++++-------------
 tests/subworkflows/test_lint.py          |  42 +++--
 17 files changed, 232 insertions(+), 232 deletions(-)

diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 8d200021c2..13a6fed338 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -38,7 +38,6 @@ def __init__(
         self.hide_progress = hide_progress
         self.no_prompts = no_prompts
         self._configure_repo_and_paths()
-        self.repo_type: Optional[str] = None
 
     def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
         """
diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py
index 743efd386d..e4e2ff092b 100644
--- a/nf_core/components/components_utils.py
+++ b/nf_core/components/components_utils.py
@@ -27,7 +27,9 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P
 
     # Figure out the repository type from the .nf-core.yml config file if we can
     config_fn, tools_config = nf_core.utils.load_tools_config(base_dir)
-    repo_type = tools_config.get("repository_type", None)
+    if config_fn is None:
+        raise UserWarning(f"Could not find a config file in directory: {base_dir}")
+    repo_type = getattr(tools_config, "repository_type", None) or None
 
     # If not set, prompt the user
     if not repo_type and use_prompt:
@@ -55,13 +57,11 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P
     # Check if it's a valid answer
     if repo_type not in ["pipeline", "modules"]:
         raise UserWarning(f"Invalid repository type: '{repo_type}'")
-
+    org: str = ""
     # Check for org if modules repo
-    if repo_type == "pipeline":
-        org = ""
-    elif repo_type == "modules":
-        org = tools_config.get("org_path", None)
-        if org is None:
+    if repo_type == "modules":
+        org = getattr(tools_config, "org_path", "") or ""
+        if org == "":
             log.warning("Organisation path not defined in %s [key: org_path]", config_fn.name)
             org = questionary.text(
                 "What is the organisation path under which modules and subworkflows are stored?",
@@ -70,7 +70,7 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P
             ).unsafe_ask()
             log.info("To avoid this prompt in the future, add the 'org_path' key to a root '%s' file.", config_fn.name)
             if rich.prompt.Confirm.ask("[bold][blue]?[/] Would you like me to add this config now?", default=True):
-                with open(config_fn, "a+") as fh:
+                with open(str(config_fn), "a+") as fh:
                     fh.write(f"org_path: {org}\n")
                     log.info(f"Config added to '{config_fn.name}'")
 
diff --git a/nf_core/components/create.py b/nf_core/components/create.py
index 413790099d..fdcf402b47 100644
--- a/nf_core/components/create.py
+++ b/nf_core/components/create.py
@@ -62,7 +62,7 @@ def __init__(
         self.not_empty_template = not empty_template
         self.migrate_pytest = migrate_pytest
 
-    def create(self):
+    def create(self) -> bool:
         """
         Create a new DSL2 module or subworkflow from the nf-core template.
 
@@ -106,12 +106,12 @@ def create(self):
         ```
 
         """
-
         if self.component_type == "modules":
             # Check modules directory structure
             self.check_modules_structure()
 
         # Check whether the given directory is a nf-core pipeline or a clone of nf-core/modules
+
         log.info(f"Repository type: [blue]{self.repo_type}")
         if self.directory != ".":
             log.info(f"Base directory: '{self.directory}'")
@@ -161,7 +161,7 @@ def create(self):
         self.org_alphabet = not_alphabet.sub("", self.org)
 
         # Create component template with jinja2
-        self._render_template()
+        assert self._render_template()
         log.info(f"Created component template: '{self.component_name}'")
 
         if self.migrate_pytest:
@@ -171,7 +171,9 @@ def create(self):
             self._print_and_delete_pytest_files()
 
         new_files = [str(path) for path in self.file_paths.values()]
+
         log.info("Created following files:\n  " + "\n  ".join(new_files))
+        return True
 
     def _get_bioconda_tool(self):
         """
@@ -265,7 +267,7 @@ def _get_module_structure_components(self):
                 default=True,
             )
 
-    def _render_template(self):
+    def _render_template(self) -> Optional[bool]:
         """
         Create new module/subworkflow files with Jinja2.
         """
@@ -288,7 +290,7 @@ def _render_template(self):
             # Write output to the target file
             log.debug(f"Writing output to: '{dest_fn}'")
             dest_fn.parent.mkdir(exist_ok=True, parents=True)
-            with open(dest_fn, "w") as fh:
+            with open(str(dest_fn), "w") as fh:
                 log.debug(f"Writing output to: '{dest_fn}'")
                 fh.write(rendered_output)
 
@@ -297,6 +299,7 @@ def _render_template(self):
                 Path(nf_core.__file__).parent / f"{self.component_type[:-1]}-template" / template_fn
             ).stat()
             dest_fn.chmod(template_stat.st_mode)
+        return True
 
     def _collect_name_prompt(self):
         """
@@ -340,7 +343,7 @@ def _collect_name_prompt(self):
                 elif self.component_type == "subworkflows":
                     self.component = rich.prompt.Prompt.ask("[violet]Name of subworkflow").strip()
 
-    def _get_component_dirs(self):
+    def _get_component_dirs(self) -> Dict[str, Path]:
         """Given a directory and a tool/subtool or subworkflow, set the file paths and check if they already exist
 
         Returns dict: keys are relative paths to template files, vals are target paths.
@@ -372,9 +375,8 @@ def _get_component_dirs(self):
             # Set file paths
             file_paths["main.nf"] = component_file
 
-        if self.repo_type == "modules":
+        elif self.repo_type == "modules":
             component_dir = Path(self.directory, self.component_type, self.org, self.component_dir)
-
             # Check if module/subworkflow directories exist already
             if component_dir.exists() and not self.force_overwrite and not self.migrate_pytest:
                 raise UserWarning(
@@ -403,7 +405,6 @@ def _get_component_dirs(self):
                     raise UserWarning(
                         f"Module subtool '{tool_glob[0]}' exists already, cannot make tool '{self.component_name}'"
                     )
-
             # Set file paths
             # For modules - can be tool/ or tool/subtool/ so can't do in template directory structure
             file_paths["main.nf"] = component_dir / "main.nf"
@@ -411,6 +412,8 @@ def _get_component_dirs(self):
             if self.component_type == "modules":
                 file_paths["environment.yml"] = component_dir / "environment.yml"
             file_paths["tests/main.nf.test.j2"] = component_dir / "tests" / "main.nf.test"
+        else:
+            raise ValueError("`repo_type` not set correctly")
 
         return file_paths
 
diff --git a/nf_core/components/info.py b/nf_core/components/info.py
index d07486f638..a296fcaccf 100644
--- a/nf_core/components/info.py
+++ b/nf_core/components/info.py
@@ -136,17 +136,17 @@ def init_mod_name(self, component):
                 ).unsafe_ask()
         else:
             if self.repo_type == "pipeline":
+                assert self.modules_json is not None  # mypy
                 # check if the module is locally installed
                 local_paths = self.modules_json.get_all_components(self.component_type).get(
                     self.modules_repo.remote_url
                 )  # type: ignore
-                if local_paths is None:
-                    raise LookupError(f"No {self.component_type[:-1]} installed from {self.modules_repo.remote_url}")
-                for directory, comp in local_paths:
-                    if comp == component:
-                        component_base_path = Path(self.directory, self.component_type)
-                        self.local_path = Path(component_base_path, directory, component)
-                        break
+                if local_paths is not None:
+                    for directory, comp in local_paths:
+                        if comp == component:
+                            component_base_path = Path(self.directory, self.component_type)
+                            self.local_path = Path(component_base_path, directory, component)
+                            break
                 if self.local_path:
                     self.local = True
 
diff --git a/nf_core/components/install.py b/nf_core/components/install.py
index aa8aac81e6..8f47913283 100644
--- a/nf_core/components/install.py
+++ b/nf_core/components/install.py
@@ -69,8 +69,12 @@ def install(self, component: str, silent: bool = False) -> bool:
         # Verify SHA
         if not self.modules_repo.verify_sha(self.prompt, self.sha):
             return False
+
+        # verify self.modules_repo entries:
         if self.modules_repo is None:
             return False
+        if self.modules_repo.repo_path is None:
+            return False
 
         # Check and verify component name
 
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index f5ce3ddb7f..e2475ef62c 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -75,6 +75,11 @@ def __init__(
         self.passed: List[LintResult] = []
         self.warned: List[LintResult] = []
         self.failed: List[LintResult] = []
+        self.all_local_components: List[NFCoreComponent] = []
+
+        self.lint_config = None
+        self.modules_json = None
+
         if self.component_type == "modules":
             self.lint_tests = self.get_all_module_lint_tests(self.repo_type == "pipeline")
         else:
@@ -107,7 +112,7 @@ def __init__(
                     f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline."
                 )
             local_component_dir = Path(self.directory, self.component_type, "local")
-            self.all_local_components = []
+
             if local_component_dir.exists():
                 self.all_local_components = [
                     NFCoreComponent(
@@ -122,7 +127,7 @@ def __init__(
                     for comp in self.get_local_components()
                 ]
             self.config = nf_core.utils.fetch_wf_config(Path(self.directory), cache_config=True)
-        else:
+        elif self.repo_type == "modules":
             component_dir = Path(
                 self.directory,
                 self.default_modules_path if self.component_type == "modules" else self.default_subworkflows_path,
@@ -146,9 +151,6 @@ def __init__(
                 self.registry = registry
             log.debug(f"Registry set to {self.registry}")
 
-        self.lint_config = None
-        self.modules_json = None
-
     def __repr__(self) -> str:
         return f"ComponentLint({self.component_type}, {self.directory})"
 
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 0c63141c73..129871d68c 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -55,6 +55,7 @@ def __init__(
         self.git_sha: Optional[str] = None
         self.is_patched: bool = False
         self.branch: Optional[str] = None
+        self.workflow_name: Optional[str] = None
 
         if remote_component:
             # Initialize the important files
diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
index fb0dc7d50d..2d8854e3c0 100644
--- a/nf_core/modules/bump_versions.py
+++ b/nf_core/modules/bump_versions.py
@@ -7,7 +7,7 @@
 import os
 import re
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import List, Optional, Tuple, Union
 
 import questionary
 import yaml
@@ -22,13 +22,13 @@
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
 from nf_core.components.nfcore_component import NFCoreComponent
-from nf_core.utils import custom_yaml_dumper, rich_force_colors
+from nf_core.utils import NFCoreYamlConfig, custom_yaml_dumper, rich_force_colors
 from nf_core.utils import plural_s as _s
 
 log = logging.getLogger(__name__)
 
 
-class ModuleVersionBumper(ComponentCommand):  # type: ignore[misc]
+class ModuleVersionBumper(ComponentCommand):
     def __init__(
         self,
         pipeline_dir: Union[str, Path],
@@ -43,7 +43,7 @@ def __init__(
         self.failed: List[Tuple[str, str]] = []
         self.ignored: List[Tuple[str, str]] = []
         self.show_up_to_date: Optional[bool] = None
-        self.tools_config: Dict[str, Any] = {}
+        self.tools_config: Optional[NFCoreYamlConfig]
 
     def bump_versions(
         self, module: Union[str, None] = None, all_modules: bool = False, show_uptodate: bool = False
@@ -160,7 +160,7 @@ def bump_module_version(self, module: NFCoreComponent) -> bool:
             return False
 
         # Don't update if blocked in blacklist
-        self.bump_versions_config = self.tools_config.get("bump-versions", {})
+        self.bump_versions_config = getattr(self.tools_config, "bump-versions", {}) or {}
         if module.component_name in self.bump_versions_config:
             config_version = self.bump_versions_config[module.component_name]
             if not config_version:
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index c0e41d1b42..02ce6fa5a2 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -922,7 +922,7 @@ def module_present(self, module_name, repo_url, install_dir):
             install_dir, {}
         )
 
-    def get_modules_json(self) -> dict:
+    def get_modules_json(self) -> ModulesJsonType:
         """
         Returns a copy of the loaded modules.json
 
@@ -932,7 +932,7 @@ def get_modules_json(self) -> dict:
         if self.modules_json is None:
             self.load()
             assert self.modules_json is not None  # mypy
-        return copy.deepcopy(self.modules_json)  # type: ignore
+        return copy.deepcopy(self.modules_json)
 
     def get_component_version(self, component_type, component_name, repo_url, install_dir):
         """
@@ -1182,6 +1182,7 @@ def resolve_missing_from_modules_json(self, missing_from_modules_json, component
         repos, _ = self.get_pipeline_module_repositories(component_type, self.modules_dir, tracked_repos)
 
         # Get tuples of components that miss installation and their install directory
+
         def components_with_repos():
             for directory in missing_from_modules_json:
                 for repo_url in repos:
@@ -1197,7 +1198,7 @@ def components_with_repos():
                                 paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:])))
                                 pass
                         paths_in_directory.append(Path(dir_name).parts[-1])
-                    if dir in paths_in_directory:
+                    if directory in paths_in_directory:
                         yield (modules_repo.repo_path, directory)
 
         # Add all components into a dictionary with install directories
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index aecba94236..b7d86c5bd7 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -8,9 +8,10 @@
 import re
 import shutil
 from pathlib import Path
-from typing import Optional, Union
+from typing import Dict, List, Optional, Union
 
 import git
+import git.config
 import jinja2
 import yaml
 
@@ -61,12 +62,15 @@ def __init__(
             self.config = template_config
         elif from_config_file:
             # Try reading config file
-            _, config_yml = nf_core.utils.load_tools_config(outdir if outdir else ".")
-            # Obtain a CreateConfig object from `.nf-core.yml` config file
-            if "template" in config_yml:
-                self.config = CreateConfig(**config_yml["template"])
-            else:
-                raise UserWarning("The template configuration was not provided in '.nf-core.yml'.")
+            try:
+                _, config_yml = nf_core.utils.load_tools_config(outdir if outdir else Path().cwd())
+                # Obtain a CreateConfig object from `.nf-core.yml` config file
+                if config_yml is not None and getattr(config_yml, "template", None) is not None:
+                    self.config = CreateConfig(**config_yml["template"])
+                else:
+                    raise UserWarning("The template configuration was not provided in '.nf-core.yml'.")
+            except (FileNotFoundError, UserWarning):
+                log.debug("The '.nf-core.yml' configuration file was not found.")
         elif (name and description and author) or (
             template_config and (isinstance(template_config, str) or isinstance(template_config, Path))
         ):
@@ -191,7 +195,10 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
             skip_paths (list<str>): List of template areas which contain paths to skip.
         """
         # Try reading config file
-        _, config_yml = nf_core.utils.load_tools_config(pipeline_dir)
+        try:
+            _, config_yml = nf_core.utils.load_tools_config(pipeline_dir)
+        except UserWarning:
+            config_yml = None
 
         # Define the different template areas, and what actions to take for each
         # if they are skipped
@@ -230,13 +237,13 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
         jinja_params["name_docker"] = jinja_params["name"].replace(jinja_params["org"], jinja_params["prefix_nodash"])
         jinja_params["logo_light"] = f"{jinja_params['name_noslash']}_logo_light.png"
         jinja_params["logo_dark"] = f"{jinja_params['name_noslash']}_logo_dark.png"
-
-        if (
-            "lint" in config_yml
-            and "nextflow_config" in config_yml["lint"]
-            and "manifest.name" in config_yml["lint"]["nextflow_config"]
-        ):
-            return jinja_params, skip_paths
+        if config_yml is not None:
+            if (
+                hasattr(config_yml, "lint")
+                and hasattr(config_yml["lint"], "nextflow_config")
+                and hasattr(config_yml["lint"]["nextflow_config"], "manifest.name")
+            ):
+                return jinja_params, skip_paths
 
         # Check that the pipeline name matches the requirements
         if not re.match(r"^[a-z]+$", jinja_params["short_name"]):
@@ -417,7 +424,7 @@ def fix_linting(self):
         """
         # Create a lint config
         short_name = self.jinja_params["short_name"]
-        lint_config = {
+        lint_config: Dict[str, List[str]] = {
             "files_exist": [
                 "CODE_OF_CONDUCT.md",
                 f"assets/nf-core-{short_name}_logo_light.png",
@@ -503,9 +510,10 @@ def fix_linting(self):
 
         # Add the lint content to the preexisting nf-core config
         config_fn, nf_core_yml = nf_core.utils.load_tools_config(self.outdir)
-        nf_core_yml["lint"] = lint_config
-        with open(self.outdir / config_fn, "w") as fh:
-            yaml.dump(nf_core_yml, fh, default_flow_style=False, sort_keys=False)
+        if config_fn is not None and nf_core_yml is not None:
+            nf_core_yml.lint = lint_config
+            with open(self.outdir / config_fn, "w") as fh:
+                yaml.dump(nf_core_yml.model_dump(), fh, default_flow_style=False, sort_keys=False)
 
         run_prettier_on_file(os.path.join(self.outdir, config_fn))
 
@@ -531,9 +539,9 @@ def git_init_pipeline(self):
         Raises:
             UserWarning: if Git default branch is set to 'dev' or 'TEMPLATE'.
         """
-        default_branch = self.default_branch
+        default_branch: Optional[str] = self.default_branch
         try:
-            default_branch = default_branch or git.config.GitConfigParser().get_value("init", "defaultBranch")
+            default_branch = default_branch or str(git.config.GitConfigParser().get_value("init", "defaultBranch"))
         except configparser.Error:
             log.debug("Could not read init.defaultBranch")
         if default_branch in ["dev", "TEMPLATE"]:
diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
index c15d61e266..88994c9361 100644
--- a/nf_core/pipelines/create/utils.py
+++ b/nf_core/pipelines/create/utils.py
@@ -3,9 +3,9 @@
 from contextvars import ContextVar
 from logging import LogRecord
 from pathlib import Path
-from typing import Any, Dict, Iterator, Optional, Union
+from typing import Any, Dict, Iterator, Union
 
-from pydantic import BaseModel, ConfigDict, ValidationError, ValidationInfo, field_validator
+from pydantic import ConfigDict, ValidationError, ValidationInfo, field_validator
 from rich.logging import RichHandler
 from textual import on
 from textual._context import active_app
@@ -16,6 +16,8 @@
 from textual.widget import Widget
 from textual.widgets import Button, Input, Markdown, RichLog, Static, Switch
 
+from nf_core.utils import NFCoreTemplateConfig
+
 # Use ContextVar to define a context on the model initialization
 _init_context_var: ContextVar = ContextVar("_init_context_var", default={})
 
@@ -33,19 +35,9 @@ def init_context(value: Dict[str, Any]) -> Iterator[None]:
 NFCORE_PIPELINE_GLOBAL: bool = True
 
 
-class CreateConfig(BaseModel):
+class CreateConfig(NFCoreTemplateConfig):
     """Pydantic model for the nf-core create config."""
 
-    org: Optional[str] = None
-    name: Optional[str] = None
-    description: Optional[str] = None
-    author: Optional[str] = None
-    version: Optional[str] = None
-    force: Optional[bool] = True
-    outdir: Optional[str] = None
-    skip_features: Optional[list] = None
-    is_nfcore: Optional[bool] = None
-
     model_config = ConfigDict(extra="allow")
 
     def __init__(self, /, **data: Any) -> None:
@@ -103,7 +95,7 @@ class TextInput(Static):
     and validation messages.
     """
 
-    def __init__(self, field_id, placeholder, description, default=None, password=None, **kwargs) -> None:
+    def __init__(self, field_id, placeholder, description, default="", password=False, **kwargs) -> None:
         """Initialise the widget with our values.
 
         Pass on kwargs upstream for standard usage."""
diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
index 93f6523709..ed833d3219 100644
--- a/nf_core/pipelines/lint/__init__.py
+++ b/nf_core/pipelines/lint/__init__.py
@@ -151,15 +151,15 @@ def _get_all_lint_tests(release_mode):
             "nfcore_yml",
         ] + (["version_consistency"] if release_mode else [])
 
-    def _load(self):
+    def _load(self) -> bool:
         """Load information about the pipeline into the PipelineLint object"""
         # Load everything using the parent object
         super()._load()
 
         # Load lint object specific stuff
-        self._load_lint_config()
+        return self._load_lint_config()
 
-    def _load_lint_config(self):
+    def _load_lint_config(self) -> bool:
         """Parse a pipeline lint config file.
 
         Load the '.nf-core.yml'  config file and extract
@@ -168,14 +168,19 @@ def _load_lint_config(self):
         Add parsed config to the `self.lint_config` class attribute.
         """
         _, tools_config = nf_core.utils.load_tools_config(self.wf_path)
-        self.lint_config = tools_config.get("lint", {})
+        self.lint_config = getattr(tools_config, "lint", {}) or {}
+        is_correct = True
 
         # Check if we have any keys that don't match lint test names
-        for k in self.lint_config:
-            if k not in self.lint_tests:
-                log.warning(f"Found unrecognised test name '{k}' in pipeline lint config")
+        if self.lint_config is not None:
+            for k in self.lint_config:
+                if k not in self.lint_tests:
+                    log.warning(f"Found unrecognised test name '{k}' in pipeline lint config")
+                    is_correct = False
 
-    def _lint_pipeline(self):
+        return is_correct
+
+    def _lint_pipeline(self) -> None:
         """Main linting function.
 
         Takes the pipeline directory as the primary input and iterates through
@@ -240,7 +245,8 @@ def _lint_pipeline(self):
                 "Running lint checks", total=len(self.lint_tests), test_name=self.lint_tests[0]
             )
             for test_name in self.lint_tests:
-                if self.lint_config.get(test_name, {}) is False:
+                lint_test = self.lint_config.get(test_name, {}) if self.lint_config is not None else {}
+                if lint_test is False:
                     log.debug(f"Skipping lint test '{test_name}'")
                     self.ignored.append((test_name, test_name))
                     continue
diff --git a/nf_core/pipelines/lint/modules_json.py b/nf_core/pipelines/lint/modules_json.py
index dd0a59d558..5ce2054036 100644
--- a/nf_core/pipelines/lint/modules_json.py
+++ b/nf_core/pipelines/lint/modules_json.py
@@ -1,9 +1,10 @@
 from pathlib import Path
+from typing import Dict, List
 
-from nf_core.modules.modules_json import ModulesJson
+from nf_core.modules.modules_json import ModulesJson, ModulesJsonType
 
 
-def modules_json(self):
+def modules_json(self) -> Dict[str, List[str]]:
     """Make sure all modules described in the ``modules.json`` file are actually installed
 
     Every module installed from ``nf-core/modules`` must have an entry in the ``modules.json`` file
@@ -18,10 +19,10 @@ def modules_json(self):
     # Load pipeline modules and modules.json
     _modules_json = ModulesJson(self.wf_path)
     _modules_json.load()
-    modules_json_dict = _modules_json.modules_json
+    modules_json_dict: ModulesJsonType | None = _modules_json.modules_json
     modules_dir = Path(self.wf_path, "modules")
 
-    if _modules_json:
+    if _modules_json and modules_json_dict is not None:
         all_modules_passed = True
 
         for repo in modules_json_dict["repos"].keys():
diff --git a/nf_core/subworkflows/lint/main_nf.py b/nf_core/subworkflows/lint/main_nf.py
index c73559502c..edca32bf30 100644
--- a/nf_core/subworkflows/lint/main_nf.py
+++ b/nf_core/subworkflows/lint/main_nf.py
@@ -4,12 +4,14 @@
 
 import logging
 import re
-from typing import List
+from typing import List, Tuple
+
+from nf_core.components.nfcore_component import NFCoreComponent
 
 log = logging.getLogger(__name__)
 
 
-def main_nf(_, subworkflow):
+def main_nf(_, subworkflow: NFCoreComponent) -> Tuple[List[str], List[str]]:
     """
     Lint a ``main.nf`` subworkflow file
 
@@ -25,8 +27,8 @@ def main_nf(_, subworkflow):
     * The subworkflow emits a software version
     """
 
-    inputs = []
-    outputs = []
+    inputs: List[str] = []
+    outputs: List[str] = []
 
     # Read the lines directly from the subworkflow
     lines = None
@@ -38,7 +40,7 @@ def main_nf(_, subworkflow):
             subworkflow.passed.append(("main_nf_exists", "Subworkflow file exists", subworkflow.main_nf))
         except FileNotFoundError:
             subworkflow.failed.append(("main_nf_exists", "Subworkflow file does not exist", subworkflow.main_nf))
-            return
+            return inputs, outputs
 
     # Go through subworkflow main.nf file and switch state according to current section
     # Perform section-specific linting
@@ -199,7 +201,7 @@ def check_subworkflow_section(self, lines: List[str]) -> List[str]:
     return includes
 
 
-def check_workflow_section(self, lines):
+def check_workflow_section(self, lines: List[str]) -> None:
     """Lint the workflow definition of a subworkflow before
     Specifically checks that the name is all capital letters
 
diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py
index 33e7f0a54a..8af0ee9a08 100644
--- a/nf_core/synced_repo.py
+++ b/nf_core/synced_repo.py
@@ -4,7 +4,7 @@
 import shutil
 from configparser import NoOptionError, NoSectionError
 from pathlib import Path
-from typing import Dict, Iterable, Optional, Union
+from typing import Dict, Iterable, List, Optional, Union
 
 import git
 from git.exc import GitCommandError
@@ -129,14 +129,16 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa
         # the WorkflowRepo define their own including custom init methods. This needs
         # fixing.
         self.setup_local_repo(remote_url, branch, hide_progress)
+
         if self.local_repo_dir is None:
             raise ValueError("Repository not initialized")
         else:
             config_fn, repo_config = load_tools_config(self.local_repo_dir)
-            try:
-                self.repo_path = repo_config["org_path"]
-            except KeyError:
-                raise UserWarning(f"'org_path' key not present in {config_fn.name}")
+            if config_fn is not None and repo_config is not None:
+                try:
+                    self.repo_path = repo_config.org_path
+                except KeyError:
+                    raise UserWarning(f"'org_path' key not present in {config_fn.name}")
 
             # Verify that the repo seems to be correctly configured
             if self.repo_path != NF_CORE_MODULES_NAME or self.branch:
@@ -148,6 +150,9 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa
 
             self.avail_module_names = None
 
+    def __repr__(self) -> str:
+        return f"SyncedRepo({self.remote_url}, {self.branch})"
+
     def setup_local_repo(self, remote_url, branch, hide_progress):
         pass
 
@@ -402,8 +407,12 @@ def get_latest_component_version(self, component_name, component_type):
         Returns the latest commit in the repository
         """
         try:
-            return list(self.get_component_git_log(component_name, component_type, depth=1))[0]["git_sha"]
-        except UserWarning:
+            git_logs = list(self.get_component_git_log(component_name, component_type, depth=1))
+            if not git_logs:
+                return None
+            return git_logs[0]["git_sha"]
+        except Exception as e:
+            log.debug(f"Could not get latest version of {component_name}: {e}")
             return None
 
     def sha_exists_on_branch(self, sha):
@@ -437,7 +446,9 @@ def get_commit_info(self, sha):
                 return message, date
         raise LookupError(f"Commit '{sha}' not found in the '{self.remote_url}'")
 
-    def get_avail_components(self, component_type, checkout=True, commit=None):
+    def get_avail_components(
+        self, component_type: str, checkout: bool = True, commit: Optional[str] = None
+    ) -> List[str]:
         """
         Gets the names of the modules/subworkflows in the repository. They are detected by
         checking which directories have a 'main.nf' file
@@ -456,9 +467,9 @@ def get_avail_components(self, component_type, checkout=True, commit=None):
             directory = self.subworkflows_dir
         # Module/Subworkflow directories are characterized by having a 'main.nf' file
         avail_component_names = [
-            os.path.relpath(dirpath, start=directory)
-            for dirpath, _, file_names in os.walk(directory)
-            if "main.nf" in file_names
+            str(Path(dirpath).relative_to(directory))
+            for dirpath, _, files in Path.walk(directory)
+            if "main.nf" in files
         ]
         return avail_component_names
 
diff --git a/tests/pipelines/test_sync.py b/tests/pipelines/test_sync.py
index d7b73c7ffb..b6955e6714 100644
--- a/tests/pipelines/test_sync.py
+++ b/tests/pipelines/test_sync.py
@@ -2,50 +2,104 @@
 
 import json
 import os
-import shutil
-import tempfile
-import unittest
 from pathlib import Path
+from typing import Dict, List, Union
 from unittest import mock
 
 import git
 import pytest
+import yaml
 
 import nf_core.pipelines.create.create
 import nf_core.pipelines.sync
+from nf_core.utils import NFCoreYamlConfig
 
+from ..test_pipelines import TestPipelines
 from ..utils import with_temporary_folder
 
 
-class TestModules(unittest.TestCase):
+class MockResponse:
+    def __init__(self, data: Union[Dict, List[Dict]], status_code: int, url: str):
+        self.url: str = url
+        self.status_code: int = status_code
+        self.from_cache: bool = False
+        self.reason: str = "Mocked response"
+        self.data: Union[Dict, List[Dict]] = data
+        self.content: str = json.dumps(data)
+        self.headers: Dict[str, str] = {"content-encoding": "test", "connection": "fake"}
+
+    def json(self):
+        return self.data
+
+
+def mocked_requests_get(url) -> MockResponse:
+    """Helper function to emulate POST requests responses from the web"""
+
+    url_template = "https://api.github.com/repos/{}/response/"
+    if url == Path(url_template.format("no_existing_pr"), "pulls?head=TEMPLATE&base=None"):
+        return MockResponse([], 200, url)
+    if url == Path(url_template.format("list_prs"), "pulls"):
+        response_data = [
+            {
+                "state": "closed",
+                "head": {"ref": "nf-core-template-merge-2"},
+                "base": {"ref": "master"},
+                "html_url": "pr_url",
+            }
+        ] + [
+            {
+                "state": "open",
+                "head": {"ref": f"nf-core-template-merge-{branch_no}"},
+                "base": {"ref": "master"},
+                "html_url": "pr_url",
+            }
+            for branch_no in range(3, 7)
+        ]
+        return MockResponse(response_data, 200, url)
+
+    return MockResponse([{"html_url": url}], 404, url)
+
+
+def mocked_requests_patch(url: str, data: str, **kwargs) -> MockResponse:
+    """Helper function to emulate POST requests responses from the web"""
+
+    if url == "url_to_update_pr":
+        return MockResponse({"html_url": "great_success"}, 200, url)
+    # convert data to dict
+    response = json.loads(data)
+    response["patch_url"] = url
+    return MockResponse(response, 404, url)
+
+
+def mocked_requests_post(url, **kwargs):
+    """Helper function to emulate POST requests responses from the web"""
+
+    if url == "https://api.github.com/repos/no_existing_pr/response/pulls":
+        return MockResponse({"html_url": "great_success"}, 201, url)
+
+    return MockResponse({}, 404, url)
+
+
+class TestModules(TestPipelines):
     """Class for modules tests"""
 
     def setUp(self):
-        """Create a new pipeline to test"""
-        self.tmp_dir = tempfile.mkdtemp()
-        self.pipeline_dir = os.path.join(self.tmp_dir, "testpipeline")
-        default_branch = "master"
-        self.create_obj = nf_core.pipelines.create.create.PipelineCreate(
-            "testing",
-            "test pipeline",
-            "tester",
-            outdir=self.pipeline_dir,
-            default_branch=default_branch,
-        )
-        self.create_obj.init_pipeline()
-        self.remote_path = os.path.join(self.tmp_dir, "remote_repo")
+        super().setUp()
+        self.remote_path = Path(self.tmp_dir, "remote_repo")
         self.remote_repo = git.Repo.init(self.remote_path, bare=True)
 
         if self.remote_repo.active_branch.name != "master":
-            self.remote_repo.active_branch.rename(default_branch)
-
-    def tearDown(self):
-        if os.path.exists(self.tmp_dir):
-            shutil.rmtree(self.tmp_dir)
+            self.remote_repo.active_branch.rename("master")
 
     @with_temporary_folder
-    def test_inspect_sync_dir_notgit(self, tmp_dir):
+    def test_inspect_sync_dir_notgit(self, tmp_dir: str):
         """Try syncing an empty directory"""
+        nf_core_yml_path = Path(tmp_dir, ".nf-core.yml")
+        nf_core_yml = NFCoreYamlConfig(repository_type="pipeline")
+
+        with open(nf_core_yml_path, "w") as fh:
+            yaml.dump(nf_core_yml.model_dump(), fh)
+
         psync = nf_core.pipelines.sync.PipelineSync(tmp_dir)
         with pytest.raises(nf_core.pipelines.sync.SyncExceptionError) as exc_info:
             psync.inspect_sync_dir()
@@ -227,88 +281,6 @@ def test_push_merge_branch_without_create_branch(self):
             psync.push_merge_branch()
         assert exc_info.value.args[0].startswith(f"Could not push branch '{psync.merge_branch}'")
 
-    def mocked_requests_get(url, **kwargs):
-        """Helper function to emulate POST requests responses from the web"""
-
-        class MockResponse:
-            def __init__(self, data, status_code):
-                self.url = kwargs.get("url")
-                self.status_code = status_code
-                self.from_cache = False
-                self.reason = "Mocked response"
-                self.data = data
-                self.content = json.dumps(data)
-                self.headers = {"content-encoding": "test", "connection": "fake"}
-
-            def json(self):
-                return self.data
-
-        url_template = "https://api.github.com/repos/{}/response/"
-        if url == os.path.join(url_template.format("no_existing_pr"), "pulls?head=TEMPLATE&base=None"):
-            response_data = []
-            return MockResponse(response_data, 200)
-        if url == os.path.join(url_template.format("list_prs"), "pulls"):
-            response_data = [
-                {
-                    "state": "closed",
-                    "head": {"ref": "nf-core-template-merge-2"},
-                    "base": {"ref": "master"},
-                    "html_url": "pr_url",
-                }
-            ] + [
-                {
-                    "state": "open",
-                    "head": {"ref": f"nf-core-template-merge-{branch_no}"},
-                    "base": {"ref": "master"},
-                    "html_url": "pr_url",
-                }
-                for branch_no in range(3, 7)
-            ]
-            return MockResponse(response_data, 200)
-
-        return MockResponse({"html_url": url}, 404)
-
-    def mocked_requests_patch(url, **kwargs):
-        """Helper function to emulate POST requests responses from the web"""
-
-        class MockResponse:
-            def __init__(self, data, status_code):
-                self.url = kwargs.get("url")
-                self.status_code = status_code
-                self.from_cache = False
-                self.reason = "Mocked"
-                self.content = json.dumps(data)
-                self.headers = {"content-encoding": "test", "connection": "fake"}
-
-        if url == "url_to_update_pr":
-            response_data = {"html_url": "great_success"}
-            return MockResponse(response_data, 200)
-
-        return MockResponse({"patch_url": url}, 404)
-
-    def mocked_requests_post(url, **kwargs):
-        """Helper function to emulate POST requests responses from the web"""
-
-        class MockResponse:
-            def __init__(self, data, status_code):
-                self.url = kwargs.get("url")
-                self.status_code = status_code
-                self.from_cache = False
-                self.reason = "Mocked"
-                self.data = data
-                self.content = json.dumps(data)
-                self.headers = {"content-encoding": "test", "connection": "fake"}
-
-            def json(self):
-                return self.data
-
-        if url == "https://api.github.com/repos/no_existing_pr/response/pulls":
-            response_data = {"html_url": "great_success"}
-            return MockResponse(response_data, 201)
-
-        response_data = {}
-        return MockResponse(response_data, 404)
-
     @mock.patch("nf_core.utils.gh_api.get", side_effect=mocked_requests_get)
     @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post)
     def test_make_pull_request_success(self, mock_post, mock_get):
@@ -354,7 +326,7 @@ def test_close_open_template_merge_prs(self, mock_get):
 
             prs = mock_get(f"https://api.github.com/repos/{psync.gh_repo}/pulls").data
             for pr in prs:
-                if pr["state"] == "open":
+                if pr.get("state", None) == "open":
                     mock_close_open_pr.assert_any_call(pr)
 
     @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post)
@@ -368,7 +340,7 @@ def test_close_open_pr(self, mock_patch, mock_post):
         psync.gh_username = "bad_url"
         psync.gh_repo = "bad_url/response"
         os.environ["GITHUB_AUTH_TOKEN"] = "test"
-        pr = {
+        pr: Dict[str, Union[str, Dict[str, str]]] = {
             "state": "open",
             "head": {"ref": "nf-core-template-merge-3"},
             "base": {"ref": "master"},
diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py
index 38bcc2b2c0..2693008707 100644
--- a/tests/subworkflows/test_lint.py
+++ b/tests/subworkflows/test_lint.py
@@ -291,10 +291,6 @@ def test_subworkflows_absent_version(self):
         with open(snap_file, "w") as fh:
             fh.write(new_content)
 
-        import ipdb
-
-        ipdb.set_trace()
-
         subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
         subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
         assert len(subworkflow_lint.failed) == 0
@@ -312,31 +308,33 @@ def test_subworkflows_missing_test_dir(self):
         test_dir_copy = shutil.copytree(test_dir, test_dir.parent / "tests_copy")
         shutil.rmtree(test_dir)
 
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(self.nfcore_modules)
         subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
-        assert len(subworkflow_lint.failed) == 0
+        assert len(subworkflow_lint.failed) == 1
         assert len(subworkflow_lint.passed) > 0
         assert len(subworkflow_lint.warned) >= 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
-        assert any([x.lint_test == "test_dir_versions" for x in subworkflow_lint.warned])
+        assert any([x.lint_test == "test_dir_exists" for x in subworkflow_lint.failed])
 
         # cleanup
         shutil.copytree(test_dir_copy, test_dir)
 
-    def test_subworkflows_missing_main_nf(self):
-        """Test linting a nf-test subworkflow if the main.nf file is missing"""
-        main_nf = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "main.nf")
-        main_nf_copy = shutil.copy(main_nf, main_nf.parent / "main_nf_copy")
-        main_nf.unlink()
-
-        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
-        subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
-        assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
-        assert len(subworkflow_lint.passed) > 0
-        assert len(subworkflow_lint.warned) >= 0
-        assert subworkflow_lint.failed[0].lint_test == "main_nf_exists"
-
-        # cleanup
-        shutil.copy(main_nf_copy, main_nf)
+    # There are many steps before the actual main_nf linting where we rely on the main_nf file to exist, so this test is not possible for now
+    # def test_subworkflows_missing_main_nf(self):
+    #     """Test linting a nf-test subworkflow if the main.nf file is missing"""
+
+    #     subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
+    #     main_nf = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "main.nf")
+    #     main_nf_copy = shutil.copy(main_nf, main_nf.parent / "main_nf_copy")
+    #     main_nf.unlink()
+    #     subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+    #     assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+    #     assert len(subworkflow_lint.passed) > 0
+    #     assert len(subworkflow_lint.warned) >= 0
+    #     assert subworkflow_lint.failed[0].lint_test == "main_nf_exists"
+
+    #     # cleanup
+    #     shutil.copy(main_nf_copy, main_nf)
+    #     shutil.rmtree(Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow_backup"))
 
     def test_subworkflows_empty_file_in_snapshot(self):
         """Test linting a nf-test subworkflow with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)"""

From 178146f75baf6322e36a752c234c628dde9953c5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 13:34:26 +0200
Subject: [PATCH 107/414] fix export of pydantic models

---
 nf_core/components/components_command.py     |  5 +-
 nf_core/components/update.py                 | 52 +++++-----
 nf_core/modules/modules_repo.py              |  1 +
 nf_core/pipelines/create/create.py           | 15 +--
 nf_core/pipelines/lint_utils.py              | 10 +-
 nf_core/utils.py                             | 50 ++++++----
 tests/pipelines/lint/test_nextflow_config.py | 15 ++-
 tests/subworkflows/test_update.py            | 20 ++--
 tests/test_modules.py                        | 44 ++++-----
 tests/test_utils.py                          | 99 +++++++-------------
 tests/utils.py                               | 29 +++++-
 11 files changed, 182 insertions(+), 158 deletions(-)

diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 13a6fed338..a6b46d1b61 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -181,7 +181,10 @@ def load_lint_config(self) -> None:
         Add parsed config to the `self.lint_config` class attribute.
         """
         _, tools_config = nf_core.utils.load_tools_config(self.directory)
-        self.lint_config = tools_config.get("lint", {})
+        if tools_config is None:
+            raise UserWarning("Could not load `.nf-core.yml` file.")
+        else:
+            self.lint_config = tools_config.get("lint", {})
 
     def check_modules_structure(self) -> None:
         """
diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index 9b24b6c0c9..eb15f976bf 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -97,11 +97,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
             updated = []
 
         _, tool_config = nf_core.utils.load_tools_config(self.directory)
-        self.update_config = tool_config.get("update", {})
-
-        if self.update_config is None:
-            raise UserWarning("Could not find '.nf-core.yml' file in pipeline directory")
-
+        self.update_config = getattr(tool_config, "update", {}) or {}
         self._parameter_checks()
 
         # Check modules directory structure
@@ -396,27 +392,26 @@ def get_single_component_info(self, component):
 
         sha = self.sha
         config_entry = None
-        if self.update_config is None:
-            raise UserWarning("Could not find '.nf-core.yml' file in pipeline directory")
-        if any(
-            [
-                entry.count("/") == 1
-                and (entry.endswith("modules") or entry.endswith("subworkflows"))
-                and not (entry.endswith(".git") or entry.endswith(".git/"))
-                for entry in self.update_config.keys()
-            ]
-        ):
-            raise UserWarning(
-                "Your '.nf-core.yml' file format is outdated. "
-                "The format should be of the form:\n"
-                "update:\n  <repo_url>:\n    <component_install_directory>:\n      <component_name>:"
-            )
-        if isinstance(self.update_config.get(self.modules_repo.remote_url, {}), str):
-            # If the repo entry is a string, it's the sha to update to
-            config_entry = self.update_config.get(self.modules_repo.remote_url, {})
-        elif component in self.update_config.get(self.modules_repo.remote_url, {}).get(install_dir, {}):
-            # If the component to update is in .nf-core.yml config file
-            config_entry = self.update_config[self.modules_repo.remote_url][install_dir].get(component)
+        if self.update_config is not None:
+            if any(
+                [
+                    entry.count("/") == 1
+                    and (entry.endswith("modules") or entry.endswith("subworkflows"))
+                    and not (entry.endswith(".git") or entry.endswith(".git/"))
+                    for entry in self.update_config.keys()
+                ]
+            ):
+                raise UserWarning(
+                    "Your '.nf-core.yml' file format is outdated. "
+                    "The format should be of the form:\n"
+                    "update:\n  <repo_url>:\n    <component_install_directory>:\n      <component_name>:"
+                )
+            if isinstance(self.update_config.get(self.modules_repo.remote_url, {}), str):
+                # If the repo entry is a string, it's the sha to update to
+                config_entry = self.update_config.get(self.modules_repo.remote_url, {})
+            elif component in self.update_config.get(self.modules_repo.remote_url, {}).get(install_dir, {}):
+                # If the component to update is in .nf-core.yml config file
+                config_entry = self.update_config[self.modules_repo.remote_url][install_dir].get(component)
         if config_entry is not None and config_entry is not True:
             if config_entry is False:
                 log.warn(
@@ -481,6 +476,7 @@ def get_all_components_info(self, branch=None):
         components_info = {}
         # Loop through all the modules/subworkflows in the pipeline
         # and check if they have an entry in the '.nf-core.yml' file
+
         for repo_name, components in self.modules_json.get_all_components(self.component_type).items():
             if isinstance(self.update_config, dict) and (
                 repo_name not in self.update_config or self.update_config[repo_name] is True
@@ -630,10 +626,8 @@ def get_all_components_info(self, branch=None):
                     overridden_repos.append(repo_name)
             elif isinstance(self.update_config, dict) and self.update_config[repo_name] is False:
                 skipped_repos.append(repo_name)
-            elif not isinstance(self.update_config, dict):
-                raise UserWarning("`.nf-core.yml` is not correctly formatted.")
             else:
-                raise UserWarning(f"Repo '{repo_name}' has an invalid entry in '.nf-core.yml'")
+                log.debug(f"no update config for {repo_name} in `.nf-core.yml`")
 
         if skipped_repos:
             skipped_str = "', '".join(skipped_repos)
diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py
index daa7b59811..7d576d4aef 100644
--- a/nf_core/modules/modules_repo.py
+++ b/nf_core/modules/modules_repo.py
@@ -63,6 +63,7 @@ def __init__(
         self.setup_local_repo(remote_url, branch, hide_progress)
 
         config_fn, repo_config = load_tools_config(self.local_repo_dir)
+        assert config_fn is not None and repo_config is not None  # mypy
         try:
             self.repo_path = repo_config["org_path"]
         except KeyError:
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index b7d86c5bd7..deeb5554af 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -376,13 +376,14 @@ def render_template(self):
 
         if self.config:
             config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir)
-            with open(config_fn, "w") as fh:
-                config_yml.update(template=self.config.model_dump())
-                # convert posix path to string for yaml dump
-                config_yml["template"]["outdir"] = str(config_yml["template"]["outdir"])
-                yaml.safe_dump(config_yml, fh)
-                log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
-                run_prettier_on_file(self.outdir / config_fn)
+            if config_fn is not None and config_yml is not None:
+                with open(str(config_fn), "w") as fh:
+                    config_yml.template = self.config.model_dump()
+                    # convert posix path to string for yaml dump
+                    config_yml["template"]["outdir"] = str(config_yml["template"]["outdir"])
+                    yaml.safe_dump(config_yml.model_dump(), fh)
+                    log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
+                    run_prettier_on_file(self.outdir / config_fn)
 
     def update_nextflow_schema(self):
         """
diff --git a/nf_core/pipelines/lint_utils.py b/nf_core/pipelines/lint_utils.py
index 4ccf790076..ccab76295f 100644
--- a/nf_core/pipelines/lint_utils.py
+++ b/nf_core/pipelines/lint_utils.py
@@ -110,9 +110,13 @@ def ignore_file(lint_name: str, file_path: Path, dir_path: Path) -> List[List[st
     passed: List[str] = []
     failed: List[str] = []
     ignored: List[str] = []
-    _, lint_conf = nf_core.utils.load_tools_config(dir_path)
-    lint_conf = lint_conf.get("lint", {})
-    ignore_entry: List[str] | bool = lint_conf.get(lint_name, [])
+    _, pipeline_conf = nf_core.utils.load_tools_config(dir_path)
+    lint_conf = getattr(pipeline_conf, "lint", None) or None
+
+    if lint_conf is None:
+        ignore_entry: List[str] = []
+    else:
+        ignore_entry = lint_conf.get(lint_name, [])
     full_path = dir_path / file_path
     # Return a failed status if we can't find the file
     if not full_path.is_file():
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 4d0566b1af..6794cf04fe 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -19,7 +19,7 @@
 import time
 from contextlib import contextmanager
 from pathlib import Path
-from typing import Dict, Generator, List, Optional, Tuple, Union
+from typing import Any, Dict, Generator, List, Optional, Tuple, Union
 
 import git
 import prompt_toolkit.styles
@@ -1042,25 +1042,37 @@ def get_repo_releases_branches(pipeline, wfs):
 
 
 class NFCoreTemplateConfig(BaseModel):
-    org: str
-    name: str
-    description: str
-    author: str
-    version: Optional[str]
-    force: Optional[bool]
-    outdir: Optional[str]
-    skip_features: Optional[list]
-    is_nfcore: Optional[bool]
+    org: Optional[str] = None
+    name: Optional[str] = None
+    description: Optional[str] = None
+    author: Optional[str] = None
+    version: Optional[str] = None
+    force: Optional[bool] = None
+    outdir: Optional[str] = None
+    skip_features: Optional[list] = None
+    is_nfcore: Optional[bool] = None
+
+
+LintConfigType = Optional[Dict[str, Union[List[str], List[Dict[str, List[str]]], bool]]]
 
 
 class NFCoreYamlConfig(BaseModel):
-    nf_core_version: str
     repository_type: str
-    org_path: str
-    template: NFCoreTemplateConfig
+    nf_core_version: Optional[str] = None
+    org_path: Optional[str] = None
+    lint: LintConfigType = None
+    template: Optional[NFCoreTemplateConfig] = None
+    bump_version: Optional[Dict[str, bool]] = None
+    update: Optional[Dict[str, Union[str, bool, Dict[str, Union[str, Dict[str, Union[str, bool]]]]]]] = None
+
+    def __getitem__(self, item: str) -> Any:
+        return getattr(self, item)
+
+    def get(self, item: str, default: Any = None) -> Any:
+        return getattr(self, item, default)
 
 
-def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, NFCoreYamlConfig]:
+def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path], Optional[NFCoreYamlConfig]]:
     """
     Parse the nf-core.yml configuration file
 
@@ -1078,11 +1090,12 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, NFCoreYa
     if config_fn is None:
         depr_path = get_first_available_path(directory, DEPRECATED_CONFIG_PATHS)
         if depr_path:
-            raise AssertionError(
+            raise UserWarning(
                 f"Deprecated `{depr_path.name}` file found! Please rename the file to `{CONFIG_PATHS[0]}`."
             )
         else:
-            raise AssertionError(f"Could not find a config file in the directory '{directory}'")
+            log.debug(f"Could not find a config file in the directory '{directory}'")
+            return Path(directory, CONFIG_PATHS[0]), None
     with open(str(config_fn)) as fh:
         tools_config = yaml.safe_load(fh)
 
@@ -1094,7 +1107,10 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, NFCoreYa
     try:
         nf_core_yaml_config = NFCoreYamlConfig(**tools_config)
     except ValidationError as e:
-        raise AssertionError(f"Config file '{config_fn}' is invalid: {e}")
+        error_message = f"Config file '{config_fn}' is invalid"
+        for error in e.errors():
+            error_message += f"\n{error['loc'][0]}: {error['msg']}"
+        raise AssertionError(error_message)
 
     log.debug("Using config file: %s", config_fn)
     return config_fn, nf_core_yaml_config
diff --git a/tests/pipelines/lint/test_nextflow_config.py b/tests/pipelines/lint/test_nextflow_config.py
index 01173aec34..3cc9355452 100644
--- a/tests/pipelines/lint/test_nextflow_config.py
+++ b/tests/pipelines/lint/test_nextflow_config.py
@@ -2,8 +2,11 @@
 import re
 from pathlib import Path
 
+import yaml
+
 import nf_core.pipelines.create.create
 import nf_core.pipelines.lint
+from nf_core.utils import NFCoreYamlConfig
 
 from ..test_lint import TestLint
 
@@ -124,11 +127,13 @@ def test_allow_params_reference_in_main_nf(self):
     def test_default_values_ignored(self):
         """Test ignoring linting of default values."""
         # Add max_cpus to the ignore list
-        nf_core_yml = Path(self.new_pipeline) / ".nf-core.yml"
-        with open(nf_core_yml, "w") as f:
-            f.write(
-                "repository_type: pipeline\nlint:\n  nextflow_config:\n    - config_defaults:\n      - params.max_cpus\n"
-            )
+        nf_core_yml_path = Path(self.new_pipeline) / ".nf-core.yml"
+        nf_core_yml = NFCoreYamlConfig(
+            repository_type="pipeline", lint={"nextflow_config": [{"config_defaults": ["params.max_cpus"]}]}
+        )
+        with open(nf_core_yml_path, "w") as f:
+            yaml.dump(nf_core_yml.model_dump(), f)
+
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
         lint_obj.load_pipeline_config()
         lint_obj._load_lint_config()
diff --git a/tests/subworkflows/test_update.py b/tests/subworkflows/test_update.py
index d3b2433572..7b17a621bc 100644
--- a/tests/subworkflows/test_update.py
+++ b/tests/subworkflows/test_update.py
@@ -156,9 +156,10 @@ def test_update_with_config_fixed_version(self):
         # Fix the subworkflow version in the .nf-core.yml to an old version
         update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": OLD_SUBWORKFLOWS_SHA}}}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        tools_config["update"] = update_config
+        setattr(tools_config, "update", update_config)
+        assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
-            yaml.dump(tools_config, f)
+            yaml.dump(tools_config.model_dump(), f)
 
         # Update all subworkflows in the pipeline
         update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False)
@@ -186,9 +187,10 @@ def test_update_with_config_dont_update(self):
         # Set the fastq_align_bowtie2 field to no update in the .nf-core.yml
         update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": False}}}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        tools_config["update"] = update_config
+        setattr(tools_config, "update", update_config)
+        assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
-            yaml.dump(tools_config, f)
+            yaml.dump(tools_config.model_dump(), f)
 
         # Update all modules in the pipeline
         update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False)
@@ -216,9 +218,10 @@ def test_update_with_config_fix_all(self):
         # Fix the version of all nf-core subworkflows in the .nf-core.yml to an old version
         update_config = {NF_CORE_MODULES_REMOTE: OLD_SUBWORKFLOWS_SHA}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        tools_config["update"] = update_config
+        setattr(tools_config, "update", update_config)
+        assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
-            yaml.dump(tools_config, f)
+            yaml.dump(tools_config.model_dump(), f)
 
         # Update fastq_align_bowtie2
         update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=False, update_deps=True, show_diff=False)
@@ -246,9 +249,10 @@ def test_update_with_config_no_updates(self):
         # Set all repository updates to False
         update_config = {NF_CORE_MODULES_REMOTE: False}
         config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir)
-        tools_config["update"] = update_config
+        setattr(tools_config, "update", update_config)
+        assert config_fn is not None and tools_config is not None  # mypy
         with open(Path(self.pipeline_dir, config_fn), "w") as f:
-            yaml.dump(tools_config, f)
+            yaml.dump(tools_config.model_dump(), f)
 
         # Update all subworkflows in the pipeline
         update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False)
diff --git a/tests/test_modules.py b/tests/test_modules.py
index 13bf32f971..9ce74fd4e1 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -1,8 +1,6 @@
 """Tests covering the modules commands"""
 
 import json
-import os
-import shutil
 import unittest
 from pathlib import Path
 
@@ -12,7 +10,13 @@
 import yaml
 
 import nf_core.modules
+import nf_core.modules.create
+import nf_core.modules.install
+import nf_core.modules.modules_repo
+import nf_core.modules.remove
 import nf_core.pipelines.create.create
+from nf_core import __version__
+from nf_core.utils import NFCoreYamlConfig
 
 from .utils import (
     GITLAB_BRANCH_TEST_BRANCH,
@@ -34,24 +38,28 @@ def create_modules_repo_dummy(tmp_dir):
     Path(root_dir, "modules", "nf-core").mkdir(parents=True)
     Path(root_dir, "tests", "modules", "nf-core").mkdir(parents=True)
     Path(root_dir, "tests", "config").mkdir(parents=True)
+
+    nf_core_yml = NFCoreYamlConfig(nf_core_version=__version__, repository_type="modules", org_path="nf-core")
     with open(Path(root_dir, ".nf-core.yml"), "w") as fh:
-        fh.writelines(["repository_type: modules", "\n", "org_path: nf-core", "\n"])
+        yaml.dump(nf_core_yml.model_dump(), fh)
     # mock biocontainers and anaconda response
     with responses.RequestsMock() as rsps:
         mock_anaconda_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0")
         mock_biocontainers_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0")
         # bpipe is a valid package on bioconda that is very unlikely to ever be added to nf-core/modules
-        module_create = nf_core.modules.ModuleCreate(root_dir, "bpipe/test", "@author", "process_single", False, False)
+        module_create = nf_core.modules.create.ModuleCreate(
+            root_dir, "bpipe/test", "@author", "process_single", False, False
+        )
         with requests_cache.disabled():
-            module_create.create()
+            assert module_create.create()
 
     # Remove doi from meta.yml which makes lint fail
     meta_yml_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "meta.yml")
 
-    with open(meta_yml_path) as fh:
+    with open(str(meta_yml_path)) as fh:
         meta_yml = yaml.safe_load(fh)
     del meta_yml["tools"][0]["bpipe"]["doi"]
-    with open(meta_yml_path, "w") as fh:
+    with open(str(meta_yml_path), "w") as fh:
         yaml.dump(meta_yml, fh)
     # Add dummy content to main.nf.test.snap
     test_snap_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap")
@@ -102,8 +110,8 @@ def setUp(self):
         self.tmp_dir, self.template_dir, self.pipeline_name, self.pipeline_dir = create_tmp_pipeline()
 
         # Set up install objects
-        self.mods_install = nf_core.modules.ModuleInstall(self.pipeline_dir, prompt=False, force=True)
-        self.mods_install_old = nf_core.modules.ModuleInstall(
+        self.mods_install = nf_core.modules.install.ModuleInstall(self.pipeline_dir, prompt=False, force=True)
+        self.mods_install_old = nf_core.modules.install.ModuleInstall(
             self.pipeline_dir,
             prompt=False,
             force=False,
@@ -111,21 +119,21 @@ def setUp(self):
             remote_url=GITLAB_URL,
             branch=OLD_TRIMGALORE_BRANCH,
         )
-        self.mods_install_trimgalore = nf_core.modules.ModuleInstall(
+        self.mods_install_trimgalore = nf_core.modules.install.ModuleInstall(
             self.pipeline_dir,
             prompt=False,
             force=False,
             remote_url=GITLAB_URL,
             branch=OLD_TRIMGALORE_BRANCH,
         )
-        self.mods_install_gitlab = nf_core.modules.ModuleInstall(
+        self.mods_install_gitlab = nf_core.modules.install.ModuleInstall(
             self.pipeline_dir,
             prompt=False,
             force=False,
             remote_url=GITLAB_URL,
             branch=GITLAB_DEFAULT_BRANCH,
         )
-        self.mods_install_gitlab_old = nf_core.modules.ModuleInstall(
+        self.mods_install_gitlab_old = nf_core.modules.install.ModuleInstall(
             self.pipeline_dir,
             prompt=False,
             force=False,
@@ -135,8 +143,8 @@ def setUp(self):
         )
 
         # Set up remove objects
-        self.mods_remove = nf_core.modules.ModuleRemove(self.pipeline_dir)
-        self.mods_remove_gitlab = nf_core.modules.ModuleRemove(
+        self.mods_remove = nf_core.modules.remove.ModuleRemove(self.pipeline_dir)
+        self.mods_remove_gitlab = nf_core.modules.remove.ModuleRemove(
             self.pipeline_dir,
             remote_url=GITLAB_URL,
             branch=GITLAB_DEFAULT_BRANCH,
@@ -145,15 +153,9 @@ def setUp(self):
         # Set up the nf-core/modules repo dummy
         self.nfcore_modules = create_modules_repo_dummy(self.tmp_dir)
 
-    def tearDown(self):
-        """Clean up temporary files and folders"""
-
-        if os.path.exists(self.tmp_dir):
-            shutil.rmtree(self.tmp_dir)
-
     def test_modulesrepo_class(self):
         """Initialise a modules repo object"""
-        modrepo = nf_core.modules.ModulesRepo()
+        modrepo = nf_core.modules.modules_repo.ModulesRepo()
         assert modrepo.repo_path == "nf-core"
         assert modrepo.branch == "master"
 
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 860cba5ba6..0d012716a9 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -1,9 +1,6 @@
 """Tests covering for utility functions."""
 
 import os
-import shutil
-import tempfile
-import unittest
 from pathlib import Path
 from unittest import mock
 
@@ -14,6 +11,7 @@
 import nf_core.pipelines.list
 import nf_core.utils
 
+from .test_pipelines import TestPipelines
 from .utils import with_temporary_folder
 
 TEST_DATA_DIR = Path(__file__).parent / "data"
@@ -28,31 +26,9 @@ def test_strip_ansi_codes():
     assert stripped == "ls examplefile.zip"
 
 
-class TestUtils(unittest.TestCase):
+class TestUtils(TestPipelines):
     """Class for utils tests"""
 
-    def setUp(self):
-        """Function that runs at start of tests for common resources
-
-        Use nf_core.pipelines.create() to make a pipeline that we can use for testing
-        """
-        self.tmp_dir = tempfile.mkdtemp()
-        self.test_pipeline_dir = os.path.join(self.tmp_dir, "nf-core-testpipeline")
-        self.create_obj = nf_core.pipelines.create.create.PipelineCreate(
-            "testpipeline",
-            "This is a test pipeline",
-            "Test McTestFace",
-            no_git=True,
-            outdir=self.test_pipeline_dir,
-        )
-        self.create_obj.init_pipeline()
-        # Base Pipeline object on this directory
-        self.pipeline_obj = nf_core.utils.Pipeline(self.test_pipeline_dir)
-
-    def tearDown(self):
-        if os.path.exists(self.tmp_dir):
-            shutil.rmtree(self.tmp_dir)
-
     def test_check_if_outdated_1(self):
         current_version = "1.0"
         remote_version = "2.0"
@@ -110,7 +86,7 @@ def testload_pipeline_config(self):
     def test_list_files_git(self):
         """Test listing pipeline files using `git ls`"""
         files = self.pipeline_obj.list_files()
-        assert Path(self.test_pipeline_dir, "main.nf") in files
+        assert Path(self.pipeline_dir, "main.nf") in files
 
     @with_temporary_folder
     def test_list_files_no_git(self, tmpdir):
@@ -193,46 +169,39 @@ def test_get_repo_releases_branches_not_exists_slash(self):
         with pytest.raises(AssertionError):
             nf_core.utils.get_repo_releases_branches("made-up/pipeline", wfs)
 
-
-def test_validate_file_md5():
-    # MD5(test) = d8e8fca2dc0f896fd7cb4cb0031ba249
-    test_file = TEST_DATA_DIR / "test.txt"
-    test_file_md5 = "d8e8fca2dc0f896fd7cb4cb0031ba249"
-    different_md5 = "9e7b964750cf0bb08ee960fce356b6d6"
-    non_hex_string = "s"
-    assert nf_core.utils.validate_file_md5(test_file, test_file_md5)
-    with pytest.raises(IOError):
-        nf_core.utils.validate_file_md5(test_file, different_md5)
-    with pytest.raises(ValueError):
-        nf_core.utils.validate_file_md5(test_file, non_hex_string)
-
-
-def test_nested_setitem():
-    d = {"a": {"b": {"c": "value"}}}
-    nf_core.utils.nested_setitem(d, ["a", "b", "c"], "value new")
-    assert d["a"]["b"]["c"] == "value new"
-    assert d == {"a": {"b": {"c": "value new"}}}
-
-
-def test_nested_delitem():
-    d = {"a": {"b": {"c": "value"}}}
-    nf_core.utils.nested_delitem(d, ["a", "b", "c"])
-    assert "c" not in d["a"]["b"]
-    assert d == {"a": {"b": {}}}
-
-
-def test_set_wd():
-    with tempfile.TemporaryDirectory() as tmpdirname:
-        with nf_core.utils.set_wd(tmpdirname):
+    def test_validate_file_md5(self):
+        # MD5(test) = d8e8fca2dc0f896fd7cb4cb0031ba249
+        test_file = TEST_DATA_DIR / "test.txt"
+        test_file_md5 = "d8e8fca2dc0f896fd7cb4cb0031ba249"
+        different_md5 = "9e7b964750cf0bb08ee960fce356b6d6"
+        non_hex_string = "s"
+        assert nf_core.utils.validate_file_md5(test_file, test_file_md5)
+        with pytest.raises(IOError):
+            nf_core.utils.validate_file_md5(test_file, different_md5)
+        with pytest.raises(ValueError):
+            nf_core.utils.validate_file_md5(test_file, non_hex_string)
+
+    def test_nested_setitem(self):
+        d = {"a": {"b": {"c": "value"}}}
+        nf_core.utils.nested_setitem(d, ["a", "b", "c"], "value new")
+        assert d["a"]["b"]["c"] == "value new"
+        assert d == {"a": {"b": {"c": "value new"}}}
+
+    def test_nested_delitem(self):
+        d = {"a": {"b": {"c": "value"}}}
+        nf_core.utils.nested_delitem(d, ["a", "b", "c"])
+        assert "c" not in d["a"]["b"]
+        assert d == {"a": {"b": {}}}
+
+    def test_set_wd(self):
+        with nf_core.utils.set_wd(self.tmp_dir):
             context_wd = Path().resolve()
-        assert context_wd == Path(tmpdirname).resolve()
+        assert context_wd == Path(self.tmp_dir).resolve()
         assert context_wd != Path().resolve()
 
-
-def test_set_wd_revert_on_raise():
-    wd_before_context = Path().resolve()
-    with tempfile.TemporaryDirectory() as tmpdirname:
+    def test_set_wd_revert_on_raise(self):
+        wd_before_context = Path().resolve()
         with pytest.raises(Exception):
-            with nf_core.utils.set_wd(tmpdirname):
+            with nf_core.utils.set_wd(self.tmp_dir):
                 raise Exception
-    assert wd_before_context == Path().resolve()
+        assert wd_before_context == Path().resolve()
diff --git a/tests/utils.py b/tests/utils.py
index 90c4ae0418..1d5a8a115d 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -9,9 +9,12 @@
 from typing import Any, Callable, Tuple
 
 import responses
+import yaml
 
 import nf_core.modules
 import nf_core.pipelines.create.create
+from nf_core import __version__
+from nf_core.utils import NFCoreTemplateConfig, NFCoreYamlConfig
 
 TEST_DATA_DIR = Path(__file__).parent / "data"
 OLD_TRIMGALORE_SHA = "9b7a3bdefeaad5d42324aa7dd50f87bea1b04386"
@@ -95,7 +98,7 @@ def mock_biocontainers_api_calls(rsps: responses.RequestsMock, module: str, vers
     rsps.get(biocontainers_api_url, json=biocontainers_mock, status=200)
 
 
-def create_tmp_pipeline() -> Tuple[Path, Path, str, Path]:
+def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]:
     """Create a new Pipeline for testing"""
 
     tmp_dir = Path(tempfile.TemporaryDirectory().name)
@@ -103,9 +106,31 @@ def create_tmp_pipeline() -> Tuple[Path, Path, str, Path]:
     template_dir = root_repo_dir / "nf_core" / "pipeline-template"
     pipeline_name = "mypipeline"
     pipeline_dir = tmp_dir / pipeline_name
+    pipeline_dir.mkdir(parents=True)
+
+    nf_core_yml = NFCoreYamlConfig(
+        nf_core_version=__version__,
+        repository_type="modules",
+        org_path="nf-core",
+        lint=None,
+        template=NFCoreTemplateConfig(
+            name="mypipeline",
+            author="me",
+            description="it is mine",
+            org="nf-core",
+            version=None,
+            force=True,
+            is_nfcore=None,
+            skip_features=None,
+            outdir=None,
+        ),
+        bump_version=None,
+    )
+    with open(str(Path(pipeline_dir, ".nf-core.yml")), "w") as fh:
+        yaml.dump(nf_core_yml.model_dump(), fh)
 
     nf_core.pipelines.create.create.PipelineCreate(
-        pipeline_name, "it is mine", "me", no_git=False, outdir=pipeline_dir
+        pipeline_name, "it is mine", "me", no_git=no_git, outdir=pipeline_dir, force=True
     ).init_pipeline()
 
     # return values to instance variables for later use in test methods

From d0a968ceb3ffe85e87303cc0d63838dbbc6a71b9 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 13:35:06 +0200
Subject: [PATCH 108/414] fix tests

---
 nf_core/modules/lint/__init__.py              |  4 +-
 nf_core/pipelines/lint/files_exist.py         |  2 +-
 nf_core/pipelines/lint/nfcore_yml.py          |  3 +-
 nf_core/pipelines/lint/schema_description.py  |  2 +-
 nf_core/pipelines/lint/template_strings.py    |  2 +-
 nf_core/pipelines/sync.py                     | 45 ++++++++++---------
 .../subworkflows/lint/subworkflow_tests.py    | 11 +++--
 tests/modules/test_modules_json.py            |  2 +-
 tests/pipelines/test_lint.py                  |  4 +-
 9 files changed, 39 insertions(+), 36 deletions(-)

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index 2b10b4df5a..cea75d8f2e 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -228,7 +228,7 @@ def lint_module(
         # TODO: consider unifying modules and subworkflows lint_module() function and add it to the ComponentLint class
         # Only check the main script in case of a local module
         if local:
-            self.main_nf(mod, fix_version, self.registry, progress_bar)
+            self.main_nf(mod, fix_version, registry, progress_bar)
             self.passed += [LintResult(mod, *m) for m in mod.passed]
             warned = [LintResult(mod, *m) for m in (mod.warned + mod.failed)]
             if not self.fail_warned:
@@ -245,7 +245,7 @@ def lint_module(
 
             for test_name in self.lint_tests:
                 if test_name == "main_nf":
-                    getattr(self, test_name)(mod, fix_version, self.registry, progress_bar)
+                    getattr(self, test_name)(mod, fix_version, registry, progress_bar)
                 else:
                     getattr(self, test_name)(mod)
 
diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index edad62aab8..ad0605dcf7 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -205,7 +205,7 @@ def files_exist(self) -> Dict[str, List[str]]:
     ]
 
     # Remove files that should be ignored according to the linting config
-    ignore_files = self.lint_config.get("files_exist", [])
+    ignore_files = self.lint_config.get("files_exist", []) if self.lint_config is not None else []
 
     def pf(file_path: Union[str, Path]) -> Path:
         return Path(self.wf_path, file_path)
diff --git a/nf_core/pipelines/lint/nfcore_yml.py b/nf_core/pipelines/lint/nfcore_yml.py
index f23b2f1a84..e0d5fb2005 100644
--- a/nf_core/pipelines/lint/nfcore_yml.py
+++ b/nf_core/pipelines/lint/nfcore_yml.py
@@ -27,8 +27,7 @@ def nfcore_yml(self) -> Dict[str, List[str]]:
     ignored: List[str] = []
 
     # Remove field that should be ignored according to the linting config
-    ignore_configs = self.lint_config.get(".nf-core", [])
-
+    ignore_configs = self.lint_config.get(".nf-core", []) if self.lint_config is not None else []
     try:
         with open(Path(self.wf_path, ".nf-core.yml")) as fh:
             content = fh.read()
diff --git a/nf_core/pipelines/lint/schema_description.py b/nf_core/pipelines/lint/schema_description.py
index 82165b6e7d..d617e40949 100644
--- a/nf_core/pipelines/lint/schema_description.py
+++ b/nf_core/pipelines/lint/schema_description.py
@@ -24,7 +24,7 @@ def schema_description(self):
     self.schema_obj.load_lint_schema()
 
     # Get parameters that should be ignored according to the linting config
-    ignore_params = self.lint_config.get("schema_description", [])
+    ignore_params = self.lint_config.get("schema_description", []) if self.lint_config is not None else []
 
     # Get ungrouped params
     if "properties" in self.schema_obj.schema.keys():
diff --git a/nf_core/pipelines/lint/template_strings.py b/nf_core/pipelines/lint/template_strings.py
index 90c47203f6..37a1f64daf 100644
--- a/nf_core/pipelines/lint/template_strings.py
+++ b/nf_core/pipelines/lint/template_strings.py
@@ -38,7 +38,7 @@ def template_strings(self):
     failed = []
     ignored = []
     # Files that should be ignored according to the linting config
-    ignore_files = self.lint_config.get("template_strings", [])
+    ignore_files = self.lint_config.get("template_strings", []) if self.lint_config is not None else []
     files = self.list_files()
 
     # Loop through files, searching for string
diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index a309fa8c3b..b1da99a626 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -10,6 +10,7 @@
 import git
 import questionary
 import requests
+import requests.auth
 import requests_cache
 import rich
 import yaml
@@ -86,23 +87,23 @@ def __init__(
         self.pr_url = ""
 
         self.config_yml_path, self.config_yml = nf_core.utils.load_tools_config(self.pipeline_dir)
-
+        assert self.config_yml_path is not None  # mypy
         # Throw deprecation warning if template_yaml_path is set
         if template_yaml_path is not None:
             log.warning(
                 f"The `template_yaml_path` argument is deprecated. Saving pipeline creation settings in .nf-core.yml instead. Please remove {template_yaml_path} file."
             )
-            if "template" in self.config_yml:
+            if getattr(self.config_yml, "template", None) is not None:
                 overwrite_template = questionary.confirm(
                     f"A template section already exists in '{self.config_yml_path}'. Do you want to overwrite?",
                     style=nf_core.utils.nfcore_question_style,
                     default=False,
                 ).unsafe_ask()
-            if overwrite_template or "template" not in self.config_yml:
+            if overwrite_template or getattr(self.config_yml, "template", None) is None:
                 with open(template_yaml_path) as f:
-                    self.config_yml["template"] = yaml.safe_load(f)
+                    self.config_yml.template = yaml.safe_load(f)
                 with open(self.config_yml_path, "w") as fh:
-                    yaml.safe_dump(self.config_yml, fh)
+                    yaml.safe_dump(self.config_yml.model_dump(), fh)
                 log.info(f"Saved pipeline creation settings to '{self.config_yml_path}'")
                 raise SystemExit(
                     f"Please commit your changes and delete the {template_yaml_path} file. Then run the sync command again."
@@ -259,11 +260,12 @@ def make_template_pipeline(self):
 
         # Only show error messages from pipeline creation
         logging.getLogger("nf_core.pipelines.create").setLevel(logging.ERROR)
-
+        assert self.config_yml_path is not None
+        assert self.config_yml is not None
         # Re-write the template yaml info from .nf-core.yml config
-        if "template" in self.config_yml:
+        if getattr(self.config_yml, "template", None) is not None:
             with open(self.config_yml_path, "w") as config_path:
-                yaml.safe_dump(self.config_yml, config_path)
+                yaml.safe_dump(self.config_yml.model_dump(), config_path)
 
         try:
             nf_core.pipelines.create.create.PipelineCreate(
@@ -411,21 +413,24 @@ def close_open_template_merge_prs(self):
             return False
 
         for pr in list_prs_json:
-            log.debug(f"Looking at PR from '{pr['head']['ref']}': {pr['html_url']}")
-            # Ignore closed PRs
-            if pr["state"] != "open":
-                log.debug(f"Ignoring PR as state not open ({pr['state']}): {pr['html_url']}")
-                continue
+            if isinstance(pr, int):
+                log.debug(f"Incorrect PR format: {pr}")
+            else:
+                log.debug(f"Looking at PR from '{pr['head']['ref']}': {pr['html_url']}")
+                # Ignore closed PRs
+                if pr["state"] != "open":
+                    log.debug(f"Ignoring PR as state not open ({pr['state']}): {pr['html_url']}")
+                    continue
 
-            # Don't close the new PR that we just opened
-            if pr["head"]["ref"] == self.merge_branch:
-                continue
+                # Don't close the new PR that we just opened
+                if pr["head"]["ref"] == self.merge_branch:
+                    continue
 
-            # PR is from an automated branch and goes to our target base
-            if pr["head"]["ref"].startswith("nf-core-template-merge-") and pr["base"]["ref"] == self.from_branch:
-                self.close_open_pr(pr)
+                # PR is from an automated branch and goes to our target base
+                if pr["head"]["ref"].startswith("nf-core-template-merge-") and pr["base"]["ref"] == self.from_branch:
+                    self.close_open_pr(pr)
 
-    def close_open_pr(self, pr):
+    def close_open_pr(self, pr) -> bool:
         """Given a PR API response, add a comment and close."""
         log.debug(f"Attempting to close PR: '{pr['html_url']}'")
 
diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py
index af39334744..7ca825f04f 100644
--- a/nf_core/subworkflows/lint/subworkflow_tests.py
+++ b/nf_core/subworkflows/lint/subworkflow_tests.py
@@ -27,14 +27,14 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
     repo_dir = subworkflow.component_dir.parts[
         : subworkflow.component_dir.parts.index(subworkflow.component_name.split("/")[0])
     ][-1]
-    test_dir = Path(
+    pytest_dir = Path(
         subworkflow.base_dir,
         "tests",
         "subworkflows",
         repo_dir,
         subworkflow.component_name,
     )
-    pytest_main_nf = Path(test_dir, "main.nf")
+    pytest_main_nf = Path(pytest_dir, "main.nf")
     is_pytest = pytest_main_nf.is_file()
     log.debug(f"{pytest_main_nf} is pytest: {is_pytest}")
     if subworkflow.nftest_testdir.is_dir():
@@ -265,8 +265,7 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
 
     # Check that the old test directory does not exist
     if not is_pytest:
-        old_test_dir = Path(subworkflow.base_dir, "tests", "subworkflows", subworkflow.component_name)
-        if old_test_dir.is_dir():
-            subworkflow.failed.append(("test_old_test_dir", "old test directory exists", old_test_dir))
+        if pytest_dir.is_dir():
+            subworkflow.failed.append(("test_old_test_dir", "old test directory exists", pytest_dir))
         else:
-            subworkflow.passed.append(("test_old_test_dir", "old test directory does not exist", old_test_dir))
+            subworkflow.passed.append(("test_old_test_dir", "old test directory does not exist", pytest_dir))
diff --git a/tests/modules/test_modules_json.py b/tests/modules/test_modules_json.py
index 2ab058fa70..845f9c3e34 100644
--- a/tests/modules/test_modules_json.py
+++ b/tests/modules/test_modules_json.py
@@ -220,7 +220,7 @@ def test_mod_json_with_empty_modules_value(self):
         mod_json_obj.create()  # Create modules.json explicitly to get correct module sha
         mod_json_orig = mod_json_obj.get_modules_json()
         mod_json = copy.deepcopy(mod_json_orig)
-        mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"] = ""
+        mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"] = {}
         # save the altered module.json and load it again to check if it will fix itself
         mod_json_obj.modules_json = mod_json
         mod_json_obj.dump()
diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py
index ab8bcf6b24..9ca29d249f 100644
--- a/tests/pipelines/test_lint.py
+++ b/tests/pipelines/test_lint.py
@@ -47,7 +47,7 @@ def test_init_pipeline_lint(self):
 
     def test_load_lint_config_not_found(self):
         """Try to load a linting config file that doesn't exist"""
-        self.lint_obj._load_lint_config()
+        assert self.lint_obj._load_lint_config()
         assert self.lint_obj.lint_config == {}
 
     def test_load_lint_config_ignore_all_tests(self):
@@ -58,7 +58,7 @@ def test_load_lint_config_ignore_all_tests(self):
         lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
 
         # Make a config file listing all test names
-        config_dict = {"lint": {test_name: False for test_name in lint_obj.lint_tests}}
+        config_dict = {"repository_type": "pipeline", "lint": {test_name: False for test_name in lint_obj.lint_tests}}
         with open(Path(new_pipeline, ".nf-core.yml"), "w") as fh:
             yaml.dump(config_dict, fh)
 

From 33f461aa5a3a888dd0914796c99b3201b2a06f3e Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 13:35:26 +0200
Subject: [PATCH 109/414] migrate to pathlib

---
 nf_core/modules/modules_json.py    |  2 +-
 nf_core/pipelines/create/create.py |  2 +-
 tests/pipelines/test_create.py     | 11 +++++++----
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 02ce6fa5a2..01785c6d65 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -1192,7 +1192,7 @@ def components_with_repos():
                         self.modules_dir,
                         modules_repo.repo_path,
                     )
-                    for dir_name, _, _ in os.walk(repo_url_path):
+                    for dir_name, _, _ in Path.walk(repo_url_path):
                         if component_type == "modules":
                             if len(Path(directory).parts) > 1:  # The module name is TOOL/SUBTOOL
                                 paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:])))
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index deeb5554af..f032db7f69 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -516,7 +516,7 @@ def fix_linting(self):
             with open(self.outdir / config_fn, "w") as fh:
                 yaml.dump(nf_core_yml.model_dump(), fh, default_flow_style=False, sort_keys=False)
 
-        run_prettier_on_file(os.path.join(self.outdir, config_fn))
+            run_prettier_on_file(Path(self.outdir, config_fn))
 
     def make_pipeline_logo(self):
         """Fetch a logo for the new pipeline from the nf-core website"""
diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py
index bb27445e70..35cff5cab6 100644
--- a/tests/pipelines/test_create.py
+++ b/tests/pipelines/test_create.py
@@ -2,6 +2,7 @@
 
 import os
 import unittest
+from pathlib import Path
 
 import git
 import yaml
@@ -22,7 +23,8 @@ def setUp(self):
         self.pipeline_version = "1.0.0"
         self.default_branch = "default"
 
-    def test_pipeline_creation(self):
+    @with_temporary_folder
+    def test_pipeline_creation(self, tmp_path):
         pipeline = nf_core.pipelines.create.create.PipelineCreate(
             name=self.pipeline_name,
             description=self.pipeline_description,
@@ -30,6 +32,7 @@ def test_pipeline_creation(self):
             version=self.pipeline_version,
             no_git=False,
             force=True,
+            outdir=tmp_path,
             default_branch=self.default_branch,
         )
 
@@ -51,10 +54,10 @@ def test_pipeline_creation_initiation(self, tmp_path):
             default_branch=self.default_branch,
         )
         pipeline.init_pipeline()
-        assert os.path.isdir(os.path.join(pipeline.outdir, ".git"))
+        assert Path(pipeline.outdir, ".git").is_dir()
         assert f" {self.default_branch}\n" in git.Repo.init(pipeline.outdir).git.branch()
-        assert not os.path.exists(os.path.join(pipeline.outdir, "pipeline_template.yml"))
-        with open(os.path.join(pipeline.outdir, ".nf-core.yml")) as fh:
+        assert not Path(pipeline.outdir, "pipeline_template.yml").exists()
+        with open(Path(pipeline.outdir, ".nf-core.yml")) as fh:
             assert "template" in fh.read()
 
     @with_temporary_folder

From 1473611b9025ec4221e91fdbe0709723c59962b8 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 13:35:44 +0200
Subject: [PATCH 110/414] change import  strategy for lint tests

---
 nf_core/subworkflows/lint/__init__.py | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py
index a073710884..b366ddfb51 100644
--- a/nf_core/subworkflows/lint/__init__.py
+++ b/nf_core/subworkflows/lint/__init__.py
@@ -19,6 +19,14 @@
 
 log = logging.getLogger(__name__)
 
+# Import lint functions
+from .main_nf import main_nf  # type: ignore[misc]
+from .meta_yml import meta_yml  # type: ignore[misc]
+from .subworkflow_changes import subworkflow_changes  # type: ignore[misc]
+from .subworkflow_tests import subworkflow_tests  # type: ignore[misc]
+from .subworkflow_todos import subworkflow_todos  # type: ignore[misc]
+from .subworkflow_version import subworkflow_version  # type: ignore[misc]
+
 
 class SubworkflowLint(ComponentLint):
     """
@@ -26,13 +34,12 @@ class SubworkflowLint(ComponentLint):
     repository or in any nf-core pipeline directory
     """
 
-    # Import lint functions
-    from .main_nf import main_nf  # type: ignore[misc]
-    from .meta_yml import meta_yml  # type: ignore[misc]
-    from .subworkflow_changes import subworkflow_changes  # type: ignore[misc]
-    from .subworkflow_tests import subworkflow_tests  # type: ignore[misc]
-    from .subworkflow_todos import subworkflow_todos  # type: ignore[misc]
-    from .subworkflow_version import subworkflow_version  # type: ignore[misc]
+    main_nf = main_nf
+    meta_yml = meta_yml
+    subworkflow_changes = subworkflow_changes
+    subworkflow_tests = subworkflow_tests
+    subworkflow_todos = subworkflow_todos
+    subworkflow_version = subworkflow_version
 
     def __init__(
         self,

From 9dc61d61059bb2cb2b2bed4c7001251b01e863df Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 13:37:36 +0200
Subject: [PATCH 111/414] migrate to pathlib

---
 nf_core/components/components_command.py      | 40 +++++++++++--------
 nf_core/components/list.py                    |  3 +-
 nf_core/modules/modules_repo.py               | 10 +++--
 nf_core/pipelines/lint/actions_awsfulltest.py |  9 +++--
 nf_core/pipelines/lint/actions_awstest.py     |  6 +--
 nf_core/pipelines/lint/actions_ci.py          |  6 +--
 .../lint/actions_schema_validation.py         |  7 ++--
 nf_core/pipelines/lint/files_unchanged.py     |  8 ++--
 nf_core/pipelines/lint/merge_markers.py       | 32 +++++++--------
 nf_core/pipelines/lint/modules_structure.py   |  3 +-
 nf_core/pipelines/lint/nextflow_config.py     | 19 ++++-----
 nf_core/pipelines/lint/pipeline_todos.py      | 20 +++++-----
 nf_core/pipelines/lint/readme.py              |  6 +--
 13 files changed, 90 insertions(+), 79 deletions(-)

diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index a6b46d1b61..4440dc32a4 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -1,6 +1,5 @@
 import logging
 import mmap
-import os
 import shutil
 from pathlib import Path
 from typing import Dict, List, Optional, Union
@@ -22,7 +21,9 @@ class ComponentCommand:
     def __init__(
         self,
         component_type: str,
-        directory: Union[str, Path],
+        directory: Union[
+            str, Path
+        ],  # TODO: This is actually None sometimes (e.g. in test_modules_list_remote), need to rewrite the logic here to handle these cases elegantly, for example setting a default path
         remote_url: Optional[str] = None,
         branch: Optional[str] = None,
         no_pull: bool = False,
@@ -33,7 +34,7 @@ def __init__(
         Initialise the ComponentClass object
         """
         self.component_type = component_type
-        self.directory = Path(directory)
+        self.directory = directory
         self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)
         self.hide_progress = hide_progress
         self.no_prompts = no_prompts
@@ -47,18 +48,21 @@ def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
         Args:
             nf_dir_req (bool, optional): Whether this command requires being run in the nf-core modules repo or a nf-core pipeline repository. Defaults to True.
         """
-
         try:
             if self.directory:
-                self.directory, self.repo_type, self.org = get_repo_info(self.directory, use_prompt=not self.no_prompts)
+                self.directory, self.repo_type, self.org = get_repo_info(
+                    Path(self.directory), use_prompt=not self.no_prompts
+                )
             else:
                 self.repo_type = None
                 self.org = ""
+
         except UserWarning:
             if nf_dir_req:
                 raise
             self.repo_type = None
             self.org = ""
+
         self.default_modules_path = Path("modules", self.org)
         self.default_tests_path = Path("tests", "modules", self.org)
         self.default_subworkflows_path = Path("subworkflows", self.org)
@@ -82,8 +86,8 @@ def get_components_clone_modules(self) -> List[str]:
         elif self.component_type == "subworkflows":
             component_base_path = Path(self.directory, self.default_subworkflows_path)
         return [
-            str(Path(dir).relative_to(component_base_path))
-            for dir, _, files in os.walk(component_base_path)
+            str(Path(directory).relative_to(component_base_path))
+            for directory, _, files in Path.walk(component_base_path)
             if "main.nf" in files
         ]
 
@@ -91,12 +95,12 @@ def has_valid_directory(self) -> bool:
         """Check that we were given a pipeline or clone of nf-core/modules"""
         if self.repo_type == "modules":
             return True
-        if self.directory is None or not os.path.exists(self.directory):
+        if self.directory is None or not Path(self.directory).exists():
             log.error(f"Could not find directory: {self.directory}")
             return False
-        main_nf = os.path.join(self.directory, "main.nf")
-        nf_config = os.path.join(self.directory, "nextflow.config")
-        if not os.path.exists(main_nf) and not os.path.exists(nf_config):
+        main_nf = Path(self.directory, "main.nf")
+        nf_config = Path(self.directory, "nextflow.config")
+        if not main_nf.exists() and not nf_config.exists():
             if Path(self.directory).resolve().parts[-1].startswith("nf-core"):
                 raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'")
             log.warning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'")
@@ -104,8 +108,8 @@ def has_valid_directory(self) -> bool:
 
     def has_modules_file(self) -> None:
         """Checks whether a module.json file has been created and creates one if it is missing"""
-        modules_json_path = os.path.join(self.directory, "modules.json")
-        if not os.path.exists(modules_json_path):
+        modules_json_path = Path(self.directory, "modules.json")
+        if not modules_json_path.exists():
             log.info("Creating missing 'module.json' file.")
             ModulesJson(self.directory).create()
 
@@ -122,10 +126,10 @@ def clear_component_dir(self, component_name: str, component_dir: Union[str, Pat
         try:
             shutil.rmtree(component_dir)
             # remove all empty directories
-            for dir_path, dir_names, filenames in os.walk(self.directory, topdown=False):
+            for dir_path, dir_names, filenames in Path.walk(Path(self.directory), top_down=False):
                 if not dir_names and not filenames:
                     try:
-                        os.rmdir(dir_path)
+                        dir_path.rmdir()
                     except OSError:
                         pass
                     else:
@@ -152,7 +156,9 @@ def components_from_repo(self, install_dir: str) -> List[str]:
             raise LookupError(f"Nothing installed from {install_dir} in pipeline")
 
         return [
-            str(Path(dir_path).relative_to(repo_dir)) for dir_path, _, files in os.walk(repo_dir) if "main.nf" in files
+            str(Path(dir_path).relative_to(repo_dir))
+            for dir_path, _, files in Path.walk(repo_dir)
+            if "main.nf" in files
         ]
 
     def install_component_files(
@@ -196,7 +202,7 @@ def check_modules_structure(self) -> None:
         """
         if self.repo_type == "pipeline":
             wrong_location_modules: List[Path] = []
-            for directory, _, files in os.walk(Path(self.directory, "modules")):
+            for directory, _, files in Path.walk(Path(self.directory, "modules")):
                 if "main.nf" in files:
                     module_path = Path(directory).relative_to(Path(self.directory, "modules"))
                     parts = module_path.parts
diff --git a/nf_core/components/list.py b/nf_core/components/list.py
index 67468b4a5a..0a6b654467 100644
--- a/nf_core/components/list.py
+++ b/nf_core/components/list.py
@@ -1,5 +1,6 @@
 import json
 import logging
+from pathlib import Path
 from typing import Dict, List, Optional, Union, cast
 
 import rich.table
@@ -15,7 +16,7 @@ class ComponentList(ComponentCommand):
     def __init__(
         self,
         component_type: str,
-        pipeline_dir: str,
+        pipeline_dir: Union[str, Path],
         remote: bool = True,
         remote_url: Optional[str] = None,
         branch: Optional[str] = None,
diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py
index 7d576d4aef..bc92072e3b 100644
--- a/nf_core/modules/modules_repo.py
+++ b/nf_core/modules/modules_repo.py
@@ -63,16 +63,18 @@ def __init__(
         self.setup_local_repo(remote_url, branch, hide_progress)
 
         config_fn, repo_config = load_tools_config(self.local_repo_dir)
-        assert config_fn is not None and repo_config is not None  # mypy
+        if config_fn is None or repo_config is None:
+            raise UserWarning(f"Could not find a configuration file in {self.local_repo_dir}")
         try:
-            self.repo_path = repo_config["org_path"]
+            self.repo_path = repo_config.org_path
         except KeyError:
             raise UserWarning(f"'org_path' key not present in {config_fn.name}")
 
         # Verify that the repo seems to be correctly configured
         if self.repo_path != NF_CORE_MODULES_NAME or self.branch:
             self.verify_branch()
-
+        if self.repo_path is None:
+            raise UserWarning(f"Could not find the org_path in the configuration file: {config_fn.name}")
         # Convenience variable
         self.modules_dir = Path(self.local_repo_dir, "modules", self.repo_path)
         self.subworkflows_dir = Path(self.local_repo_dir, "subworkflows", self.repo_path)
@@ -96,7 +98,7 @@ def setup_local_repo(self, remote, branch, hide_progress=True, in_cache=False):
             branch (str): name of branch to use
         Sets self.repo
         """
-        self.local_repo_dir = os.path.join(NFCORE_DIR if not in_cache else NFCORE_CACHE_DIR, self.fullname)
+        self.local_repo_dir = Path(NFCORE_DIR if not in_cache else NFCORE_CACHE_DIR, self.fullname)
         try:
             if not os.path.exists(self.local_repo_dir):
                 try:
diff --git a/nf_core/pipelines/lint/actions_awsfulltest.py b/nf_core/pipelines/lint/actions_awsfulltest.py
index 4cf3bece28..7ea167f6c9 100644
--- a/nf_core/pipelines/lint/actions_awsfulltest.py
+++ b/nf_core/pipelines/lint/actions_awsfulltest.py
@@ -1,9 +1,10 @@
-import os
+from pathlib import Path
+from typing import Dict, List
 
 import yaml
 
 
-def actions_awsfulltest(self):
+def actions_awsfulltest(self) -> Dict[str, List[str]]:
     """Checks the GitHub Actions awsfulltest is valid.
 
     In addition to small test datasets run on GitHub Actions, we provide the possibility of testing the pipeline on full size datasets on AWS.
@@ -29,8 +30,8 @@ def actions_awsfulltest(self):
     warned = []
     failed = []
 
-    fn = os.path.join(self.wf_path, ".github", "workflows", "awsfulltest.yml")
-    if os.path.isfile(fn):
+    fn = Path(self.wf_path, ".github", "workflows", "awsfulltest.yml")
+    if fn.is_file():
         try:
             with open(fn) as fh:
                 wf = yaml.safe_load(fh)
diff --git a/nf_core/pipelines/lint/actions_awstest.py b/nf_core/pipelines/lint/actions_awstest.py
index 7c55998944..7e4c0fc497 100644
--- a/nf_core/pipelines/lint/actions_awstest.py
+++ b/nf_core/pipelines/lint/actions_awstest.py
@@ -1,4 +1,4 @@
-import os
+from pathlib import Path
 
 import yaml
 
@@ -22,8 +22,8 @@ def actions_awstest(self):
     * Must be turned on for ``workflow_dispatch``.
 
     """
-    fn = os.path.join(self.wf_path, ".github", "workflows", "awstest.yml")
-    if not os.path.isfile(fn):
+    fn = Path(self.wf_path, ".github", "workflows", "awstest.yml")
+    if not fn.is_file():
         return {"ignored": [f"'awstest.yml' workflow not found: `{fn}`"]}
 
     try:
diff --git a/nf_core/pipelines/lint/actions_ci.py b/nf_core/pipelines/lint/actions_ci.py
index a3e7d54b66..74f433ef80 100644
--- a/nf_core/pipelines/lint/actions_ci.py
+++ b/nf_core/pipelines/lint/actions_ci.py
@@ -1,4 +1,4 @@
-import os
+from pathlib import Path
 
 import yaml
 
@@ -40,10 +40,10 @@ def actions_ci(self):
     """
     passed = []
     failed = []
-    fn = os.path.join(self.wf_path, ".github", "workflows", "ci.yml")
+    fn = Path(self.wf_path, ".github", "workflows", "ci.yml")
 
     # Return an ignored status if we can't find the file
-    if not os.path.isfile(fn):
+    if not fn.is_file():
         return {"ignored": ["'.github/workflows/ci.yml' not found"]}
 
     try:
diff --git a/nf_core/pipelines/lint/actions_schema_validation.py b/nf_core/pipelines/lint/actions_schema_validation.py
index b4be42b54c..a057d80589 100644
--- a/nf_core/pipelines/lint/actions_schema_validation.py
+++ b/nf_core/pipelines/lint/actions_schema_validation.py
@@ -1,6 +1,5 @@
-import glob
 import logging
-import os
+from pathlib import Path
 from typing import Any, Dict, List
 
 import jsonschema
@@ -26,7 +25,7 @@ def actions_schema_validation(self) -> Dict[str, List[str]]:
     logging.getLogger("nf_core.pipelines.schema").setLevel(logging.ERROR)
 
     # Get all workflow files
-    action_workflows = glob.glob(os.path.join(self.wf_path, ".github/workflows/*.y*ml"))
+    action_workflows = list(Path(self.wf_path).glob(".github/workflows/*.y*ml"))
 
     # Load the GitHub workflow schema
     r = requests.get("https://json.schemastore.org/github-workflow", allow_redirects=True)
@@ -40,7 +39,7 @@ def actions_schema_validation(self) -> Dict[str, List[str]]:
 
     # Validate all workflows against the schema
     for wf_path in action_workflows:
-        wf = os.path.basename(wf_path)
+        wf = wf_path.name
 
         # load workflow
         try:
diff --git a/nf_core/pipelines/lint/files_unchanged.py b/nf_core/pipelines/lint/files_unchanged.py
index bafd8aec78..300b3674b2 100644
--- a/nf_core/pipelines/lint/files_unchanged.py
+++ b/nf_core/pipelines/lint/files_unchanged.py
@@ -112,7 +112,8 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]:
     logging.getLogger("nf_core.pipelines.create").setLevel(logging.ERROR)
 
     # Generate a new pipeline with nf-core create that we can compare to
-    tmp_dir = tempfile.mkdtemp()
+    tmp_dir = Path(tempfile.TemporaryDirectory().name)
+    tmp_dir.mkdir(parents=True)
 
     # Create a template.yaml file for the pipeline creation
     template_yaml = {
@@ -123,10 +124,11 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]:
     }
 
     template_yaml_path = Path(tmp_dir, "template.yaml")
+
     with open(template_yaml_path, "w") as fh:
         yaml.dump(template_yaml, fh, default_flow_style=False)
 
-    test_pipeline_dir = os.path.join(tmp_dir, f"{prefix}-{short_name}")
+    test_pipeline_dir = Path(tmp_dir, f"{prefix}-{short_name}")
     create_obj = nf_core.pipelines.create.create.PipelineCreate(
         None, None, None, no_git=True, outdir=test_pipeline_dir, template_config=template_yaml_path
     )
@@ -141,7 +143,7 @@ def _tf(file_path: Union[str, Path]) -> Path:
         """Helper function - get file path for template file"""
         return Path(test_pipeline_dir, file_path)
 
-    ignore_files = self.lint_config.get("files_unchanged", [])
+    ignore_files = self.lint_config.get("files_unchanged", []) if self.lint_config is not None else []
 
     # Files that must be completely unchanged from template
     for files in files_exact:
diff --git a/nf_core/pipelines/lint/merge_markers.py b/nf_core/pipelines/lint/merge_markers.py
index d57b63fd19..208c9f4bcc 100644
--- a/nf_core/pipelines/lint/merge_markers.py
+++ b/nf_core/pipelines/lint/merge_markers.py
@@ -1,6 +1,6 @@
 import fnmatch
 import logging
-import os
+from pathlib import Path
 
 import nf_core.utils
 
@@ -35,36 +35,36 @@ def merge_markers(self):
     failed = []
     ignored = []
 
-    ignored_config = self.lint_config.get("merge_markers", [])
+    ignored_config = self.lint_config.get("merge_markers", []) if self.lint_config is not None else []
 
     ignore = [".git"]
-    if os.path.isfile(os.path.join(self.wf_path, ".gitignore")):
-        with open(os.path.join(self.wf_path, ".gitignore"), encoding="latin1") as fh:
+    if Path(self.wf_path, ".gitignore").is_file():
+        with open(Path(self.wf_path, ".gitignore"), encoding="latin1") as fh:
             for line in fh:
-                ignore.append(os.path.basename(line.strip().rstrip("/")))
-    for root, dirs, files in os.walk(self.wf_path, topdown=True):
+                ignore.append(Path(line.strip().rstrip("/")).name)
+    for root, dirs, files in Path.walk(self.wf_path, top_down=True):
         # Ignore files
         for i_base in ignore:
-            i = os.path.join(root, i_base)
-            dirs[:] = [d for d in dirs if not fnmatch.fnmatch(os.path.join(root, d), i)]
-            files[:] = [f for f in files if not fnmatch.fnmatch(os.path.join(root, f), i)]
+            i = str(Path(root, i_base))
+            dirs[:] = [d for d in dirs if not fnmatch.fnmatch(str(Path(root, d)), i)]
+            files[:] = [f for f in files if not fnmatch.fnmatch(str(Path(root, f)), i)]
         for fname in files:
             # File ignored in config
-            if os.path.relpath(os.path.join(root, fname), self.wf_path) in ignored_config:
-                ignored.append(f"Ignoring file `{os.path.join(root, fname)}`")
+            if str(Path(root, fname).relative_to(self.wf_path)) in ignored_config:
+                ignored.append(f"Ignoring file `{Path(root, fname)}`")
                 continue
             # Skip binary files
-            if nf_core.utils.is_file_binary(os.path.join(root, fname)):
+            if nf_core.utils.is_file_binary(Path(root, fname)):
                 continue
             try:
-                with open(os.path.join(root, fname), encoding="latin1") as fh:
+                with open(Path(root, fname), encoding="latin1") as fh:
                     for line in fh:
                         if ">>>>>>>" in line:
-                            failed.append(f"Merge marker '>>>>>>>' in `{os.path.join(root, fname)}`: {line[:30]}")
+                            failed.append(f"Merge marker '>>>>>>>' in `{Path(root, fname)}`: {line[:30]}")
                         if "<<<<<<<" in line:
-                            failed.append(f"Merge marker '<<<<<<<' in `{os.path.join(root, fname)}`: {line[:30]}")
+                            failed.append(f"Merge marker '<<<<<<<' in `{Path(root, fname)}`: {line[:30]}")
             except FileNotFoundError:
-                log.debug(f"Could not open file {os.path.join(root, fname)} in merge_markers lint test")
+                log.debug(f"Could not open file {Path(root, fname)} in merge_markers lint test")
     if len(failed) == 0:
         passed.append("No merge markers found in pipeline files")
     return {"passed": passed, "failed": failed, "ignored": ignored}
diff --git a/nf_core/pipelines/lint/modules_structure.py b/nf_core/pipelines/lint/modules_structure.py
index 9d9b4c9fc0..fd29942ed6 100644
--- a/nf_core/pipelines/lint/modules_structure.py
+++ b/nf_core/pipelines/lint/modules_structure.py
@@ -1,5 +1,4 @@
 import logging
-import os
 from pathlib import Path
 
 log = logging.getLogger(__name__)
@@ -20,7 +19,7 @@ def modules_structure(self):
         modules/nf-core/modules/TOOL/SUBTOOL
     """
     wrong_location_modules = []
-    for directory, _, files in os.walk(Path(self.wf_path, "modules")):
+    for directory, _, files in Path.walk(Path(self.wf_path, "modules")):
         if "main.nf" in files:
             module_path = Path(directory).relative_to(Path(self.wf_path, "modules"))
             parts = module_path.parts
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index f62100a70a..96323af94d 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -1,14 +1,14 @@
 import logging
-import os
 import re
 from pathlib import Path
+from typing import Dict, List, Optional, Union
 
 from nf_core.pipelines.schema import PipelineSchema
 
 log = logging.getLogger(__name__)
 
 
-def nextflow_config(self):
+def nextflow_config(self) -> Dict[str, List[str]]:
     """Checks the pipeline configuration for required variables.
 
     All nf-core pipelines are required to be configured with a minimal set of variable
@@ -173,7 +173,7 @@ def nextflow_config(self):
     ]
 
     # Remove field that should be ignored according to the linting config
-    ignore_configs = self.lint_config.get("nextflow_config", [])
+    ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else []
 
     for cfs in config_fail:
         for cf in cfs:
@@ -205,12 +205,13 @@ def nextflow_config(self):
             failed.append(f"Config variable (incorrectly) found: {self._wrap_quotes(cf)}")
 
     # Check and warn if the process configuration is done with deprecated syntax
+
     process_with_deprecated_syntax = list(
         set(
             [
-                re.search(r"^(process\.\$.*?)\.+.*$", ck).group(1)
+                match.group(1)
                 for ck in self.nf_config.keys()
-                if re.match(r"^(process\.\$.*?)\.+.*$", ck)
+                if (match := re.match(r"^(process\.\$.*?)\.+.*$", ck)) is not None
             ]
         )
     )
@@ -313,7 +314,7 @@ def nextflow_config(self):
             r'System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")',
             r"}",
         ]
-        path = os.path.join(self.wf_path, "nextflow.config")
+        path = Path(self.wf_path, "nextflow.config")
         i = 0
         with open(path) as f:
             for line in f:
@@ -335,7 +336,7 @@ def nextflow_config(self):
             )
 
     # Check for the availability of the "test" configuration profile by parsing nextflow.config
-    with open(os.path.join(self.wf_path, "nextflow.config")) as f:
+    with open(Path(self.wf_path, "nextflow.config")) as f:
         content = f.read()
 
         # Remove comments
@@ -379,8 +380,8 @@ def nextflow_config(self):
         if param in ignore_defaults:
             ignored.append(f"Config default ignored: {param}")
         elif param in self.nf_config.keys():
-            config_default = None
-            schema_default = None
+            config_default: Optional[Union[str, float, int]] = None
+            schema_default: Optional[Union[str, float, int]] = None
             if schema.schema_types[param_name] == "boolean":
                 schema_default = str(schema.schema_defaults[param_name]).lower()
                 config_default = str(self.nf_config[param]).lower()
diff --git a/nf_core/pipelines/lint/pipeline_todos.py b/nf_core/pipelines/lint/pipeline_todos.py
index ba6ec79150..530d853764 100644
--- a/nf_core/pipelines/lint/pipeline_todos.py
+++ b/nf_core/pipelines/lint/pipeline_todos.py
@@ -1,6 +1,6 @@
 import fnmatch
 import logging
-import os
+from pathlib import Path
 
 log = logging.getLogger(__name__)
 
@@ -39,19 +39,19 @@ def pipeline_todos(self, root_dir=None):
         root_dir = self.wf_path
 
     ignore = [".git"]
-    if os.path.isfile(os.path.join(root_dir, ".gitignore")):
-        with open(os.path.join(root_dir, ".gitignore"), encoding="latin1") as fh:
+    if Path(root_dir, ".gitignore").is_file():
+        with open(Path(root_dir, ".gitignore"), encoding="latin1") as fh:
             for line in fh:
-                ignore.append(os.path.basename(line.strip().rstrip("/")))
-    for root, dirs, files in os.walk(root_dir, topdown=True):
+                ignore.append(Path(line.strip().rstrip("/")).name)
+    for root, dirs, files in Path.walk(root_dir, top_down=True):
         # Ignore files
         for i_base in ignore:
-            i = os.path.join(root, i_base)
-            dirs[:] = [d for d in dirs if not fnmatch.fnmatch(os.path.join(root, d), i)]
-            files[:] = [f for f in files if not fnmatch.fnmatch(os.path.join(root, f), i)]
+            i = str(Path(root, i_base))
+            dirs[:] = [d for d in dirs if not fnmatch.fnmatch(str(Path(root, d)), i)]
+            files[:] = [f for f in files if not fnmatch.fnmatch(str(Path(root, f)), i)]
         for fname in files:
             try:
-                with open(os.path.join(root, fname), encoding="latin1") as fh:
+                with open(Path(root, fname), encoding="latin1") as fh:
                     for line in fh:
                         if "TODO nf-core" in line:
                             line = (
@@ -63,7 +63,7 @@ def pipeline_todos(self, root_dir=None):
                                 .strip()
                             )
                             warned.append(f"TODO string in `{fname}`: _{line}_")
-                            file_paths.append(os.path.join(root, fname))
+                            file_paths.append(Path(root, fname))
             except FileNotFoundError:
                 log.debug(f"Could not open file {fname} in pipeline_todos lint test")
 
diff --git a/nf_core/pipelines/lint/readme.py b/nf_core/pipelines/lint/readme.py
index cade9ca3ea..4c16243690 100644
--- a/nf_core/pipelines/lint/readme.py
+++ b/nf_core/pipelines/lint/readme.py
@@ -1,5 +1,5 @@
-import os
 import re
+from pathlib import Path
 
 
 def readme(self):
@@ -29,9 +29,9 @@ def readme(self):
     failed = []
 
     # Remove field that should be ignored according to the linting config
-    ignore_configs = self.lint_config.get("readme", [])
+    ignore_configs = self.lint_config.get("readme", []) if self.lint_config is not None else []
 
-    with open(os.path.join(self.wf_path, "README.md")) as fh:
+    with open(Path(self.wf_path, "README.md")) as fh:
         content = fh.read()
 
     if "nextflow_badge" not in ignore_configs:

From 0a3cb5ffaea2026f55e6291f1f4f1ea73dc3cc4a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 14:09:35 +0200
Subject: [PATCH 112/414] fix mypy linting

---
 nf_core/modules/bump_versions.py   |  2 +-
 nf_core/pipelines/create/create.py | 13 +++++++------
 tests/pipelines/test_sync.py       |  2 +-
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
index 2d8854e3c0..6546cccc9a 100644
--- a/nf_core/modules/bump_versions.py
+++ b/nf_core/modules/bump_versions.py
@@ -76,7 +76,7 @@ def bump_versions(
             )
 
         # Get list of all modules
-        _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.directory)
+        _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(Path(self.directory))
 
         # Load the .nf-core.yml config
         _, self.tools_config = nf_core.utils.load_tools_config(self.directory)
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index f032db7f69..be07c0c290 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -8,7 +8,7 @@
 import re
 import shutil
 from pathlib import Path
-from typing import Dict, List, Optional, Union
+from typing import Dict, List, Optional, Union, cast
 
 import git
 import git.config
@@ -21,6 +21,7 @@
 from nf_core.pipelines.create.utils import CreateConfig
 from nf_core.pipelines.create_logo import create_logo
 from nf_core.pipelines.lint_utils import run_prettier_on_file
+from nf_core.utils import LintConfigType
 
 log = logging.getLogger(__name__)
 
@@ -57,7 +58,7 @@ def __init__(
         from_config_file: bool = False,
         default_branch: Optional[str] = None,
         is_interactive: bool = False,
-    ):
+    ) -> None:
         if isinstance(template_config, CreateConfig):
             self.config = template_config
         elif from_config_file:
@@ -418,13 +419,13 @@ def remove_nf_core_in_bug_report_template(self):
 
         run_prettier_on_file(bug_report_path)
 
-    def fix_linting(self):
+    def fix_linting(self) -> None:
         """
         Updates the .nf-core.yml with linting configurations
         for a customized pipeline.
         """
         # Create a lint config
-        short_name = self.jinja_params["short_name"]
+        short_name: str = self.jinja_params["short_name"]
         lint_config: Dict[str, List[str]] = {
             "files_exist": [
                 "CODE_OF_CONDUCT.md",
@@ -512,7 +513,7 @@ def fix_linting(self):
         # Add the lint content to the preexisting nf-core config
         config_fn, nf_core_yml = nf_core.utils.load_tools_config(self.outdir)
         if config_fn is not None and nf_core_yml is not None:
-            nf_core_yml.lint = lint_config
+            nf_core_yml.lint = cast(LintConfigType, lint_config)
             with open(self.outdir / config_fn, "w") as fh:
                 yaml.dump(nf_core_yml.model_dump(), fh, default_flow_style=False, sort_keys=False)
 
@@ -534,7 +535,7 @@ def make_pipeline_logo(self):
                 force=bool(self.force),
             )
 
-    def git_init_pipeline(self):
+    def git_init_pipeline(self) -> None:
         """Initialises the new pipeline as a Git repository and submits first commit.
 
         Raises:
diff --git a/tests/pipelines/test_sync.py b/tests/pipelines/test_sync.py
index b6955e6714..ffbe75510b 100644
--- a/tests/pipelines/test_sync.py
+++ b/tests/pipelines/test_sync.py
@@ -331,7 +331,7 @@ def test_close_open_template_merge_prs(self, mock_get):
 
     @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post)
     @mock.patch("nf_core.utils.gh_api.patch", side_effect=mocked_requests_patch)
-    def test_close_open_pr(self, mock_patch, mock_post):
+    def test_close_open_pr(self, mock_patch, mock_post) -> None:
         psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir)
         psync.inspect_sync_dir()
         psync.get_wf_config()

From b7b45dfab771a2a84ed05d368719f204133ec8a0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 14:09:47 +0200
Subject: [PATCH 113/414] fix circular import

---
 nf_core/__main__.py                    |  2 +-
 nf_core/components/components_utils.py | 16 +++++++++++++---
 nf_core/components/info.py             |  2 +-
 nf_core/components/install.py          |  2 +-
 nf_core/modules/modules_json.py        |  8 ++------
 nf_core/modules/modules_repo.py        |  6 +-----
 nf_core/synced_repo.py                 |  9 ++++-----
 tests/modules/test_modules_json.py     |  4 ++--
 tests/modules/test_update.py           |  2 +-
 tests/subworkflows/test_update.py      |  2 +-
 10 files changed, 27 insertions(+), 26 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index f33c63e87c..b86f8f4bad 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -52,7 +52,7 @@
     subworkflows_test,
     subworkflows_update,
 )
-from nf_core.modules.modules_repo import NF_CORE_MODULES_REMOTE
+from nf_core.components.components_utils import NF_CORE_MODULES_REMOTE
 from nf_core.pipelines.download import DownloadError
 from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir
 
diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py
index e4e2ff092b..4e9c0ac601 100644
--- a/nf_core/components/components_utils.py
+++ b/nf_core/components/components_utils.py
@@ -1,16 +1,23 @@
 import logging
 import re
 from pathlib import Path
-from typing import List, Optional, Tuple, Union
+from typing import TYPE_CHECKING, List, Optional, Tuple, Union
 
 import questionary
 import rich.prompt
 
+if TYPE_CHECKING:
+    from nf_core.modules.modules_repo import ModulesRepo
+
 import nf_core.utils
-from nf_core.modules.modules_repo import ModulesRepo
 
 log = logging.getLogger(__name__)
 
+# Constants for the nf-core/modules repo used throughout the module files
+NF_CORE_MODULES_NAME = "nf-core"
+NF_CORE_MODULES_REMOTE = "https://github.com/nf-core/modules.git"
+NF_CORE_MODULES_DEFAULT_BRANCH = "master"
+
 
 def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[Path, Optional[str], str]:
     """
@@ -82,7 +89,10 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P
 
 
 def prompt_component_version_sha(
-    component_name: str, component_type: str, modules_repo: ModulesRepo, installed_sha: Optional[str] = None
+    component_name: str,
+    component_type: str,
+    modules_repo: "ModulesRepo",
+    installed_sha: Optional[str] = None,
 ) -> str:
     """
     Creates an interactive questionary prompt for selecting the module/subworkflow version
diff --git a/nf_core/components/info.py b/nf_core/components/info.py
index a296fcaccf..55a95593f9 100644
--- a/nf_core/components/info.py
+++ b/nf_core/components/info.py
@@ -15,8 +15,8 @@
 
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
+from nf_core.components.components_utils import NF_CORE_MODULES_REMOTE
 from nf_core.modules.modules_json import ModulesJson
-from nf_core.modules.modules_repo import NF_CORE_MODULES_REMOTE
 
 log = logging.getLogger(__name__)
 
diff --git a/nf_core/components/install.py b/nf_core/components/install.py
index 8f47913283..f2849f85bc 100644
--- a/nf_core/components/install.py
+++ b/nf_core/components/install.py
@@ -12,11 +12,11 @@
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
 from nf_core.components.components_utils import (
+    NF_CORE_MODULES_NAME,
     get_components_to_install,
     prompt_component_version_sha,
 )
 from nf_core.modules.modules_json import ModulesJson
-from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME
 
 log = logging.getLogger(__name__)
 
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 01785c6d65..e9b4aa1025 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -14,12 +14,8 @@
 from git.exc import GitCommandError
 
 import nf_core.utils
-from nf_core.components.components_utils import get_components_to_install
-from nf_core.modules.modules_repo import (
-    NF_CORE_MODULES_NAME,
-    NF_CORE_MODULES_REMOTE,
-    ModulesRepo,
-)
+from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE, get_components_to_install
+from nf_core.modules.modules_repo import ModulesRepo
 from nf_core.pipelines.lint_utils import dump_json_with_prettier
 
 from .modules_differ import ModulesDiffer
diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py
index bc92072e3b..5b50205484 100644
--- a/nf_core/modules/modules_repo.py
+++ b/nf_core/modules/modules_repo.py
@@ -12,16 +12,12 @@
 
 import nf_core.modules.modules_json
 import nf_core.modules.modules_utils
+from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
 from nf_core.synced_repo import RemoteProgressbar, SyncedRepo
 from nf_core.utils import NFCORE_CACHE_DIR, NFCORE_DIR, load_tools_config
 
 log = logging.getLogger(__name__)
 
-# Constants for the nf-core/modules repo used throughout the module files
-NF_CORE_MODULES_NAME = "nf-core"
-NF_CORE_MODULES_REMOTE = "https://github.com/nf-core/modules.git"
-NF_CORE_MODULES_DEFAULT_BRANCH = "master"
-
 
 class ModulesRepo(SyncedRepo):
     """
diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py
index 8af0ee9a08..8efdd0e488 100644
--- a/nf_core/synced_repo.py
+++ b/nf_core/synced_repo.py
@@ -9,15 +9,14 @@
 import git
 from git.exc import GitCommandError
 
+from nf_core.components.components_utils import (
+    NF_CORE_MODULES_NAME,
+    NF_CORE_MODULES_REMOTE,
+)
 from nf_core.utils import load_tools_config
 
 log = logging.getLogger(__name__)
 
-# Constants for the nf-core/modules repo used throughout the module files
-NF_CORE_MODULES_NAME = "nf-core"
-NF_CORE_MODULES_REMOTE = "https://github.com/nf-core/modules.git"
-NF_CORE_MODULES_DEFAULT_BRANCH = "master"
-
 
 class RemoteProgressbar(git.RemoteProgress):
     """
diff --git a/tests/modules/test_modules_json.py b/tests/modules/test_modules_json.py
index 845f9c3e34..b2cac99e6d 100644
--- a/tests/modules/test_modules_json.py
+++ b/tests/modules/test_modules_json.py
@@ -3,13 +3,13 @@
 import shutil
 from pathlib import Path
 
-from nf_core.modules.modules_json import ModulesJson
-from nf_core.modules.modules_repo import (
+from nf_core.components.components_utils import (
     NF_CORE_MODULES_DEFAULT_BRANCH,
     NF_CORE_MODULES_NAME,
     NF_CORE_MODULES_REMOTE,
     ModulesRepo,
 )
+from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.patch import ModulePatch
 
 from ..test_modules import TestModules
diff --git a/tests/modules/test_update.py b/tests/modules/test_update.py
index 1f81eab487..6c8eacc666 100644
--- a/tests/modules/test_update.py
+++ b/tests/modules/test_update.py
@@ -8,9 +8,9 @@
 import yaml
 
 import nf_core.utils
+from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
 from nf_core.modules.install import ModuleInstall
 from nf_core.modules.modules_json import ModulesJson
-from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
 from nf_core.modules.patch import ModulePatch
 from nf_core.modules.update import ModuleUpdate
 
diff --git a/tests/subworkflows/test_update.py b/tests/subworkflows/test_update.py
index 7b17a621bc..153038cd1d 100644
--- a/tests/subworkflows/test_update.py
+++ b/tests/subworkflows/test_update.py
@@ -8,8 +8,8 @@
 import yaml
 
 import nf_core.utils
+from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
 from nf_core.modules.modules_json import ModulesJson
-from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
 from nf_core.modules.update import ModuleUpdate
 from nf_core.subworkflows.update import SubworkflowUpdate
 

From c6227a7cac8a909e54a46423a9626159ec6589b8 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 14:17:18 +0200
Subject: [PATCH 114/414] fix module command imports

---
 nf_core/commands_modules.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py
index 3d96d332b0..b93bd7bcb0 100644
--- a/nf_core/commands_modules.py
+++ b/nf_core/commands_modules.py
@@ -13,7 +13,7 @@ def modules_list_remote(ctx, keywords, json):
     """
     List modules in a remote GitHub repo [dim i](e.g [link=https://github.com/nf-core/modules]nf-core/modules[/])[/].
     """
-    from nf_core.modules import ModuleList
+    from nf_core.modules.list import ModuleList
 
     try:
         module_list = ModuleList(
@@ -33,7 +33,7 @@ def modules_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-b
     """
     List modules installed locally in a pipeline
     """
-    from nf_core.modules import ModuleList
+    from nf_core.modules.list import ModuleList
 
     try:
         module_list = ModuleList(
@@ -55,7 +55,7 @@ def modules_install(ctx, tool, dir, prompt, force, sha):
 
     Fetches and installs module files from a remote repo e.g. nf-core/modules.
     """
-    from nf_core.modules import ModuleInstall
+    from nf_core.modules.install import ModuleInstall
 
     try:
         module_install = ModuleInstall(
@@ -93,7 +93,7 @@ def modules_update(
 
     Fetches and updates module files from a remote repo e.g. nf-core/modules.
     """
-    from nf_core.modules import ModuleUpdate
+    from nf_core.modules.update import ModuleUpdate
 
     try:
         module_install = ModuleUpdate(
@@ -125,7 +125,7 @@ def modules_patch(ctx, tool, dir, remove):
     Checks if a module has been modified locally and creates a patch file
     describing how the module has changed from the remote version
     """
-    from nf_core.modules import ModulePatch
+    from nf_core.modules.patch import ModulePatch
 
     try:
         module_patch = ModulePatch(
@@ -147,7 +147,7 @@ def modules_remove(ctx, dir, tool):
     """
     Remove a module from a pipeline.
     """
-    from nf_core.modules import ModuleRemove
+    from nf_core.modules.remove import ModuleRemove
 
     try:
         module_remove = ModuleRemove(
@@ -194,7 +194,7 @@ def modules_create(
     elif no_meta:
         has_meta = False
 
-    from nf_core.modules import ModuleCreate
+    from nf_core.modules.create import ModuleCreate
 
     # Run function
     try:
@@ -257,7 +257,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed,
     nf-core/modules repository.
     """
     from nf_core.components.lint import LintExceptionError
-    from nf_core.modules import ModuleLint
+    from nf_core.modules.lint import ModuleLint
 
     try:
         module_lint = ModuleLint(
@@ -302,7 +302,7 @@ def modules_info(ctx, tool, dir):
     will print this usage info.
     If not, usage from the remote modules repo will be shown.
     """
-    from nf_core.modules import ModuleInfo
+    from nf_core.modules.info import ModuleInfo
 
     try:
         module_info = ModuleInfo(

From 847c683d22a44cb20129afb4b63bf94d529badb9 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 14:20:10 +0200
Subject: [PATCH 115/414] fix: cannot import name 'NotRequired'

---
 requirements-dev.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements-dev.txt b/requirements-dev.txt
index 82087edcba..aa43ee3fe3 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -14,6 +14,7 @@ types-Markdown
 types-PyYAML
 types-requests
 types-setuptools
+typing_extensions >=4.0.0
 pytest-asyncio
 pytest-textual-snapshot==0.4.0
 pytest-workflow>=2.0.0

From e7ac7812422e1d76fc67898c72058b6decb23322 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 16:12:12 +0200
Subject: [PATCH 116/414] more dir-> directory conversions

---
 nf_core/__main__.py           | 135 ++++++++++++++++++++--------------
 nf_core/commands_pipelines.py |  29 ++++----
 2 files changed, 95 insertions(+), 69 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index b86f8f4bad..91af979586 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -126,7 +126,7 @@
 # because they are actually preliminary, but intended program terminations.
 # (Custom exceptions are cleaner than `sys.exit(1)`, which we used before)
 def selective_traceback_hook(exctype, value, traceback):
-    if exctype in {DownloadError}:  # extend set as needed
+    if exctype in {DownloadError, UserWarning}:  # extend set as needed
         log.error(value)
     else:
         # print the colored traceback for all other exceptions with rich as usual
@@ -278,6 +278,7 @@ def command_pipelines_create(ctx, name, description, author, version, force, out
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory [dim]\[default: current working directory][/]",
@@ -331,7 +332,7 @@ def command_pipelines_create(ctx, name, description, author, version, force, out
 @click.pass_context
 def command_pipelines_lint(
     ctx,
-    dir,
+    directory,
     release,
     fix,
     key,
@@ -345,7 +346,7 @@ def command_pipelines_lint(
     """
     Check pipeline code against nf-core guidelines.
     """
-    pipelines_lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, sort_by)
+    pipelines_lint(ctx, directory, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, sort_by)
 
 
 # nf-core pipelines download
@@ -584,6 +585,7 @@ def command_pipelines_list(ctx, keywords, sort, json, show_archived):
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
@@ -610,11 +612,13 @@ def command_pipelines_list(ctx, keywords, sort, json, show_archived):
 @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.")
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
 @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
-def command_pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr):
+def command_pipelines_sync(
+    ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr
+):
     """
     Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template.
     """
-    pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr)
+    pipelines_sync(ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr)
 
 
 # nf-core pipelines bump-version
@@ -624,6 +628,7 @@ def command_pipelines_sync(ctx, dir, from_branch, pull_request, github_repositor
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
@@ -635,11 +640,11 @@ def command_pipelines_sync(ctx, dir, from_branch, pull_request, github_repositor
     default=False,
     help="Bump required nextflow version instead of pipeline version",
 )
-def command_pipelines_bump_version(ctx, new_version, dir, nextflow):
+def command_pipelines_bump_version(ctx, new_version, directory, nextflow):
     """
     Update nf-core pipeline version number with `nf-core pipelines bump-version`.
     """
-    pipelines_bump_version(ctx, new_version, dir, nextflow)
+    pipelines_bump_version(ctx, new_version, directory, nextflow)
 
 
 # nf-core pipelines create-logo
@@ -680,11 +685,11 @@ def command_pipelines_bump_version(ctx, new_version, dir, nextflow):
     default=False,
     help="Overwrite any files if they already exist",
 )
-def command_pipelines_create_logo(logo_text, dir, name, theme, width, format, force):
+def command_pipelines_create_logo(logo_text, directory, name, theme, width, format, force):
     """
     Generate a logo with the nf-core logo template.
     """
-    pipelines_create_logo(logo_text, dir, name, theme, width, format, force)
+    pipelines_create_logo(logo_text, directory, name, theme, width, format, force)
 
 
 # nf-core pipelines schema subcommands
@@ -715,6 +720,7 @@ def command_pipelines_schema_validate(pipeline, params):
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
@@ -735,11 +741,11 @@ def command_pipelines_schema_validate(pipeline, params):
     default="https://nf-co.re/pipeline_schema_builder",
     help="Customise the builder URL (for development work)",
 )
-def command_pipelines_schema_build(dir, no_prompts, web_only, url):
+def command_pipelines_schema_build(directory, no_prompts, web_only, url):
     """
     Interactively build a pipeline schema from Nextflow params.
     """
-    pipelines_schema_build(dir, no_prompts, web_only, url)
+    pipelines_schema_build(directory, no_prompts, web_only, url)
 
 
 # nf-core pipelines schema lint
@@ -864,15 +870,16 @@ def command_modules_list_remote(ctx, keywords, json):
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def command_modules_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
+def command_modules_list_local(ctx, keywords, json, directory):  # pylint: disable=redefined-builtin
     """
     List modules installed locally in a pipeline
     """
-    modules_list_local(ctx, keywords, json, dir)
+    modules_list_local(ctx, keywords, json, directory)
 
 
 # nf-core modules install
@@ -882,6 +889,7 @@ def command_modules_list_local(ctx, keywords, json, dir):  # pylint: disable=red
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
@@ -901,11 +909,11 @@ def command_modules_list_local(ctx, keywords, json, dir):  # pylint: disable=red
     help="Force reinstallation of module if it already exists",
 )
 @click.option("-s", "--sha", type=str, metavar="<commit sha>", help="Install module at commit SHA")
-def command_modules_install(ctx, tool, dir, prompt, force, sha):
+def command_modules_install(ctx, tool, directory, prompt, force, sha):
     """
     Install DSL2 modules within a pipeline.
     """
-    modules_install(ctx, tool, dir, prompt, force, sha)
+    modules_install(ctx, tool, directory, prompt, force, sha)
 
 
 # nf-core modules update
@@ -992,16 +1000,17 @@ def command_modules_update(
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
 @click.option("-r", "--remove", is_flag=True, default=False)
-def command_modules_patch(ctx, tool, dir, remove):
+def command_modules_patch(ctx, tool, directory, remove):
     """
     Create a patch file for minor changes in a module
     """
-    modules_patch(ctx, tool, dir, remove)
+    modules_patch(ctx, tool, directory, remove)
 
 
 # nf-core modules remove
@@ -1011,15 +1020,16 @@ def command_modules_patch(ctx, tool, dir, remove):
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
-def command_modules_remove(ctx, dir, tool):
+def command_modules_remove(ctx, directory, tool):
     """
     Remove a module from a pipeline.
     """
-    modules_remove(ctx, dir, tool)
+    modules_remove(ctx, directory, tool)
 
 
 # nf-core modules create
@@ -1092,7 +1102,7 @@ def command_modules_remove(ctx, dir, tool):
 def command_modules_create(
     ctx,
     tool,
-    dir,
+    directory,
     author,
     label,
     meta,
@@ -1109,7 +1119,7 @@ def command_modules_create(
     modules_create(
         ctx,
         tool,
-        dir,
+        directory,
         author,
         label,
         meta,
@@ -1129,6 +1139,7 @@ def command_modules_create(
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     metavar="<nf-core/modules directory>",
@@ -1154,11 +1165,11 @@ def command_modules_create(
     default=None,
     help="Run tests with a specific profile",
 )
-def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile):
+def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile):
     """
     Run nf-test for a module.
     """
-    modules_test(ctx, tool, dir, no_prompts, update, once, profile)
+    modules_test(ctx, tool, directory, no_prompts, update, once, profile)
 
 
 # nf-core modules lint
@@ -1168,6 +1179,7 @@ def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile):
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     metavar="<pipeline/modules directory>",
@@ -1204,11 +1216,11 @@ def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile):
     is_flag=True,
     help="Fix the module version if a newer version is available",
 )
-def command_modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version):
+def command_modules_lint(ctx, tool, directory, registry, key, all, fail_warned, local, passed, sort_by, fix_version):
     """
     Lint one or more modules in a directory.
     """
-    modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version)
+    modules_lint(ctx, tool, directory, registry, key, all, fail_warned, local, passed, sort_by, fix_version)
 
 
 # nf-core modules info
@@ -1218,15 +1230,16 @@ def command_modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local,
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def command_modules_info(ctx, tool, dir):
+def command_modules_info(ctx, tool, directory):
     """
     Show developer usage information about a given module.
     """
-    modules_info(ctx, tool, dir)
+    modules_info(ctx, tool, directory)
 
 
 # nf-core modules bump-versions
@@ -1236,18 +1249,19 @@ def command_modules_info(ctx, tool, dir):
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     metavar="<nf-core/modules directory>",
 )
 @click.option("-a", "--all", is_flag=True, help="Run on all modules")
 @click.option("-s", "--show-all", is_flag=True, help="Show up-to-date modules in results too")
-def command_modules_bump_versions(ctx, tool, dir, all, show_all):
+def command_modules_bump_versions(ctx, tool, directory, all, show_all):
     """
     Bump versions for one or more modules in a clone of
     the nf-core/modules repo.
     """
-    modules_bump_versions(ctx, tool, dir, all, show_all)
+    modules_bump_versions(ctx, tool, directory, all, show_all)
 
 
 # nf-core subworkflows click command
@@ -1313,11 +1327,11 @@ def subworkflows(ctx, git_remote, branch, no_pull):
     default=False,
     help="Migrate a module with pytest tests to nf-test",
 )
-def command_subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest):
+def command_subworkflows_create(ctx, subworkflow, directory, author, force, migrate_pytest):
     """
     Create a new subworkflow from the nf-core template.
     """
-    subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest)
+    subworkflows_create(ctx, subworkflow, directory, author, force, migrate_pytest)
 
 
 # nf-core subworkflows test
@@ -1327,6 +1341,7 @@ def command_subworkflows_create(ctx, subworkflow, dir, author, force, migrate_py
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     metavar="<nf-core/modules directory>",
@@ -1352,11 +1367,11 @@ def command_subworkflows_create(ctx, subworkflow, dir, author, force, migrate_py
     default=None,
     help="Run tests with a specific profile",
 )
-def command_subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile):
+def command_subworkflows_test(ctx, subworkflow, directory, no_prompts, update, once, profile):
     """
     Run nf-test for a subworkflow.
     """
-    subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile)
+    subworkflows_test(ctx, subworkflow, directory, no_prompts, update, once, profile)
 
 
 # nf-core subworkflows list subcommands
@@ -1389,15 +1404,16 @@ def command_subworkflows_list_remote(ctx, keywords, json):
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def command_subworkflows_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
+def command_subworkflows_list_local(ctx, keywords, json, directory):  # pylint: disable=redefined-builtin
     """
     List subworkflows installed locally in a pipeline
     """
-    subworkflows_list_local(ctx, keywords, json, dir)
+    subworkflows_list_local(ctx, keywords, json, directory)
 
 
 # nf-core subworkflows lint
@@ -1407,6 +1423,7 @@ def command_subworkflows_list_local(ctx, keywords, json, dir):  # pylint: disabl
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     metavar="<pipeline/modules directory>",
@@ -1438,11 +1455,11 @@ def command_subworkflows_list_local(ctx, keywords, json, dir):  # pylint: disabl
     help="Sort lint output by subworkflow or test name.",
     show_default=True,
 )
-def command_subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by):
+def command_subworkflows_lint(ctx, subworkflow, directory, registry, key, all, fail_warned, local, passed, sort_by):
     """
     Lint one or more subworkflows in a directory.
     """
-    subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by)
+    subworkflows_lint(ctx, subworkflow, directory, registry, key, all, fail_warned, local, passed, sort_by)
 
 
 # nf-core subworkflows info
@@ -1452,15 +1469,16 @@ def command_subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_wa
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def command_subworkflows_info(ctx, subworkflow, dir):
+def command_subworkflows_info(ctx, subworkflow, directory):
     """
     Show developer usage information about a given subworkflow.
     """
-    subworkflows_info(ctx, subworkflow, dir)
+    subworkflows_info(ctx, subworkflow, directory)
 
 
 # nf-core subworkflows install
@@ -1470,6 +1488,7 @@ def command_subworkflows_info(ctx, subworkflow, dir):
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
@@ -1495,11 +1514,11 @@ def command_subworkflows_info(ctx, subworkflow, dir):
     metavar="<commit sha>",
     help="Install subworkflow at commit SHA",
 )
-def command_subworkflows_install(ctx, subworkflow, dir, prompt, force, sha):
+def command_subworkflows_install(ctx, subworkflow, directory, prompt, force, sha):
     """
     Install DSL2 subworkflow within a pipeline.
     """
-    subworkflows_install(ctx, subworkflow, dir, prompt, force, sha)
+    subworkflows_install(ctx, subworkflow, directory, prompt, force, sha)
 
 
 # nf-core subworkflows remove
@@ -1509,15 +1528,16 @@ def command_subworkflows_install(ctx, subworkflow, dir, prompt, force, sha):
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
-def command_subworkflows_remove(ctx, dir, subworkflow):
+def command_subworkflows_remove(ctx, directory, subworkflow):
     """
     Remove a subworkflow from a pipeline.
     """
-    subworkflows_remove(ctx, dir, subworkflow)
+    subworkflows_remove(ctx, directory, subworkflow)
 
 
 # nf-core subworkflows update
@@ -1527,6 +1547,7 @@ def command_subworkflows_remove(ctx, dir, subworkflow):
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
@@ -1587,7 +1608,7 @@ def command_subworkflows_remove(ctx, dir, subworkflow):
 def command_subworkflows_update(
     ctx,
     subworkflow,
-    dir,
+    directory,
     force,
     prompt,
     sha,
@@ -1601,7 +1622,7 @@ def command_subworkflows_update(
     Update DSL2 subworkflow within a pipeline.
     """
     subworkflows_update(
-        ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save_diff, update_deps, limit_output
+        ctx, subworkflow, directory, force, prompt, sha, install_all, preview, save_diff, update_deps, limit_output
     )
 
 
@@ -1636,6 +1657,7 @@ def command_schema_validate(pipeline, params):
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
@@ -1656,14 +1678,14 @@ def command_schema_validate(pipeline, params):
     default="https://nf-co.re/pipeline_schema_builder",
     help="Customise the builder URL (for development work)",
 )
-def command_schema_build(dir, no_prompts, web_only, url):
+def command_schema_build(directory, no_prompts, web_only, url):
     """
     Use `nf-core pipelines schema build` instead.
     """
     log.warning(
         "The `[magenta]nf-core schema build[/]` command is deprecated. Use `[magenta]nf-core pipelines schema build[/]` instead."
     )
-    pipelines_schema_build(dir, no_prompts, web_only, url)
+    pipelines_schema_build(directory, no_prompts, web_only, url)
 
 
 # nf-core schema lint (deprecated)
@@ -1764,14 +1786,14 @@ def command_schema_docs(schema_path, output, format, force, columns):
     default=False,
     help="Overwrite any files if they already exist",
 )
-def command_create_logo(logo_text, dir, name, theme, width, format, force):
+def command_create_logo(logo_text, directory, name, theme, width, format, force):
     """
     Use `nf-core pipelines create-logo` instead.
     """
     log.warning(
         "The `[magenta]nf-core create-logo[/]` command is deprecated. Use `[magenta]nf-core pipelines screate-logo[/]` instead."
     )
-    pipelines_create_logo(logo_text, dir, name, theme, width, format, force)
+    pipelines_create_logo(logo_text, directory, name, theme, width, format, force)
 
 
 # nf-core sync (deprecated)
@@ -1779,6 +1801,7 @@ def command_create_logo(logo_text, dir, name, theme, width, format, force):
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
@@ -1805,14 +1828,14 @@ def command_create_logo(logo_text, dir, name, theme, width, format, force):
 @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.")
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
 @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
-def command_sync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr):
+def command_sync(directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr):
     """
     Use `nf-core pipelines sync` instead.
     """
     log.warning(
         "The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead."
     )
-    pipelines_sync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr)
+    pipelines_sync(directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr)
 
 
 # nf-core bump-version (deprecated)
@@ -1822,6 +1845,7 @@ def command_sync(dir, from_branch, pull_request, github_repository, username, te
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
@@ -1833,14 +1857,14 @@ def command_sync(dir, from_branch, pull_request, github_repository, username, te
     default=False,
     help="Bump required nextflow version instead of pipeline version",
 )
-def command_bump_version(ctx, new_version, dir, nextflow):
+def command_bump_version(ctx, new_version, directory, nextflow):
     """
     Use `nf-core pipelines bump-version` instead.
     """
     log.warning(
         "The `[magenta]nf-core bump-version[/]` command is deprecated. Use `[magenta]nf-core pipelines bump-version[/]` instead."
     )
-    pipelines_bump_version(ctx, new_version, dir, nextflow)
+    pipelines_bump_version(ctx, new_version, directory, nextflow)
 
 
 # nf-core list (deprecated)
@@ -2086,6 +2110,7 @@ def command_download(
 @click.option(
     "-d",
     "--dir",
+    "directory",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory [dim]\[default: current working directory][/]",
@@ -2139,7 +2164,7 @@ def command_download(
 @click.pass_context
 def command_lint(
     ctx,
-    dir,
+    directory,
     release,
     fix,
     key,
@@ -2156,7 +2181,7 @@ def command_lint(
     log.warning(
         "The `[magenta]nf-core lint[/]` command is deprecated. Use `[magenta]nf-core pipelines lint[/]` instead."
     )
-    pipelines_lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, sort_by)
+    pipelines_lint(ctx, directory, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, sort_by)
 
 
 # nf-core create (deprecated)
diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py
index 432a36aaee..c586534b22 100644
--- a/nf_core/commands_pipelines.py
+++ b/nf_core/commands_pipelines.py
@@ -60,7 +60,7 @@ def pipelines_create(ctx, name, description, author, version, force, outdir, tem
 
 
 # nf-core pipelines bump-version
-def pipelines_bump_version(ctx, new_version, dir, nextflow):
+def pipelines_bump_version(ctx, new_version, directory, nextflow):
     """
     Update nf-core pipeline version number.
 
@@ -78,10 +78,10 @@ def pipelines_bump_version(ctx, new_version, dir, nextflow):
 
     try:
         # Check if pipeline directory contains necessary files
-        is_pipeline_directory(dir)
+        is_pipeline_directory(directory)
 
         # Make a pipeline object and load config etc
-        pipeline_obj = Pipeline(dir)
+        pipeline_obj = Pipeline(directory)
         pipeline_obj._load()
 
         # Bump the pipeline version number
@@ -97,7 +97,7 @@ def pipelines_bump_version(ctx, new_version, dir, nextflow):
 # nf-core pipelines lint
 def pipelines_lint(
     ctx,
-    dir,
+    directory,
     release,
     fix,
     key,
@@ -123,7 +123,7 @@ def pipelines_lint(
 
     # Check if pipeline directory is a pipeline
     try:
-        is_pipeline_directory(dir)
+        is_pipeline_directory(directory)
     except UserWarning as e:
         log.error(e)
         sys.exit(1)
@@ -131,7 +131,7 @@ def pipelines_lint(
     # Run the lint tests!
     try:
         lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting(
-            dir,
+            directory,
             release,
             fix,
             key,
@@ -279,7 +279,7 @@ def pipelines_list(ctx, keywords, sort, json, show_archived):
 
 
 # nf-core pipelines sync
-def pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr):
+def pipelines_sync(ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr):
     """
     Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template.
 
@@ -295,12 +295,13 @@ def pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, usern
     from nf_core.pipelines.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError
     from nf_core.utils import is_pipeline_directory
 
-    # Check if pipeline directory contains necessary files
-    is_pipeline_directory(dir)
-
-    # Sync the given pipeline dir
-    sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr)
     try:
+        # Check if pipeline directory contains necessary files
+        is_pipeline_directory(directory)
+        # Sync the given pipeline dir
+        sync_obj = PipelineSync(
+            directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr
+        )
         sync_obj.sync()
     except (SyncExceptionError, PullRequestExceptionError) as e:
         log.error(e)
@@ -360,7 +361,7 @@ def pipelines_schema_validate(pipeline, params):
 
 
 # nf-core pipelines schema build
-def pipelines_schema_build(dir, no_prompts, web_only, url):
+def pipelines_schema_build(directory, no_prompts, web_only, url):
     """
     Interactively build a pipeline schema from Nextflow params.
 
@@ -376,7 +377,7 @@ def pipelines_schema_build(dir, no_prompts, web_only, url):
 
     try:
         schema_obj = PipelineSchema()
-        if schema_obj.build_schema(dir, no_prompts, web_only, url) is False:
+        if schema_obj.build_schema(directory, no_prompts, web_only, url) is False:
             sys.exit(1)
     except (UserWarning, AssertionError) as e:
         log.error(e)

From 5a8ae1240e646413d3c483cb8d67f8d1581495cb Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 16:18:50 +0200
Subject: [PATCH 117/414] fix pydantic warnings

---
 nf_core/pipelines/create/create.py | 28 ++++++++++++----------------
 nf_core/pipelines/sync.py          |  2 +-
 nf_core/utils.py                   |  8 ++++++--
 3 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index be07c0c290..a2df9aeefc 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -21,7 +21,7 @@
 from nf_core.pipelines.create.utils import CreateConfig
 from nf_core.pipelines.create_logo import create_logo
 from nf_core.pipelines.lint_utils import run_prettier_on_file
-from nf_core.utils import LintConfigType
+from nf_core.utils import LintConfigType, NFCoreTemplateConfig
 
 log = logging.getLogger(__name__)
 
@@ -111,7 +111,7 @@ def __init__(
         self.is_interactive = is_interactive
         self.force = self.config.force
         if self.config.outdir is None:
-            self.config.outdir = os.getcwd()
+            self.config.outdir = str(Path.cwd())
         if self.config.outdir == ".":
             self.outdir = Path(self.config.outdir, self.jinja_params["name_noslash"]).absolute()
         else:
@@ -289,13 +289,13 @@ def render_template(self):
                 log.info("Use -f / --force to overwrite existing files")
                 raise UserWarning(f"Output directory '{self.outdir}' exists!")
         else:
-            os.makedirs(self.outdir)
+            self.outdir.mkdir(parents=True, exist_ok=True)
 
         # Run jinja2 for each file in the template folder
         env = jinja2.Environment(
             loader=jinja2.PackageLoader("nf_core", "pipeline-template"), keep_trailing_newline=True
         )
-        template_dir = os.path.join(os.path.dirname(nf_core.__file__), "pipeline-template")
+        template_dir = Path(nf_core.__file__).parent / "pipeline-template"
         object_attrs = self.jinja_params
         object_attrs["nf_core_version"] = nf_core.__version__
 
@@ -310,26 +310,24 @@ def render_template(self):
         }
 
         # Set the paths to skip according to customization
-        for template_fn_path_obj in template_files:
-            template_fn_path = str(template_fn_path_obj)
-
+        for template_fn_path in template_files:
             # Skip files that are in the self.skip_paths list
             for skip_path in self.skip_paths:
-                if os.path.relpath(template_fn_path, template_dir).startswith(skip_path):
+                if str(template_fn_path.relative_to(template_dir)).startswith(skip_path):
                     break
             else:
-                if os.path.isdir(template_fn_path):
+                if template_fn_path.is_dir():
                     continue
-                if any([s in template_fn_path for s in ignore_strs]):
+                if any([s in str(template_fn_path) for s in ignore_strs]):
                     log.debug(f"Ignoring '{template_fn_path}' in jinja2 template creation")
                     continue
 
                 # Set up vars and directories
-                template_fn = os.path.relpath(template_fn_path, template_dir)
+                template_fn = template_fn_path.relative_to(template_dir)
                 output_path = self.outdir / template_fn
                 if template_fn in rename_files:
                     output_path = self.outdir / rename_files[template_fn]
-                os.makedirs(os.path.dirname(output_path), exist_ok=True)
+                output_path.parent.mkdir(parents=True, exist_ok=True)
 
                 try:
                     # Just copy binary files
@@ -338,7 +336,7 @@ def render_template(self):
 
                     # Got this far - render the template
                     log.debug(f"Rendering template file: '{template_fn}'")
-                    j_template = env.get_template(template_fn)
+                    j_template = env.get_template(str(template_fn))
                     rendered_output = j_template.render(object_attrs)
 
                     # Write to the pipeline output file
@@ -379,9 +377,7 @@ def render_template(self):
             config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir)
             if config_fn is not None and config_yml is not None:
                 with open(str(config_fn), "w") as fh:
-                    config_yml.template = self.config.model_dump()
-                    # convert posix path to string for yaml dump
-                    config_yml["template"]["outdir"] = str(config_yml["template"]["outdir"])
+                    config_yml.template = NFCoreTemplateConfig(**self.config.model_dump())
                     yaml.safe_dump(config_yml.model_dump(), fh)
                     log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
                     run_prettier_on_file(self.outdir / config_fn)
diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index b1da99a626..d044be84e4 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -274,7 +274,7 @@ def make_template_pipeline(self):
                 version=self.wf_config["manifest.version"].strip('"').strip("'"),
                 no_git=True,
                 force=True,
-                outdir=self.pipeline_dir,
+                outdir=str(self.pipeline_dir),
                 author=self.wf_config["manifest.author"].strip('"').strip("'"),
             ).init_pipeline()
         except Exception as err:
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 6794cf04fe..0beb8c7366 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -1052,6 +1052,12 @@ class NFCoreTemplateConfig(BaseModel):
     skip_features: Optional[list] = None
     is_nfcore: Optional[bool] = None
 
+    def __getitem__(self, item: str) -> Any:
+        return getattr(self, item)
+
+    def get(self, item: str, default: Any = None) -> Any:
+        return getattr(self, item, default)
+
 
 LintConfigType = Optional[Dict[str, Union[List[str], List[Dict[str, List[str]]], bool]]]
 
@@ -1086,7 +1092,6 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path]
     tools_config = {}
 
     config_fn = get_first_available_path(directory, CONFIG_PATHS)
-
     if config_fn is None:
         depr_path = get_first_available_path(directory, DEPRECATED_CONFIG_PATHS)
         if depr_path:
@@ -1102,7 +1107,6 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path]
     # If the file is empty
     if tools_config is None:
         raise AssertionError(f"Config file '{config_fn}' is empty")
-
     # Check for required fields
     try:
         nf_core_yaml_config = NFCoreYamlConfig(**tools_config)

From ac1ea23974df7182c02a2619a2363010590c1b23 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 16:30:53 +0200
Subject: [PATCH 118/414] fix notrequired not found

---
 nf_core/modules/modules_json.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index e9b4aa1025..f992271741 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -6,12 +6,13 @@
 import shutil
 import tempfile
 from pathlib import Path
-from typing import Dict, List, NotRequired, Optional, Tuple, TypedDict, Union
+from typing import Dict, List, Optional, Tuple, Union
 
 import git
 import questionary
 import rich.prompt
 from git.exc import GitCommandError
+from typing_extensions import NotRequired, TypedDict  # for py<3.11
 
 import nf_core.utils
 from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE, get_components_to_install

From 79727c0b430f495468011233ec3b761d275a7be7 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 17:28:53 +0200
Subject: [PATCH 119/414] fix pydantic type

---
 nf_core/pipelines/create/create.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index a2df9aeefc..127b1f607a 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -378,6 +378,7 @@ def render_template(self):
             if config_fn is not None and config_yml is not None:
                 with open(str(config_fn), "w") as fh:
                     config_yml.template = NFCoreTemplateConfig(**self.config.model_dump())
+                    config_yml.template.outdir = str(config_yml.template.outdir)
                     yaml.safe_dump(config_yml.model_dump(), fh)
                     log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
                     run_prettier_on_file(self.outdir / config_fn)

From ee67c5fdd7f764f1f16f10f28e75f6f1f45941f5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 17:31:34 +0200
Subject: [PATCH 120/414] fix before model creation

---
 nf_core/pipelines/create/create.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 127b1f607a..acbe7efd5c 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -377,8 +377,9 @@ def render_template(self):
             config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir)
             if config_fn is not None and config_yml is not None:
                 with open(str(config_fn), "w") as fh:
+                    self.config.outdir = str(self.config.outdir)
                     config_yml.template = NFCoreTemplateConfig(**self.config.model_dump())
-                    config_yml.template.outdir = str(config_yml.template.outdir)
+
                     yaml.safe_dump(config_yml.model_dump(), fh)
                     log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
                     run_prettier_on_file(self.outdir / config_fn)

From dae348e4de483f5b24f92bcc41ddb1b843f688bf Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Thu, 25 Jul 2024 17:33:33 +0200
Subject: [PATCH 121/414] fix modules repo import error

---
 tests/modules/test_modules_json.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/test_modules_json.py b/tests/modules/test_modules_json.py
index b2cac99e6d..0368c146c4 100644
--- a/tests/modules/test_modules_json.py
+++ b/tests/modules/test_modules_json.py
@@ -7,9 +7,9 @@
     NF_CORE_MODULES_DEFAULT_BRANCH,
     NF_CORE_MODULES_NAME,
     NF_CORE_MODULES_REMOTE,
-    ModulesRepo,
 )
 from nf_core.modules.modules_json import ModulesJson
+from nf_core.modules.modules_repo import ModulesRepo
 from nf_core.modules.patch import ModulePatch
 
 from ..test_modules import TestModules

From 9ed6cdcc28d4be17175ae5a4a98f5278949c3db9 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Wed, 24 Jul 2024 15:55:30 +0000
Subject: [PATCH 122/414] Update python:3.12-slim Docker digest to 740d94a

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 8943b70627..c88abcb1ce 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:f11725aba18c19664a408902103365eaf8013823ffc56270f921d1dc78a198cb
+FROM python:3.12-slim@sha256:740d94a19218c8dd584b92f804b1158f85b0d241e5215ea26ed2dcade2b9d138
 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for nf-core/tools"
 

From 7b4d135569320507bdbfb99ff459aa4d195d9357 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 25 Jul 2024 17:51:32 +0000
Subject: [PATCH 123/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b407f5349a..b27dce4b5c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -53,6 +53,7 @@
 - handle new jsonschema error type ([#3061](https://github.com/nf-core/tools/pull/3061))
 - Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071))
 - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074))
+- Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From fcc859ef3da2d369c5a5fc7e031d8dcd03d5a72b Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Thu, 25 Jul 2024 19:45:20 +0000
Subject: [PATCH 124/414] Update pre-commit hook pre-commit/mirrors-mypy to
 v1.11.0

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index fc2011cb99..63202e5178 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -19,7 +19,7 @@ repos:
         alias: ec
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.10.1"
+    rev: "v1.11.0"
     hooks:
       - id: mypy
         additional_dependencies:

From baa1a3c27c9ae947db118f22ba7a3e0b746f9dfd Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Thu, 25 Jul 2024 20:04:49 +0000
Subject: [PATCH 125/414] Update gitpod/workspace-base Docker digest to f189a41

---
 nf_core/gitpod/gitpod.Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
index 2f458dfc2a..fd0e8bb799 100644
--- a/nf_core/gitpod/gitpod.Dockerfile
+++ b/nf_core/gitpod/gitpod.Dockerfile
@@ -1,7 +1,7 @@
 # Test build locally before making a PR
 #   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
 
-FROM gitpod/workspace-base@sha256:0f3822450f94084f6a62db4a4282d895591f6a55632dc044fe496f98cb79e75c
+FROM gitpod/workspace-base@sha256:f189a4195c3861365356f9c1b438ab26fd88e1ff46ce2843afc62861fc982e0c
 
 USER root
 

From b53a4b82436f0313fa5c0896e9edd869c3043084 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 09:30:22 +0200
Subject: [PATCH 126/414] fix incorrect type name

---
 nf_core/modules/modules_differ.py | 6 +++---
 nf_core/modules/modules_json.py   | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py
index 36d927f084..e310b3bf8b 100644
--- a/nf_core/modules/modules_differ.py
+++ b/nf_core/modules/modules_differ.py
@@ -4,7 +4,7 @@
 import logging
 import os
 from pathlib import Path
-from typing import List, Union
+from typing import Dict, List, Union
 
 from rich.console import Console
 from rich.syntax import Syntax
@@ -296,7 +296,7 @@ def print_diff(
                 console.print(Syntax("".join(diff), "diff", theme="ansi_dark", padding=1))
 
     @staticmethod
-    def per_file_patch(patch_fn: Union[str, Path]) -> dict[str, List[str]]:
+    def per_file_patch(patch_fn: Union[str, Path]) -> Dict[str, List[str]]:
         """
         Splits a patch file for several files into one patch per file.
 
@@ -453,7 +453,7 @@ def try_apply_single_patch(file_lines, patch, reverse=False):
     @staticmethod
     def try_apply_patch(
         module: str, repo_path: Union[str, Path], patch_path: Union[str, Path], module_dir: Path, reverse: bool = False
-    ) -> dict[str, List[str]]:
+    ) -> Dict[str, List[str]]:
         """
         Try applying a full patch file to a module
 
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index f992271741..4f3578b02b 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -1000,7 +1000,7 @@ def get_subworkflow_version(self, subworkflow_name, repo_url, install_dir):
             .get("git_sha", None)
         )
 
-    def get_all_components(self, component_type: str) -> dict[str, List[Tuple[(str, str)]]]:
+    def get_all_components(self, component_type: str) -> Dict[str, List[Tuple[(str, str)]]]:
         """
         Retrieves all pipeline modules/subworkflows that are reported in the modules.json
 

From bdbdd17a24c8aee70339f22d0bc0994c2f65fe4e Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 11:50:17 +0200
Subject: [PATCH 127/414] fix types

---
 nf_core/pipelines/create/create.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index acbe7efd5c..5e57d27c3b 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -81,8 +81,11 @@ def __init__(
         else:
             raise UserWarning("The template configuration was not provided.")
 
+        if self.config.outdir is None:
+            self.config.outdir = str(Path.cwd())
+
         self.jinja_params, skip_paths = self.obtain_jinja_params_dict(
-            self.config.skip_features or [], self.config.outdir
+            self.config.skip_features or [], Path(self.config.outdir)
         )
 
         skippable_paths = {
@@ -110,8 +113,7 @@ def __init__(
         self.default_branch = default_branch
         self.is_interactive = is_interactive
         self.force = self.config.force
-        if self.config.outdir is None:
-            self.config.outdir = str(Path.cwd())
+
         if self.config.outdir == ".":
             self.outdir = Path(self.config.outdir, self.jinja_params["name_noslash"]).absolute()
         else:
@@ -184,7 +186,7 @@ def update_config(self, organisation, version, force, outdir):
         if self.config.is_nfcore is None:
             self.config.is_nfcore = self.config.org == "nf-core"
 
-    def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
+    def obtain_jinja_params_dict(self, features_to_skip: List[str], pipeline_dir: Union[str, Path]):
         """Creates a dictionary of parameters for the new pipeline.
 
         Args:
@@ -379,7 +381,6 @@ def render_template(self):
                 with open(str(config_fn), "w") as fh:
                     self.config.outdir = str(self.config.outdir)
                     config_yml.template = NFCoreTemplateConfig(**self.config.model_dump())
-
                     yaml.safe_dump(config_yml.model_dump(), fh)
                     log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
                     run_prettier_on_file(self.outdir / config_fn)

From 98c3fb0178a4548fcab1db5055cedd1586f0c915 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 11:54:07 +0200
Subject: [PATCH 128/414] fix type definition for older python version

---
 nf_core/modules/modules_json.py        | 2 +-
 nf_core/pipelines/lint/modules_json.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 4f3578b02b..9f17add6ae 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -115,7 +115,7 @@ def create(self) -> None:
         self.dump()
 
     def get_component_names_from_repo(
-        self, repos: Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, str | List[str]]]]]], directory: Path
+        self, repos: Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, Union[str, List[str]]]]]]], directory: Path
     ) -> List[Tuple[str, List[str], str]]:
         """
         Get component names from repositories in a pipeline.
diff --git a/nf_core/pipelines/lint/modules_json.py b/nf_core/pipelines/lint/modules_json.py
index 5ce2054036..2b7c266848 100644
--- a/nf_core/pipelines/lint/modules_json.py
+++ b/nf_core/pipelines/lint/modules_json.py
@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import Dict, List
+from typing import Dict, List, Union
 
 from nf_core.modules.modules_json import ModulesJson, ModulesJsonType
 
@@ -19,7 +19,7 @@ def modules_json(self) -> Dict[str, List[str]]:
     # Load pipeline modules and modules.json
     _modules_json = ModulesJson(self.wf_path)
     _modules_json.load()
-    modules_json_dict: ModulesJsonType | None = _modules_json.modules_json
+    modules_json_dict: Union[ModulesJsonType, None] = _modules_json.modules_json
     modules_dir = Path(self.wf_path, "modules")
 
     if _modules_json and modules_json_dict is not None:

From 7b883eb1f01bac9249428a3821c9a4454dc715ca Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 12:11:41 +0200
Subject: [PATCH 129/414] fix incorrect types and missing cli option names

---
 nf_core/__main__.py                |  6 +++---
 nf_core/pipelines/create/create.py |  9 +++++----
 nf_core/pipelines/sync.py          | 21 +++++++++++----------
 3 files changed, 19 insertions(+), 17 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 91af979586..d0aad63e80 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1036,7 +1036,7 @@ def command_modules_remove(ctx, directory, tool):
 @modules.command("create")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
-@click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<directory>")
+@click.option("-d", "--dir", "directory", type=click.Path(exists=True), default=".", metavar="<directory>")
 @click.option(
     "-a",
     "--author",
@@ -1306,7 +1306,7 @@ def subworkflows(ctx, git_remote, branch, no_pull):
 @subworkflows.command("create")
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
-@click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<directory>")
+@click.option("-d", "--dir", "directory", type=click.Path(exists=True), default=".", metavar="<directory>")
 @click.option(
     "-a",
     "--author",
@@ -1751,7 +1751,7 @@ def command_schema_docs(schema_path, output, format, force, columns):
 # nf-core create-logo (deprecated)
 @nf_core_cli.command("create-logo", deprecated=True, hidden=True)
 @click.argument("logo-text", metavar="<logo_text>")
-@click.option("-d", "--dir", type=click.Path(), default=".", help="Directory to save the logo in.")
+@click.option("-d", "--dir", "directory", type=click.Path(), default=".", help="Directory to save the logo in.")
 @click.option(
     "-n",
     "--name",
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 5e57d27c3b..15eed46dce 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -278,7 +278,7 @@ def init_pipeline(self):
                 "https://nf-co.re/docs/tutorials/adding_a_pipeline/overview#join-the-community[/link]"
             )
 
-    def render_template(self):
+    def render_template(self) -> None:
         """Runs Jinja to create a new nf-core pipeline."""
         log.info(f"Creating new pipeline: '{self.name}'")
 
@@ -306,7 +306,7 @@ def render_template(self):
         template_files += list(Path(template_dir).glob("*"))
         ignore_strs = [".pyc", "__pycache__", ".pyo", ".pyd", ".DS_Store", ".egg"]
         short_name = self.jinja_params["short_name"]
-        rename_files = {
+        rename_files: Dict[str, str] = {
             "workflows/pipeline.nf": f"workflows/{short_name}.nf",
             "subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf": f"subworkflows/local/utils_nfcore_{short_name}_pipeline/main.nf",
         }
@@ -327,8 +327,9 @@ def render_template(self):
                 # Set up vars and directories
                 template_fn = template_fn_path.relative_to(template_dir)
                 output_path = self.outdir / template_fn
-                if template_fn in rename_files:
-                    output_path = self.outdir / rename_files[template_fn]
+
+                if str(template_fn) in rename_files:
+                    output_path = self.outdir / rename_files[str(template_fn)]
                 output_path.parent.mkdir(parents=True, exist_ok=True)
 
                 try:
diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index d044be84e4..741bdd751a 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -6,6 +6,7 @@
 import re
 import shutil
 from pathlib import Path
+from typing import Dict, Optional, Union
 
 import git
 import questionary
@@ -61,24 +62,24 @@ class PipelineSync:
 
     def __init__(
         self,
-        pipeline_dir,
-        from_branch=None,
-        make_pr=False,
-        gh_repo=None,
-        gh_username=None,
-        template_yaml_path=None,
-        force_pr=False,
+        pipeline_dir: Union[str, Path],
+        from_branch: Optional[str] = None,
+        make_pr: bool = False,
+        gh_repo: Optional[str] = None,
+        gh_username: Optional[str] = None,
+        template_yaml_path: Optional[str] = None,
+        force_pr: bool = False,
     ):
         """Initialise syncing object"""
 
-        self.pipeline_dir = Path(pipeline_dir).resolve()
+        self.pipeline_dir: Path = Path(pipeline_dir).resolve()
         self.from_branch = from_branch
         self.original_branch = None
         self.original_merge_branch = f"nf-core-template-merge-{nf_core.__version__}"
         self.merge_branch = self.original_merge_branch
         self.made_changes = False
         self.make_pr = make_pr
-        self.gh_pr_returned_data = {}
+        self.gh_pr_returned_data: Dict = {}
         self.required_config_vars = ["manifest.name", "manifest.description", "manifest.version", "manifest.author"]
         self.force_pr = force_pr
 
@@ -87,7 +88,7 @@ def __init__(
         self.pr_url = ""
 
         self.config_yml_path, self.config_yml = nf_core.utils.load_tools_config(self.pipeline_dir)
-        assert self.config_yml_path is not None  # mypy
+        assert self.config_yml_path is not None and self.config_yml is not None  # mypy
         # Throw deprecation warning if template_yaml_path is set
         if template_yaml_path is not None:
             log.warning(

From 0fe3910c54251b005a0cbc493de556d865310c1e Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 12:28:30 +0200
Subject: [PATCH 130/414] fix create-logo cli command

---
 nf_core/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index d0aad63e80..11ab574ccc 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -650,7 +650,7 @@ def command_pipelines_bump_version(ctx, new_version, directory, nextflow):
 # nf-core pipelines create-logo
 @pipelines.command("create-logo")
 @click.argument("logo-text", metavar="<logo_text>")
-@click.option("-d", "--dir", type=click.Path(), default=".", help="Directory to save the logo in.")
+@click.option("-d", "--dir", "directory", type=click.Path(), default=".", help="Directory to save the logo in.")
 @click.option(
     "-n",
     "--name",

From ce325366e04551b46d109b572e95320c7dc39023 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 14:47:53 +0200
Subject: [PATCH 131/414] add types, include review comments, add pydantic mypy
 plugin

---
 .pre-commit-config.yaml                  | 1 +
 mypy.ini                                 | 1 +
 nf_core/components/components_command.py | 6 +++++-
 nf_core/components/components_utils.py   | 2 +-
 nf_core/components/info.py               | 2 +-
 nf_core/components/lint/__init__.py      | 5 +++--
 6 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index bcf7ff65ce..f763fa6658 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -28,3 +28,4 @@ repos:
           - types-jsonschema
           - types-Markdown
           - types-setuptools
+          - pydantic
diff --git a/mypy.ini b/mypy.ini
index c48aa5884b..5a95223162 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -1,3 +1,4 @@
 [mypy]
 warn_unused_configs = True
 ignore_missing_imports = true
+plugins = pydantic.mypy
diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 4440dc32a4..91e14d0606 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -254,7 +254,11 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None:
                 # Update path in modules.json if the file is in the correct format
                 modules_json = ModulesJson(self.directory)
                 modules_json.load()
-                if modules_json.has_git_url_and_modules() and modules_json.modules_json is not None:
+                if (
+                    modules_json.has_git_url_and_modules()
+                    and self.modules_repo.repo_path is not None
+                    and modules_json.modules_json is not None
+                ):
                     modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][
                         self.modules_repo.repo_path
                     ][module_name]["patch"] = str(patch_path.relative_to(Path(self.directory).resolve()))
diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py
index 4e9c0ac601..3d64dc1bb6 100644
--- a/nf_core/components/components_utils.py
+++ b/nf_core/components/components_utils.py
@@ -77,7 +77,7 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P
             ).unsafe_ask()
             log.info("To avoid this prompt in the future, add the 'org_path' key to a root '%s' file.", config_fn.name)
             if rich.prompt.Confirm.ask("[bold][blue]?[/] Would you like me to add this config now?", default=True):
-                with open(str(config_fn), "a+") as fh:
+                with open(config_fn, "a+") as fh:
                     fh.write(f"org_path: {org}\n")
                     log.info(f"Config added to '{config_fn.name}'")
 
diff --git a/nf_core/components/info.py b/nf_core/components/info.py
index 55a95593f9..726586b5b7 100644
--- a/nf_core/components/info.py
+++ b/nf_core/components/info.py
@@ -107,7 +107,7 @@ def init_mod_name(self, component):
                 elif self.repo_type == "pipeline":
                     assert self.modules_json is not None  # mypy
                     all_components = self.modules_json.get_all_components(self.component_type).get(
-                        self.modules_repo.remote_url, []
+                        self.modules_repo.remote_url, {}
                     )
                     components = [
                         component if directory == self.modules_repo.repo_path else f"{directory}/{component}"
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index e2475ef62c..ddf5e1e165 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -22,6 +22,7 @@
 from nf_core.components.nfcore_component import NFCoreComponent
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.pipelines.lint_utils import console
+from nf_core.utils import LintConfigType
 from nf_core.utils import plural_s as _s
 
 log = logging.getLogger(__name__)
@@ -77,8 +78,8 @@ def __init__(
         self.failed: List[LintResult] = []
         self.all_local_components: List[NFCoreComponent] = []
 
-        self.lint_config = None
-        self.modules_json = None
+        self.lint_config: Optional[LintConfigType] = None
+        self.modules_json: Optional[ModulesJson] = None
 
         if self.component_type == "modules":
             self.lint_tests = self.get_all_module_lint_tests(self.repo_type == "pipeline")

From 8eeaf28402013b4f54af693f80836de92c8d2cf7 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 14:50:35 +0200
Subject: [PATCH 132/414] fix mypy error

---
 nf_core/modules/lint/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index cea75d8f2e..fcf2d7d066 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -238,7 +238,7 @@ def lint_module(
 
         # Otherwise run all the lint tests
         else:
-            if self.repo_type == "pipeline" and self.modules_json:
+            if self.repo_type == "pipeline" and self.modules_json and mod.repo_url:
                 # Set correct sha
                 version = self.modules_json.get_module_version(mod.component_name, mod.repo_url, mod.org)
                 mod.git_sha = version

From 95de96b7bddf192cd5ef3ea75218236ec73e02c4 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 15:27:31 +0200
Subject: [PATCH 133/414] allow dashes in pipeilne short name (why didn't this
 fail before?)

---
 nf_core/pipelines/create/create.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 15eed46dce..dcb6d2c994 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -249,7 +249,7 @@ def obtain_jinja_params_dict(self, features_to_skip: List[str], pipeline_dir: Un
                 return jinja_params, skip_paths
 
         # Check that the pipeline name matches the requirements
-        if not re.match(r"^[a-z]+$", jinja_params["short_name"]):
+        if not re.match(r"^[a-z-]+$", jinja_params["short_name"]):
             if jinja_params["is_nfcore"]:
                 raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")
             else:

From 1b6f231ebc41665a7cad108fe4fdbc7b38d218f0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 15:27:59 +0200
Subject: [PATCH 134/414] Revert "allow dashes in pipeilne short name (why
 didn't this fail before?)"

This reverts commit 95de96b7bddf192cd5ef3ea75218236ec73e02c4.
---
 nf_core/pipelines/create/create.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index dcb6d2c994..15eed46dce 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -249,7 +249,7 @@ def obtain_jinja_params_dict(self, features_to_skip: List[str], pipeline_dir: Un
                 return jinja_params, skip_paths
 
         # Check that the pipeline name matches the requirements
-        if not re.match(r"^[a-z-]+$", jinja_params["short_name"]):
+        if not re.match(r"^[a-z]+$", jinja_params["short_name"]):
             if jinja_params["is_nfcore"]:
                 raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")
             else:

From 5186ac71523c0fe16978c3857325365f02d1093b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 16:25:41 +0200
Subject: [PATCH 135/414] use path.walk correctly

---
 nf_core/components/components_command.py    | 8 ++++----
 nf_core/modules/modules_json.py             | 4 ++--
 nf_core/pipelines/lint/merge_markers.py     | 2 +-
 nf_core/pipelines/lint/modules_structure.py | 2 +-
 nf_core/pipelines/lint/pipeline_todos.py    | 2 +-
 nf_core/synced_repo.py                      | 2 +-
 6 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 91e14d0606..5cde00ef69 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -87,7 +87,7 @@ def get_components_clone_modules(self) -> List[str]:
             component_base_path = Path(self.directory, self.default_subworkflows_path)
         return [
             str(Path(directory).relative_to(component_base_path))
-            for directory, _, files in Path.walk(component_base_path)
+            for directory, _, files in Path(component_base_path).walk()
             if "main.nf" in files
         ]
 
@@ -126,7 +126,7 @@ def clear_component_dir(self, component_name: str, component_dir: Union[str, Pat
         try:
             shutil.rmtree(component_dir)
             # remove all empty directories
-            for dir_path, dir_names, filenames in Path.walk(Path(self.directory), top_down=False):
+            for dir_path, dir_names, filenames in Path(self.directory).walk(top_down=False):
                 if not dir_names and not filenames:
                     try:
                         dir_path.rmdir()
@@ -157,7 +157,7 @@ def components_from_repo(self, install_dir: str) -> List[str]:
 
         return [
             str(Path(dir_path).relative_to(repo_dir))
-            for dir_path, _, files in Path.walk(repo_dir)
+            for dir_path, _, files in Path(repo_dir).walk()
             if "main.nf" in files
         ]
 
@@ -202,7 +202,7 @@ def check_modules_structure(self) -> None:
         """
         if self.repo_type == "pipeline":
             wrong_location_modules: List[Path] = []
-            for directory, _, files in Path.walk(Path(self.directory, "modules")):
+            for directory, _, files in Path(self.directory, "modules").walk():
                 if "main.nf" in files:
                     module_path = Path(directory).relative_to(Path(self.directory, "modules"))
                     parts = module_path.parts
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 9f17add6ae..3f4fb46f2d 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -134,7 +134,7 @@ def get_component_names_from_repo(
                 repo_url,
                 [
                     str(component_name.relative_to(directory / modules_repo.repo_path))
-                    for component_name, _, file_names in Path.walk(directory / modules_repo.repo_path)
+                    for component_name, _, file_names in Path(directory / modules_repo.repo_path).walk()
                     if "main.nf" in file_names
                 ],
                 modules_repo.repo_path,
@@ -1189,7 +1189,7 @@ def components_with_repos():
                         self.modules_dir,
                         modules_repo.repo_path,
                     )
-                    for dir_name, _, _ in Path.walk(repo_url_path):
+                    for dir_name, _, _ in repo_url_path.walk():
                         if component_type == "modules":
                             if len(Path(directory).parts) > 1:  # The module name is TOOL/SUBTOOL
                                 paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:])))
diff --git a/nf_core/pipelines/lint/merge_markers.py b/nf_core/pipelines/lint/merge_markers.py
index 208c9f4bcc..4e2f73fb85 100644
--- a/nf_core/pipelines/lint/merge_markers.py
+++ b/nf_core/pipelines/lint/merge_markers.py
@@ -42,7 +42,7 @@ def merge_markers(self):
         with open(Path(self.wf_path, ".gitignore"), encoding="latin1") as fh:
             for line in fh:
                 ignore.append(Path(line.strip().rstrip("/")).name)
-    for root, dirs, files in Path.walk(self.wf_path, top_down=True):
+    for root, dirs, files in Path(self.wf_path).walk(top_down=True):
         # Ignore files
         for i_base in ignore:
             i = str(Path(root, i_base))
diff --git a/nf_core/pipelines/lint/modules_structure.py b/nf_core/pipelines/lint/modules_structure.py
index fd29942ed6..34cdc89561 100644
--- a/nf_core/pipelines/lint/modules_structure.py
+++ b/nf_core/pipelines/lint/modules_structure.py
@@ -19,7 +19,7 @@ def modules_structure(self):
         modules/nf-core/modules/TOOL/SUBTOOL
     """
     wrong_location_modules = []
-    for directory, _, files in Path.walk(Path(self.wf_path, "modules")):
+    for directory, _, files in Path(self.wf_path, "modules").walk():
         if "main.nf" in files:
             module_path = Path(directory).relative_to(Path(self.wf_path, "modules"))
             parts = module_path.parts
diff --git a/nf_core/pipelines/lint/pipeline_todos.py b/nf_core/pipelines/lint/pipeline_todos.py
index 530d853764..0a21d0d05a 100644
--- a/nf_core/pipelines/lint/pipeline_todos.py
+++ b/nf_core/pipelines/lint/pipeline_todos.py
@@ -43,7 +43,7 @@ def pipeline_todos(self, root_dir=None):
         with open(Path(root_dir, ".gitignore"), encoding="latin1") as fh:
             for line in fh:
                 ignore.append(Path(line.strip().rstrip("/")).name)
-    for root, dirs, files in Path.walk(root_dir, top_down=True):
+    for root, dirs, files in Path(root_dir).walk(top_down=True):  #
         # Ignore files
         for i_base in ignore:
             i = str(Path(root, i_base))
diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py
index 8efdd0e488..22cdcd1577 100644
--- a/nf_core/synced_repo.py
+++ b/nf_core/synced_repo.py
@@ -467,7 +467,7 @@ def get_avail_components(
         # Module/Subworkflow directories are characterized by having a 'main.nf' file
         avail_component_names = [
             str(Path(dirpath).relative_to(directory))
-            for dirpath, _, files in Path.walk(directory)
+            for dirpath, _, files in Path(directory).walk()
             if "main.nf" in files
         ]
         return avail_component_names

From 873398727b6dd8e6a1046f6a91c45bad8fd26825 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 16:37:19 +0200
Subject: [PATCH 136/414] Revert "use path.walk correctly"

This reverts commit 5186ac71523c0fe16978c3857325365f02d1093b.
---
 nf_core/components/components_command.py    | 8 ++++----
 nf_core/modules/modules_json.py             | 4 ++--
 nf_core/pipelines/lint/merge_markers.py     | 2 +-
 nf_core/pipelines/lint/modules_structure.py | 2 +-
 nf_core/pipelines/lint/pipeline_todos.py    | 2 +-
 nf_core/synced_repo.py                      | 2 +-
 6 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 5cde00ef69..91e14d0606 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -87,7 +87,7 @@ def get_components_clone_modules(self) -> List[str]:
             component_base_path = Path(self.directory, self.default_subworkflows_path)
         return [
             str(Path(directory).relative_to(component_base_path))
-            for directory, _, files in Path(component_base_path).walk()
+            for directory, _, files in Path.walk(component_base_path)
             if "main.nf" in files
         ]
 
@@ -126,7 +126,7 @@ def clear_component_dir(self, component_name: str, component_dir: Union[str, Pat
         try:
             shutil.rmtree(component_dir)
             # remove all empty directories
-            for dir_path, dir_names, filenames in Path(self.directory).walk(top_down=False):
+            for dir_path, dir_names, filenames in Path.walk(Path(self.directory), top_down=False):
                 if not dir_names and not filenames:
                     try:
                         dir_path.rmdir()
@@ -157,7 +157,7 @@ def components_from_repo(self, install_dir: str) -> List[str]:
 
         return [
             str(Path(dir_path).relative_to(repo_dir))
-            for dir_path, _, files in Path(repo_dir).walk()
+            for dir_path, _, files in Path.walk(repo_dir)
             if "main.nf" in files
         ]
 
@@ -202,7 +202,7 @@ def check_modules_structure(self) -> None:
         """
         if self.repo_type == "pipeline":
             wrong_location_modules: List[Path] = []
-            for directory, _, files in Path(self.directory, "modules").walk():
+            for directory, _, files in Path.walk(Path(self.directory, "modules")):
                 if "main.nf" in files:
                     module_path = Path(directory).relative_to(Path(self.directory, "modules"))
                     parts = module_path.parts
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 3f4fb46f2d..9f17add6ae 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -134,7 +134,7 @@ def get_component_names_from_repo(
                 repo_url,
                 [
                     str(component_name.relative_to(directory / modules_repo.repo_path))
-                    for component_name, _, file_names in Path(directory / modules_repo.repo_path).walk()
+                    for component_name, _, file_names in Path.walk(directory / modules_repo.repo_path)
                     if "main.nf" in file_names
                 ],
                 modules_repo.repo_path,
@@ -1189,7 +1189,7 @@ def components_with_repos():
                         self.modules_dir,
                         modules_repo.repo_path,
                     )
-                    for dir_name, _, _ in repo_url_path.walk():
+                    for dir_name, _, _ in Path.walk(repo_url_path):
                         if component_type == "modules":
                             if len(Path(directory).parts) > 1:  # The module name is TOOL/SUBTOOL
                                 paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:])))
diff --git a/nf_core/pipelines/lint/merge_markers.py b/nf_core/pipelines/lint/merge_markers.py
index 4e2f73fb85..208c9f4bcc 100644
--- a/nf_core/pipelines/lint/merge_markers.py
+++ b/nf_core/pipelines/lint/merge_markers.py
@@ -42,7 +42,7 @@ def merge_markers(self):
         with open(Path(self.wf_path, ".gitignore"), encoding="latin1") as fh:
             for line in fh:
                 ignore.append(Path(line.strip().rstrip("/")).name)
-    for root, dirs, files in Path(self.wf_path).walk(top_down=True):
+    for root, dirs, files in Path.walk(self.wf_path, top_down=True):
         # Ignore files
         for i_base in ignore:
             i = str(Path(root, i_base))
diff --git a/nf_core/pipelines/lint/modules_structure.py b/nf_core/pipelines/lint/modules_structure.py
index 34cdc89561..fd29942ed6 100644
--- a/nf_core/pipelines/lint/modules_structure.py
+++ b/nf_core/pipelines/lint/modules_structure.py
@@ -19,7 +19,7 @@ def modules_structure(self):
         modules/nf-core/modules/TOOL/SUBTOOL
     """
     wrong_location_modules = []
-    for directory, _, files in Path(self.wf_path, "modules").walk():
+    for directory, _, files in Path.walk(Path(self.wf_path, "modules")):
         if "main.nf" in files:
             module_path = Path(directory).relative_to(Path(self.wf_path, "modules"))
             parts = module_path.parts
diff --git a/nf_core/pipelines/lint/pipeline_todos.py b/nf_core/pipelines/lint/pipeline_todos.py
index 0a21d0d05a..530d853764 100644
--- a/nf_core/pipelines/lint/pipeline_todos.py
+++ b/nf_core/pipelines/lint/pipeline_todos.py
@@ -43,7 +43,7 @@ def pipeline_todos(self, root_dir=None):
         with open(Path(root_dir, ".gitignore"), encoding="latin1") as fh:
             for line in fh:
                 ignore.append(Path(line.strip().rstrip("/")).name)
-    for root, dirs, files in Path(root_dir).walk(top_down=True):  #
+    for root, dirs, files in Path.walk(root_dir, top_down=True):
         # Ignore files
         for i_base in ignore:
             i = str(Path(root, i_base))
diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py
index 22cdcd1577..8efdd0e488 100644
--- a/nf_core/synced_repo.py
+++ b/nf_core/synced_repo.py
@@ -467,7 +467,7 @@ def get_avail_components(
         # Module/Subworkflow directories are characterized by having a 'main.nf' file
         avail_component_names = [
             str(Path(dirpath).relative_to(directory))
-            for dirpath, _, files in Path(directory).walk()
+            for dirpath, _, files in Path.walk(directory)
             if "main.nf" in files
         ]
         return avail_component_names

From 1679594f5a52c0926f7f40800fcf43c445f8515a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 16:41:59 +0200
Subject: [PATCH 137/414] switch back to os.walk()

---
 nf_core/components/components_command.py    | 13 ++++++-------
 nf_core/modules/modules_json.py             |  4 ++--
 nf_core/pipelines/lint/merge_markers.py     |  3 ++-
 nf_core/pipelines/lint/modules_structure.py |  3 ++-
 nf_core/pipelines/lint/pipeline_todos.py    |  3 ++-
 nf_core/synced_repo.py                      |  4 +---
 6 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 91e14d0606..ada8b532e5 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -1,5 +1,6 @@
 import logging
 import mmap
+import os
 import shutil
 from pathlib import Path
 from typing import Dict, List, Optional, Union
@@ -87,7 +88,7 @@ def get_components_clone_modules(self) -> List[str]:
             component_base_path = Path(self.directory, self.default_subworkflows_path)
         return [
             str(Path(directory).relative_to(component_base_path))
-            for directory, _, files in Path.walk(component_base_path)
+            for directory, _, files in os.walk(component_base_path)
             if "main.nf" in files
         ]
 
@@ -126,10 +127,10 @@ def clear_component_dir(self, component_name: str, component_dir: Union[str, Pat
         try:
             shutil.rmtree(component_dir)
             # remove all empty directories
-            for dir_path, dir_names, filenames in Path.walk(Path(self.directory), top_down=False):
+            for dir_path, dir_names, filenames in os.walk(Path(self.directory), topdown=False):
                 if not dir_names and not filenames:
                     try:
-                        dir_path.rmdir()
+                        Path(dir_path).rmdir()
                     except OSError:
                         pass
                     else:
@@ -156,9 +157,7 @@ def components_from_repo(self, install_dir: str) -> List[str]:
             raise LookupError(f"Nothing installed from {install_dir} in pipeline")
 
         return [
-            str(Path(dir_path).relative_to(repo_dir))
-            for dir_path, _, files in Path.walk(repo_dir)
-            if "main.nf" in files
+            str(Path(dir_path).relative_to(repo_dir)) for dir_path, _, files in os.walk(repo_dir) if "main.nf" in files
         ]
 
     def install_component_files(
@@ -202,7 +201,7 @@ def check_modules_structure(self) -> None:
         """
         if self.repo_type == "pipeline":
             wrong_location_modules: List[Path] = []
-            for directory, _, files in Path.walk(Path(self.directory, "modules")):
+            for directory, _, files in os.walk(Path(self.directory, "modules")):
                 if "main.nf" in files:
                     module_path = Path(directory).relative_to(Path(self.directory, "modules"))
                     parts = module_path.parts
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 9f17add6ae..4f86bc8302 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -134,7 +134,7 @@ def get_component_names_from_repo(
                 repo_url,
                 [
                     str(component_name.relative_to(directory / modules_repo.repo_path))
-                    for component_name, _, file_names in Path.walk(directory / modules_repo.repo_path)
+                    for component_name, _, file_names in os.walk(directory / modules_repo.repo_path)
                     if "main.nf" in file_names
                 ],
                 modules_repo.repo_path,
@@ -1189,7 +1189,7 @@ def components_with_repos():
                         self.modules_dir,
                         modules_repo.repo_path,
                     )
-                    for dir_name, _, _ in Path.walk(repo_url_path):
+                    for dir_name, _, _ in os.walk(repo_url_path):
                         if component_type == "modules":
                             if len(Path(directory).parts) > 1:  # The module name is TOOL/SUBTOOL
                                 paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:])))
diff --git a/nf_core/pipelines/lint/merge_markers.py b/nf_core/pipelines/lint/merge_markers.py
index 208c9f4bcc..1c3d70a76f 100644
--- a/nf_core/pipelines/lint/merge_markers.py
+++ b/nf_core/pipelines/lint/merge_markers.py
@@ -1,5 +1,6 @@
 import fnmatch
 import logging
+import os
 from pathlib import Path
 
 import nf_core.utils
@@ -42,7 +43,7 @@ def merge_markers(self):
         with open(Path(self.wf_path, ".gitignore"), encoding="latin1") as fh:
             for line in fh:
                 ignore.append(Path(line.strip().rstrip("/")).name)
-    for root, dirs, files in Path.walk(self.wf_path, top_down=True):
+    for root, dirs, files in os.walk(self.wf_path, topdown=True):
         # Ignore files
         for i_base in ignore:
             i = str(Path(root, i_base))
diff --git a/nf_core/pipelines/lint/modules_structure.py b/nf_core/pipelines/lint/modules_structure.py
index fd29942ed6..9d9b4c9fc0 100644
--- a/nf_core/pipelines/lint/modules_structure.py
+++ b/nf_core/pipelines/lint/modules_structure.py
@@ -1,4 +1,5 @@
 import logging
+import os
 from pathlib import Path
 
 log = logging.getLogger(__name__)
@@ -19,7 +20,7 @@ def modules_structure(self):
         modules/nf-core/modules/TOOL/SUBTOOL
     """
     wrong_location_modules = []
-    for directory, _, files in Path.walk(Path(self.wf_path, "modules")):
+    for directory, _, files in os.walk(Path(self.wf_path, "modules")):
         if "main.nf" in files:
             module_path = Path(directory).relative_to(Path(self.wf_path, "modules"))
             parts = module_path.parts
diff --git a/nf_core/pipelines/lint/pipeline_todos.py b/nf_core/pipelines/lint/pipeline_todos.py
index 530d853764..0535069f9a 100644
--- a/nf_core/pipelines/lint/pipeline_todos.py
+++ b/nf_core/pipelines/lint/pipeline_todos.py
@@ -1,5 +1,6 @@
 import fnmatch
 import logging
+import os
 from pathlib import Path
 
 log = logging.getLogger(__name__)
@@ -43,7 +44,7 @@ def pipeline_todos(self, root_dir=None):
         with open(Path(root_dir, ".gitignore"), encoding="latin1") as fh:
             for line in fh:
                 ignore.append(Path(line.strip().rstrip("/")).name)
-    for root, dirs, files in Path.walk(root_dir, top_down=True):
+    for root, dirs, files in os.walk(root_dir, topdown=True):
         # Ignore files
         for i_base in ignore:
             i = str(Path(root, i_base))
diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py
index 8efdd0e488..e2a76ccaeb 100644
--- a/nf_core/synced_repo.py
+++ b/nf_core/synced_repo.py
@@ -466,9 +466,7 @@ def get_avail_components(
             directory = self.subworkflows_dir
         # Module/Subworkflow directories are characterized by having a 'main.nf' file
         avail_component_names = [
-            str(Path(dirpath).relative_to(directory))
-            for dirpath, _, files in Path.walk(directory)
-            if "main.nf" in files
+            str(Path(dirpath).relative_to(directory)) for dirpath, _, files in os.walk(directory) if "main.nf" in files
         ]
         return avail_component_names
 

From 3c0433e68fc33be6dd35dfbb88b3989e103b6ad6 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 22:43:37 +0200
Subject: [PATCH 138/414] fix sync

---
 nf_core/modules/modules_json.py    | 2 +-
 nf_core/pipelines/create/create.py | 5 ++---
 nf_core/pipelines/sync.py          | 7 ++-----
 nf_core/utils.py                   | 2 ++
 4 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 4f86bc8302..39d70b7d78 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -133,7 +133,7 @@ def get_component_names_from_repo(
             components = (
                 repo_url,
                 [
-                    str(component_name.relative_to(directory / modules_repo.repo_path))
+                    str(Path(component_name).relative_to(directory / modules_repo.repo_path))
                     for component_name, _, file_names in os.walk(directory / modules_repo.repo_path)
                     if "main.nf" in file_names
                 ],
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 15eed46dce..9b64b53446 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -53,7 +53,7 @@ def __init__(
         no_git: bool = False,
         force: bool = False,
         outdir: Optional[Union[Path, str]] = None,
-        template_config: Optional[Union[str, CreateConfig, Path]] = None,
+        template_config: Optional[CreateConfig] = None,
         organisation: str = "nf-core",
         from_config_file: bool = False,
         default_branch: Optional[str] = None,
@@ -67,7 +67,7 @@ def __init__(
                 _, config_yml = nf_core.utils.load_tools_config(outdir if outdir else Path().cwd())
                 # Obtain a CreateConfig object from `.nf-core.yml` config file
                 if config_yml is not None and getattr(config_yml, "template", None) is not None:
-                    self.config = CreateConfig(**config_yml["template"])
+                    self.config = CreateConfig(**config_yml["template"].model_dump())
                 else:
                     raise UserWarning("The template configuration was not provided in '.nf-core.yml'.")
             except (FileNotFoundError, UserWarning):
@@ -261,7 +261,6 @@ def obtain_jinja_params_dict(self, features_to_skip: List[str], pipeline_dir: Un
 
     def init_pipeline(self):
         """Creates the nf-core pipeline."""
-
         # Make the new pipeline
         self.render_template()
 
diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index 741bdd751a..efc7212b4d 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -270,13 +270,10 @@ def make_template_pipeline(self):
 
         try:
             nf_core.pipelines.create.create.PipelineCreate(
-                name=self.wf_config["manifest.name"].strip('"').strip("'"),
-                description=self.wf_config["manifest.description"].strip('"').strip("'"),
-                version=self.wf_config["manifest.version"].strip('"').strip("'"),
+                outdir=str(self.pipeline_dir),
+                from_config_file=True,
                 no_git=True,
                 force=True,
-                outdir=str(self.pipeline_dir),
-                author=self.wf_config["manifest.author"].strip('"').strip("'"),
             ).init_pipeline()
         except Exception as err:
             # Reset to where you were to prevent git getting messed up.
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 0beb8c7366..44eafca3cc 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -1053,6 +1053,8 @@ class NFCoreTemplateConfig(BaseModel):
     is_nfcore: Optional[bool] = None
 
     def __getitem__(self, item: str) -> Any:
+        if self is None:
+            return None
         return getattr(self, item)
 
     def get(self, item: str, default: Any = None) -> Any:

From 4d6930be2da27623f5e1644785cb6bcf1a994d74 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 26 Jul 2024 22:46:57 +0200
Subject: [PATCH 139/414] fix types

---
 nf_core/pipelines/create/create.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 9b64b53446..d5c230e048 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -53,7 +53,7 @@ def __init__(
         no_git: bool = False,
         force: bool = False,
         outdir: Optional[Union[Path, str]] = None,
-        template_config: Optional[CreateConfig] = None,
+        template_config: Optional[Union[CreateConfig, str, Path]] = None,
         organisation: str = "nf-core",
         from_config_file: bool = False,
         default_branch: Optional[str] = None,

From 26b1cd13c36bc2d1234b8f97e6141bf9c0c82c5c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 11:44:02 +0200
Subject: [PATCH 140/414] set force true in sync to create a template file

---
 nf_core/pipelines/sync.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index efc7212b4d..fced35dc20 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -263,8 +263,12 @@ def make_template_pipeline(self):
         logging.getLogger("nf_core.pipelines.create").setLevel(logging.ERROR)
         assert self.config_yml_path is not None
         assert self.config_yml is not None
+
         # Re-write the template yaml info from .nf-core.yml config
-        if getattr(self.config_yml, "template", None) is not None:
+        if self.config_yml.template is not None:
+            # Set force true in config to overwrite existing files
+
+            self.config_yml.template.force = True
             with open(self.config_yml_path, "w") as config_path:
                 yaml.safe_dump(self.config_yml.model_dump(), config_path)
 
@@ -275,6 +279,14 @@ def make_template_pipeline(self):
                 no_git=True,
                 force=True,
             ).init_pipeline()
+
+            # set force to false to avoid overwriting files in the future
+            if self.config_yml.template is not None:
+                # Set force true in config to overwrite existing files
+                self.config_yml.template.force = False
+                with open(self.config_yml_path, "w") as config_path:
+                    yaml.safe_dump(self.config_yml.model_dump(), config_path)
+
         except Exception as err:
             # Reset to where you were to prevent git getting messed up.
             self.repo.git.reset("--hard")

From 59a3eb38c2f7603ed63c73ea6c1589a9b73a95c1 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 12:33:14 +0200
Subject: [PATCH 141/414] fix missing initialization in download.py

---
 nf_core/pipelines/download.py | 10 ++++++----
 nf_core/utils.py              | 14 ++++++++------
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py
index 797909636c..704fe91b2f 100644
--- a/nf_core/pipelines/download.py
+++ b/nf_core/pipelines/download.py
@@ -11,7 +11,7 @@
 import textwrap
 from datetime import datetime
 from pathlib import Path
-from typing import List, Optional, Tuple
+from typing import Any, Dict, List, Optional, Tuple
 from zipfile import ZipFile
 
 import git
@@ -24,6 +24,7 @@
 from packaging.version import Version
 
 import nf_core
+import nf_core.modules.modules_utils
 import nf_core.pipelines.list
 import nf_core.utils
 from nf_core.synced_repo import RemoteProgressbar, SyncedRepo
@@ -131,6 +132,7 @@ def __init__(
         self.compress_type = compress_type
         self.force = force
         self.platform = platform
+        self.fullname: Optional[str] = None
         # if flag is not specified, do not assume deliberate choice and prompt config inclusion interactively.
         # this implies that non-interactive "no" choice is only possible implicitly (e.g. with --platform or if prompt is suppressed by !stderr.is_interactive).
         # only alternative would have been to make it a parameter with argument, e.g. -d="yes" or -d="no".
@@ -161,8 +163,8 @@ def __init__(
         # allows to specify a container library / registry or a respective mirror to download images from
         self.parallel_downloads = parallel_downloads
 
-        self.wf_revisions = {}
-        self.wf_branches = {}
+        self.wf_revisions = []
+        self.wf_branches: Dict[str, Any] = {}
         self.wf_sha = {}
         self.wf_download_url = {}
         self.nf_config = {}
@@ -339,7 +341,7 @@ def prompt_pipeline_name(self):
             stderr.print("Specify the name of a nf-core pipeline or a GitHub repository name (user/repo).")
             self.pipeline = nf_core.utils.prompt_remote_pipeline_name(self.wfs)
 
-    def prompt_revision(self):
+    def prompt_revision(self) -> None:
         """
         Prompt for pipeline revision / branch
         Prompt user for revision tag if '--revision' was not set
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 44eafca3cc..80324fc9a8 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -903,7 +903,9 @@ def prompt_remote_pipeline_name(wfs):
     raise AssertionError(f"Not able to find pipeline '{pipeline}'")
 
 
-def prompt_pipeline_release_branch(wf_releases, wf_branches, multiple=False):
+def prompt_pipeline_release_branch(
+    wf_releases: List[Dict[str, Any]], wf_branches: Dict[str, Any], multiple: bool = False
+) -> tuple[Any, list[str]]:
     """Prompt for pipeline release / branch
 
     Args:
@@ -912,18 +914,18 @@ def prompt_pipeline_release_branch(wf_releases, wf_branches, multiple=False):
         multiple (bool): Allow selection of multiple releases & branches (for Seqera Platform)
 
     Returns:
-        choice (str): Selected release / branch name
+        choice (questionary.Choice or bool): Selected release / branch or False if no releases / branches available
     """
     # Prompt user for release tag, tag_set will contain all available.
-    choices = []
-    tag_set = []
+    choices: List[questionary.Choice] = []
+    tag_set: List[str] = []
 
     # Releases
     if len(wf_releases) > 0:
         for tag in map(lambda release: release.get("tag_name"), wf_releases):
             tag_display = [("fg:ansiblue", f"{tag}  "), ("class:choice-default", "[release]")]
             choices.append(questionary.Choice(title=tag_display, value=tag))
-            tag_set.append(tag)
+            tag_set.append(str(tag))
 
     # Branches
     for branch in wf_branches.keys():
@@ -932,7 +934,7 @@ def prompt_pipeline_release_branch(wf_releases, wf_branches, multiple=False):
         tag_set.append(branch)
 
     if len(choices) == 0:
-        return False
+        return [], []
 
     if multiple:
         return (

From fec536fd1ece3ce042a7fa32c9f05a7ddaa6ad06 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?=
 <mashehu@users.noreply.github.com>
Date: Mon, 29 Jul 2024 13:35:40 +0200
Subject: [PATCH 142/414] Apply suggestions from code review

---
 CHANGELOG.md                  | 2 +-
 nf_core/commands_pipelines.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2c47c1b887..15e92781cb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,7 +13,7 @@
 
 - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976))
 - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014))
-- Rrestructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070))
+- Restructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070))
 
 ### Download
 
diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py
index c586534b22..4b6fa75f3e 100644
--- a/nf_core/commands_pipelines.py
+++ b/nf_core/commands_pipelines.py
@@ -284,7 +284,7 @@ def pipelines_sync(ctx, directory, from_branch, pull_request, github_repository,
     Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template.
 
     To keep nf-core pipelines up to date with improvements in the main
-    template, we use a method of w that uses a special
+    template, we use a method of synchronisation that uses a special
     git branch called [cyan i]TEMPLATE[/].
 
     This command updates the [cyan i]TEMPLATE[/] branch with the latest version of

From 7f03f9e807c537c448f75d69002625b0768b4931 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 14:12:24 +0200
Subject: [PATCH 143/414] fix mypy warnings

---
 nf_core/pipelines/create/utils.py | 12 +++++++++---
 nf_core/pipelines/create_logo.py  |  6 +++---
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
index 88994c9361..e62ef328e4 100644
--- a/nf_core/pipelines/create/utils.py
+++ b/nf_core/pipelines/create/utils.py
@@ -124,10 +124,16 @@ def compose(self) -> ComposeResult:
     @on(Input.Submitted)
     def show_invalid_reasons(self, event: Union[Input.Changed, Input.Submitted]) -> None:
         """Validate the text input and show errors if invalid."""
-        if not event.validation_result.is_valid:
-            self.query_one(".validation_msg").update("\n".join(event.validation_result.failure_descriptions))
+        val_msg = self.query_one(".validation_msg")
+        if not isinstance(val_msg, Static):
+            raise ValueError("Validation message not found.")
+
+        if event.validation_result is not None and not event.validation_result.is_valid:
+            # check that val_msg is instance of Static
+            if isinstance(val_msg, Static):
+                val_msg.update("\n".join(event.validation_result.failure_descriptions))
         else:
-            self.query_one(".validation_msg").update("")
+            val_msg.update("")
 
 
 class ValidateConfig(Validator):
diff --git a/nf_core/pipelines/create_logo.py b/nf_core/pipelines/create_logo.py
index f49e98e93c..6619b910b5 100644
--- a/nf_core/pipelines/create_logo.py
+++ b/nf_core/pipelines/create_logo.py
@@ -1,6 +1,6 @@
 import logging
 from pathlib import Path
-from typing import Union
+from typing import Optional, Union
 
 from PIL import Image, ImageDraw, ImageFont
 
@@ -59,11 +59,11 @@ def create_logo(
             return logo_path
         # cache file
         cache_path = Path(NFCORE_CACHE_DIR, "logo", cache_name)
-        img = None
+        img: Optional[Image.Image] = None
         if cache_path.is_file():
             log.debug(f"Logo already exists in cache at: {cache_path}. Reusing this file.")
             img = Image.open(str(cache_path))
-        if not img:
+        if img is None:
             log.debug(f"Creating logo for {text}")
 
             # make sure the figure fits the text

From a4c829fb909f060f3c5d35486a7b293c2161757f Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 29 Jul 2024 12:40:04 +0200
Subject: [PATCH 144/414] add option to skip code linters

---
 .../create-test-lint-wf-template.yml          |   5 +
 nf_core/pipeline-template/.gitpod.yml         |   3 +-
 nf_core/pipelines/create/create.py            |   8 +
 nf_core/pipelines/create/custompipeline.py    |  16 +
 tests/__snapshots__/test_create_app.ambr      | 511 +++++++++---------
 tests/data/pipeline_create_template_skip.yml  |   1 +
 tests/test_create.py                          |  14 +-
 7 files changed, 296 insertions(+), 262 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index b823ca72d8..cfa0a50079 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -41,6 +41,7 @@ jobs:
           - "template_skip_github_badges.yml"
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
+          - "template_skip_code_linters.yml"
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
@@ -102,6 +103,10 @@ jobs:
         run: |
           printf "org: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml
 
+      - name: Create template skip code_linters
+        run: |
+          printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml
+
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |
diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml
index 105a1821a1..30e85ed977 100644
--- a/nf_core/pipeline-template/.gitpod.yml
+++ b/nf_core/pipeline-template/.gitpod.yml
@@ -10,8 +10,9 @@ tasks:
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
+    #{%- if code_linters -%}
     - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
+    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files{% endif %}
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
     # - nextflow.nextflow                    # Nextflow syntax highlighting
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 27ca8ac847..42e4a6ad7b 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -94,6 +94,13 @@ def __init__(
                 ".github/workflows/awstest.yml",
                 ".github/workflows/release-announcements.yml",
             ],
+            "code_linters": [
+                ".editorconfig",
+                ".pre-commit-config.yaml",
+                ".prettierignore",
+                ".prettierrc.yml",
+                ".github/workflows/fix-linting.yml",
+            ],
         }
         # Get list of files we're skipping with the supplied skip keys
         self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k])
@@ -202,6 +209,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
             "github_badges": {"file": False, "content": True},
             "igenomes": {"file": True, "content": True},
             "nf_core_configs": {"file": False, "content": True},
+            "code_linters": {"file": True, "content": True},
         }
 
         # Set the parameters for the jinja template
diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py
index 7d460db65d..7a94ab228a 100644
--- a/nf_core/pipelines/create/custompipeline.py
+++ b/nf_core/pipelines/create/custompipeline.py
@@ -41,6 +41,16 @@
 For more information about nf-core configuration profiles, see the [nf-core/configs repository](https://github.com/nf-core/configs)
 """
 
+markdown_code_linters = """
+Pipelines include code linters, these linters will check the formatting of your code.
+Linters will check JSON, YAML, Python and others.
+The available code linters are:
+
+- pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository.
+- editor-config (https://github.com/editorconfig-checker/editorconfig-checker): checks rules such as indentation or trailing spaces.
+- prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc).
+"""
+
 
 class CustomPipeline(Screen):
     """Select if the pipeline will use genomic data."""
@@ -80,6 +90,12 @@ def compose(self) -> ComposeResult:
                 "The pipeline will include configuration profiles containing custom parameters requried to run nf-core pipelines at different institutions",
                 "nf_core_configs",
             ),
+            PipelineFeature(
+                markdown_code_linters,
+                "Use code linters",
+                "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.",
+                "code_linters",
+            ),
             classes="features-container",
         )
         yield Center(
diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr
index 2ad0772587..5e5b005de0 100644
--- a/tests/__snapshots__/test_create_app.ambr
+++ b/tests/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
           font-weight: 700;
       }
   
-      .terminal-2971485804-matrix {
+      .terminal-2778615119-matrix {
           font-family: Fira Code, monospace;
           font-size: 20px;
           line-height: 24.4px;
           font-variant-east-asian: full-width;
       }
   
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+      .terminal-2778615119-title {
           font-size: 18px;
           font-weight: bold;
           font-family: arial;
       }
   
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-  .terminal-2971485804-r3 { fill: #989898 }
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+  .terminal-2778615119-r22 { fill: #a7a9ab }
+  .terminal-2778615119-r23 { fill: #e2e3e3 }
       </style>
   
       <defs>
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+      <clipPath id="terminal-2778615119-clip-terminal">
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diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml
index ed498cb732..d9ef405c51 100644
--- a/tests/data/pipeline_create_template_skip.yml
+++ b/tests/data/pipeline_create_template_skip.yml
@@ -11,3 +11,4 @@ skip_features:
   - github_badges
   - igenomes
   - nf_core_configs
+  - code_linters
diff --git a/tests/test_create.py b/tests/test_create.py
index 313b6f5354..896a8e7ad6 100644
--- a/tests/test_create.py
+++ b/tests/test_create.py
@@ -106,14 +106,16 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path):
         pipeline.init_pipeline()
 
         # Check pipeline template yml has been dumped to `.nf-core.yml` and matches input
-        assert not os.path.exists(os.path.join(pipeline.outdir, "pipeline_template.yml"))
-        assert os.path.exists(os.path.join(pipeline.outdir, ".nf-core.yml"))
-        with open(os.path.join(pipeline.outdir, ".nf-core.yml")) as fh:
+        assert not os.path.exists(Path(pipeline.outdir / "pipeline_template.yml"))
+        assert os.path.exists(Path(pipeline.outdir / ".nf-core.yml"))
+        with open(Path(pipeline.outdir / ".nf-core.yml")) as fh:
             nfcore_yml = yaml.safe_load(fh)
             assert "template" in nfcore_yml
             assert yaml.safe_load(PIPELINE_TEMPLATE_YML.read_text()).items() <= nfcore_yml["template"].items()
 
         # Check that some of the skipped files are not present
-        assert not os.path.exists(os.path.join(pipeline.outdir, "CODE_OF_CONDUCT.md"))
-        assert not os.path.exists(os.path.join(pipeline.outdir, ".github"))
-        assert not os.path.exists(os.path.join(pipeline.outdir, "conf", "igenomes.config"))
+        assert not os.path.exists(Path(pipeline.outdir / "CODE_OF_CONDUCT.md"))
+        assert not os.path.exists(Path(pipeline.outdir / ".github"))
+        assert not os.path.exists(Path(pipeline.outdir / "conf" / "igenomes.config"))
+        assert not os.path.exists(Path(pipeline.outdir / ".editorconfig"))
+        assert not os.path.exists(Path(pipeline.outdir / ".editorconfig"))

From d2020f511c0f5992b6919e6832d3bcd5cd3bfe75 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 14:19:36 +0200
Subject: [PATCH 145/414] set default value for self.directory and more
 dir->directory switches

---
 nf_core/commands_modules.py              | 38 ++++++++++++------------
 nf_core/commands_subworkflows.py         | 34 ++++++++++-----------
 nf_core/components/components_command.py | 12 ++++----
 nf_core/components/list.py               |  4 ++-
 nf_core/modules/list.py                  | 11 ++++++-
 nf_core/subworkflows/list.py             | 11 ++++++-
 tests/modules/test_list.py               | 18 +++++------
 tests/subworkflows/test_list.py          |  2 +-
 8 files changed, 73 insertions(+), 57 deletions(-)

diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py
index b93bd7bcb0..a889305055 100644
--- a/nf_core/commands_modules.py
+++ b/nf_core/commands_modules.py
@@ -17,7 +17,7 @@ def modules_list_remote(ctx, keywords, json):
 
     try:
         module_list = ModuleList(
-            None,
+            ".",
             True,
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
@@ -29,7 +29,7 @@ def modules_list_remote(ctx, keywords, json):
         sys.exit(1)
 
 
-def modules_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
+def modules_list_local(ctx, keywords, json, directory):  # pylint: disable=redefined-builtin
     """
     List modules installed locally in a pipeline
     """
@@ -37,7 +37,7 @@ def modules_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-b
 
     try:
         module_list = ModuleList(
-            dir,
+            directory,
             False,
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
@@ -49,7 +49,7 @@ def modules_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-b
         sys.exit(1)
 
 
-def modules_install(ctx, tool, dir, prompt, force, sha):
+def modules_install(ctx, tool, directory, prompt, force, sha):
     """
     Install DSL2 modules within a pipeline.
 
@@ -59,7 +59,7 @@ def modules_install(ctx, tool, dir, prompt, force, sha):
 
     try:
         module_install = ModuleInstall(
-            dir,
+            directory,
             force,
             prompt,
             sha,
@@ -118,7 +118,7 @@ def modules_update(
         sys.exit(1)
 
 
-def modules_patch(ctx, tool, dir, remove):
+def modules_patch(ctx, tool, directory, remove):
     """
     Create a patch file for minor changes in a module
 
@@ -129,7 +129,7 @@ def modules_patch(ctx, tool, dir, remove):
 
     try:
         module_patch = ModulePatch(
-            dir,
+            directory,
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
@@ -143,7 +143,7 @@ def modules_patch(ctx, tool, dir, remove):
         sys.exit(1)
 
 
-def modules_remove(ctx, dir, tool):
+def modules_remove(ctx, directory, tool):
     """
     Remove a module from a pipeline.
     """
@@ -151,7 +151,7 @@ def modules_remove(ctx, dir, tool):
 
     try:
         module_remove = ModuleRemove(
-            dir,
+            directory,
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
@@ -165,7 +165,7 @@ def modules_remove(ctx, dir, tool):
 def modules_create(
     ctx,
     tool,
-    dir,
+    directory,
     author,
     label,
     meta,
@@ -199,7 +199,7 @@ def modules_create(
     # Run function
     try:
         module_create = ModuleCreate(
-            dir,
+            directory,
             tool,
             author,
             label,
@@ -219,7 +219,7 @@ def modules_create(
         sys.exit(1)
 
 
-def modules_test(ctx, tool, dir, no_prompts, update, once, profile):
+def modules_test(ctx, tool, directory, no_prompts, update, once, profile):
     """
     Run nf-test for a module.
 
@@ -231,7 +231,7 @@ def modules_test(ctx, tool, dir, no_prompts, update, once, profile):
         module_tester = ComponentsTest(
             component_type="modules",
             component_name=tool,
-            directory=dir,
+            directory=directory,
             no_prompts=no_prompts,
             update=update,
             once=once,
@@ -246,7 +246,7 @@ def modules_test(ctx, tool, dir, no_prompts, update, once, profile):
         sys.exit(1)
 
 
-def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version):
+def modules_lint(ctx, tool, directory, registry, key, all, fail_warned, local, passed, sort_by, fix_version):
     """
     Lint one or more modules in a directory.
 
@@ -261,7 +261,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed,
 
     try:
         module_lint = ModuleLint(
-            dir,
+            directory,
             fail_warned=fail_warned,
             registry=ctx.params["registry"],
             remote_url=ctx.obj["modules_repo_url"],
@@ -290,7 +290,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed,
         sys.exit(1)
 
 
-def modules_info(ctx, tool, dir):
+def modules_info(ctx, tool, directory):
     """
     Show developer usage information about a given module.
 
@@ -306,7 +306,7 @@ def modules_info(ctx, tool, dir):
 
     try:
         module_info = ModuleInfo(
-            dir,
+            directory,
             tool,
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
@@ -318,7 +318,7 @@ def modules_info(ctx, tool, dir):
         sys.exit(1)
 
 
-def modules_bump_versions(ctx, tool, dir, all, show_all):
+def modules_bump_versions(ctx, tool, directory, all, show_all):
     """
     Bump versions for one or more modules in a clone of
     the nf-core/modules repo.
@@ -328,7 +328,7 @@ def modules_bump_versions(ctx, tool, dir, all, show_all):
 
     try:
         version_bumper = ModuleVersionBumper(
-            dir,
+            directory,
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py
index a3abce3f85..36fd998a68 100644
--- a/nf_core/commands_subworkflows.py
+++ b/nf_core/commands_subworkflows.py
@@ -10,7 +10,7 @@
 stdout = rich.console.Console(force_terminal=rich_force_colors())
 
 
-def subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest):
+def subworkflows_create(ctx, subworkflow, directory, author, force, migrate_pytest):
     """
     Create a new subworkflow from the nf-core template.
 
@@ -24,7 +24,7 @@ def subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest):
 
     # Run function
     try:
-        subworkflow_create = SubworkflowCreate(dir, subworkflow, author, force, migrate_pytest)
+        subworkflow_create = SubworkflowCreate(directory, subworkflow, author, force, migrate_pytest)
         subworkflow_create.create()
     except UserWarning as e:
         log.critical(e)
@@ -34,7 +34,7 @@ def subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest):
         sys.exit(1)
 
 
-def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile):
+def subworkflows_test(ctx, subworkflow, directory, no_prompts, update, once, profile):
     """
     Run nf-test for a subworkflow.
 
@@ -46,7 +46,7 @@ def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile):
         sw_tester = ComponentsTest(
             component_type="subworkflows",
             component_name=subworkflow,
-            directory=dir,
+            directory=directory,
             no_prompts=no_prompts,
             update=update,
             once=once,
@@ -69,7 +69,7 @@ def subworkflows_list_remote(ctx, keywords, json):
 
     try:
         subworkflow_list = SubworkflowList(
-            None,
+            ".",
             True,
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
@@ -82,7 +82,7 @@ def subworkflows_list_remote(ctx, keywords, json):
         sys.exit(1)
 
 
-def subworkflows_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
+def subworkflows_list_local(ctx, keywords, json, directory):  # pylint: disable=redefined-builtin
     """
     List subworkflows installed locally in a pipeline
     """
@@ -90,7 +90,7 @@ def subworkflows_list_local(ctx, keywords, json, dir):  # pylint: disable=redefi
 
     try:
         subworkflow_list = SubworkflowList(
-            dir,
+            directory,
             False,
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
@@ -102,7 +102,7 @@ def subworkflows_list_local(ctx, keywords, json, dir):  # pylint: disable=redefi
         sys.exit(1)
 
 
-def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by):
+def subworkflows_lint(ctx, subworkflow, directory, registry, key, all, fail_warned, local, passed, sort_by):
     """
     Lint one or more subworkflows in a directory.
 
@@ -117,7 +117,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo
 
     try:
         subworkflow_lint = SubworkflowLint(
-            dir,
+            directory,
             fail_warned=fail_warned,
             registry=ctx.params["registry"],
             remote_url=ctx.obj["modules_repo_url"],
@@ -145,7 +145,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo
         sys.exit(1)
 
 
-def subworkflows_info(ctx, subworkflow, dir):
+def subworkflows_info(ctx, subworkflow, directory):
     """
     Show developer usage information about a given subworkflow.
 
@@ -161,7 +161,7 @@ def subworkflows_info(ctx, subworkflow, dir):
 
     try:
         subworkflow_info = SubworkflowInfo(
-            dir,
+            directory,
             subworkflow,
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
@@ -173,7 +173,7 @@ def subworkflows_info(ctx, subworkflow, dir):
         sys.exit(1)
 
 
-def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha):
+def subworkflows_install(ctx, subworkflow, directory, prompt, force, sha):
     """
     Install DSL2 subworkflow within a pipeline.
 
@@ -183,7 +183,7 @@ def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha):
 
     try:
         subworkflow_install = SubworkflowInstall(
-            dir,
+            directory,
             force,
             prompt,
             sha,
@@ -199,7 +199,7 @@ def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha):
         sys.exit(1)
 
 
-def subworkflows_remove(ctx, dir, subworkflow):
+def subworkflows_remove(ctx, directory, subworkflow):
     """
     Remove a subworkflow from a pipeline.
     """
@@ -207,7 +207,7 @@ def subworkflows_remove(ctx, dir, subworkflow):
 
     try:
         module_remove = SubworkflowRemove(
-            dir,
+            directory,
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
@@ -221,7 +221,7 @@ def subworkflows_remove(ctx, dir, subworkflow):
 def subworkflows_update(
     ctx,
     subworkflow,
-    dir,
+    directory,
     force,
     prompt,
     sha,
@@ -240,7 +240,7 @@ def subworkflows_update(
 
     try:
         subworkflow_install = SubworkflowUpdate(
-            dir,
+            directory,
             force,
             prompt,
             sha,
diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index ada8b532e5..69f067f8fe 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -22,9 +22,7 @@ class ComponentCommand:
     def __init__(
         self,
         component_type: str,
-        directory: Union[
-            str, Path
-        ],  # TODO: This is actually None sometimes (e.g. in test_modules_list_remote), need to rewrite the logic here to handle these cases elegantly, for example setting a default path
+        directory: Union[str, Path] = ".",
         remote_url: Optional[str] = None,
         branch: Optional[str] = None,
         no_pull: bool = False,
@@ -34,11 +32,11 @@ def __init__(
         """
         Initialise the ComponentClass object
         """
-        self.component_type = component_type
-        self.directory = directory
+        self.component_type: str = component_type
+        self.directory: Path = Path(directory)
         self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)
-        self.hide_progress = hide_progress
-        self.no_prompts = no_prompts
+        self.hide_progress: bool = hide_progress
+        self.no_prompts: bool = no_prompts
         self._configure_repo_and_paths()
 
     def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
diff --git a/nf_core/components/list.py b/nf_core/components/list.py
index 0a6b654467..ded035c897 100644
--- a/nf_core/components/list.py
+++ b/nf_core/components/list.py
@@ -25,7 +25,9 @@ def __init__(
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
         self.remote = remote
 
-    def list_components(self, keywords: Optional[List[str]] = None, print_json=False) -> Union[rich.table.Table, str]:
+    def list_components(
+        self, keywords: Optional[List[str]] = None, print_json: bool = False
+    ) -> Union[rich.table.Table, str]:
         keywords = keywords or []
         """
         Get available modules/subworkflows names from GitHub tree for repo
diff --git a/nf_core/modules/list.py b/nf_core/modules/list.py
index c7dc943f9e..68da570f67 100644
--- a/nf_core/modules/list.py
+++ b/nf_core/modules/list.py
@@ -1,4 +1,6 @@
 import logging
+from pathlib import Path
+from typing import Optional, Union
 
 from nf_core.components.list import ComponentList
 
@@ -6,5 +8,12 @@
 
 
 class ModuleList(ComponentList):
-    def __init__(self, pipeline_dir, remote=True, remote_url=None, branch=None, no_pull=False):
+    def __init__(
+        self,
+        pipeline_dir: Union[str, Path] = ".",
+        remote: bool = True,
+        remote_url: Optional[str] = None,
+        branch: Optional[str] = None,
+        no_pull: bool = False,
+    ):
         super().__init__("modules", pipeline_dir, remote, remote_url, branch, no_pull)
diff --git a/nf_core/subworkflows/list.py b/nf_core/subworkflows/list.py
index ddf144ee00..9e84d6cbe0 100644
--- a/nf_core/subworkflows/list.py
+++ b/nf_core/subworkflows/list.py
@@ -1,4 +1,6 @@
 import logging
+from pathlib import Path
+from typing import Optional, Union
 
 from nf_core.components.list import ComponentList
 
@@ -6,5 +8,12 @@
 
 
 class SubworkflowList(ComponentList):
-    def __init__(self, pipeline_dir, remote=True, remote_url=None, branch=None, no_pull=False):
+    def __init__(
+        self,
+        pipeline_dir: Union[str, Path] = ".",
+        remote: bool = True,
+        remote_url: Optional[str] = None,
+        branch: Optional[str] = None,
+        no_pull: bool = False,
+    ) -> None:
         super().__init__("subworkflows", pipeline_dir, remote, remote_url, branch, no_pull)
diff --git a/tests/modules/test_list.py b/tests/modules/test_list.py
index fdbb61f69e..a170f6d6fc 100644
--- a/tests/modules/test_list.py
+++ b/tests/modules/test_list.py
@@ -13,7 +13,7 @@
 class TestModulesCreate(TestModules):
     def test_modules_list_remote(self):
         """Test listing available modules"""
-        mods_list = nf_core.modules.list.ModuleList(None, remote=True)
+        mods_list = nf_core.modules.list.ModuleList(remote=True)
         listed_mods = mods_list.list_components()
         console = Console(record=True)
         console.print(listed_mods)
@@ -22,9 +22,7 @@ def test_modules_list_remote(self):
 
     def test_modules_list_remote_gitlab(self):
         """Test listing the modules in the remote gitlab repo"""
-        mods_list = nf_core.modules.list.ModuleList(
-            None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH
-        )
+        mods_list = nf_core.modules.list.ModuleList(remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH)
         listed_mods = mods_list.list_components()
         console = Console(record=True)
         console.print(listed_mods)
@@ -64,22 +62,22 @@ def test_modules_install_gitlab_and_list_pipeline(self):
     def test_modules_list_local_json(self):
         """Test listing locally installed modules as JSON"""
         mods_list = nf_core.modules.list.ModuleList(self.pipeline_dir, remote=False)
-        listed_mods = mods_list.list_components(print_json=True)
+        listed_mods = str(mods_list.list_components(print_json=True))
         listed_mods = json.loads(listed_mods)
         assert "fastqc" in listed_mods
         assert "multiqc" in listed_mods
 
     def test_modules_list_remote_json(self):
         """Test listing available modules as JSON"""
-        mods_list = nf_core.modules.list.ModuleList(None, remote=True)
-        listed_mods = mods_list.list_components(print_json=True)
+        mods_list = nf_core.modules.list.ModuleList(remote=True)
+        listed_mods: str = str(mods_list.list_components(print_json=True))
         listed_mods = json.loads(listed_mods)
         assert "fastqc" in listed_mods
         assert "multiqc" in listed_mods
 
     def test_modules_list_with_one_keyword(self):
         """Test listing available modules with one keyword"""
-        mods_list = nf_core.modules.list.ModuleList(None, remote=True)
+        mods_list = nf_core.modules.list.ModuleList(remote=True)
         listed_mods = mods_list.list_components(keywords=["qc"])
         console = Console(record=True)
         console.print(listed_mods)
@@ -88,7 +86,7 @@ def test_modules_list_with_one_keyword(self):
 
     def test_modules_list_with_keywords(self):
         """Test listing available modules with multiple keywords"""
-        mods_list = nf_core.modules.list.ModuleList(None, remote=True)
+        mods_list = nf_core.modules.list.ModuleList(remote=True)
         listed_mods = mods_list.list_components(keywords=["fastq", "qc"])
         console = Console(record=True)
         console.print(listed_mods)
@@ -97,7 +95,7 @@ def test_modules_list_with_keywords(self):
 
     def test_modules_list_with_unused_keyword(self):
         """Test listing available modules with an unused keyword"""
-        mods_list = nf_core.modules.list.ModuleList(None, remote=True)
+        mods_list = nf_core.modules.list.ModuleList(remote=True)
         with self.assertLogs(level="INFO") as log:
             listed_mods = mods_list.list_components(keywords=["you_will_never_find_me"])
             self.assertIn("No available", log.output[0])
diff --git a/tests/subworkflows/test_list.py b/tests/subworkflows/test_list.py
index 5e4e6feb0a..aa1c4de7af 100644
--- a/tests/subworkflows/test_list.py
+++ b/tests/subworkflows/test_list.py
@@ -9,7 +9,7 @@
 class TestSubworkflowsList(TestSubworkflows):
     def test_subworkflows_list_remote(self):
         """Test listing available subworkflows"""
-        subworkflows_list = nf_core.subworkflows.SubworkflowList(None, remote=True)
+        subworkflows_list = nf_core.subworkflows.SubworkflowList(remote=True)
         listed_subworkflows = subworkflows_list.list_components()
         console = Console(record=True)
         console.print(listed_subworkflows)

From ebdb3981fec56235822f07d19dca7bc2c206e7ee Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 14:26:37 +0200
Subject: [PATCH 146/414] remove unnecessary checks

---
 nf_core/components/components_command.py | 2 +-
 nf_core/components/components_utils.py   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 69f067f8fe..7d43b387fc 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -94,7 +94,7 @@ def has_valid_directory(self) -> bool:
         """Check that we were given a pipeline or clone of nf-core/modules"""
         if self.repo_type == "modules":
             return True
-        if self.directory is None or not Path(self.directory).exists():
+        if not Path(self.directory).exists():
             log.error(f"Could not find directory: {self.directory}")
             return False
         main_nf = Path(self.directory, "main.nf")
diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py
index 3d64dc1bb6..632ae7b2aa 100644
--- a/nf_core/components/components_utils.py
+++ b/nf_core/components/components_utils.py
@@ -26,7 +26,7 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P
     """
 
     # Verify that the pipeline dir exists
-    if directory is None or not Path(directory).is_dir():
+    if not Path(directory).is_dir():
         raise UserWarning(f"Could not find directory: {directory}")
 
     # Try to find the root directory

From 15a9071886fda734d182a2ae10a2dd78074c3d48 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 14:33:20 +0200
Subject: [PATCH 147/414] remove unnecessary Path conversions

---
 nf_core/components/components_command.py | 12 +++++-------
 nf_core/components/components_test.py    |  2 +-
 nf_core/components/lint/__init__.py      | 12 +++++-------
 nf_core/modules/bump_versions.py         |  2 +-
 4 files changed, 12 insertions(+), 16 deletions(-)

diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 7d43b387fc..4e739fd6b8 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -49,9 +49,7 @@ def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
         """
         try:
             if self.directory:
-                self.directory, self.repo_type, self.org = get_repo_info(
-                    Path(self.directory), use_prompt=not self.no_prompts
-                )
+                self.directory, self.repo_type, self.org = get_repo_info(self.directory, use_prompt=not self.no_prompts)
             else:
                 self.repo_type = None
                 self.org = ""
@@ -94,13 +92,13 @@ def has_valid_directory(self) -> bool:
         """Check that we were given a pipeline or clone of nf-core/modules"""
         if self.repo_type == "modules":
             return True
-        if not Path(self.directory).exists():
+        if not self.directory.exists():
             log.error(f"Could not find directory: {self.directory}")
             return False
         main_nf = Path(self.directory, "main.nf")
         nf_config = Path(self.directory, "nextflow.config")
         if not main_nf.exists() and not nf_config.exists():
-            if Path(self.directory).resolve().parts[-1].startswith("nf-core"):
+            if self.directory.resolve().parts[-1].startswith("nf-core"):
                 raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'")
             log.warning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'")
         return True
@@ -125,7 +123,7 @@ def clear_component_dir(self, component_name: str, component_dir: Union[str, Pat
         try:
             shutil.rmtree(component_dir)
             # remove all empty directories
-            for dir_path, dir_names, filenames in os.walk(Path(self.directory), topdown=False):
+            for dir_path, dir_names, filenames in os.walk(self.directory, topdown=False):
                 if not dir_names and not filenames:
                     try:
                         Path(dir_path).rmdir()
@@ -258,7 +256,7 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None:
                 ):
                     modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][
                         self.modules_repo.repo_path
-                    ][module_name]["patch"] = str(patch_path.relative_to(Path(self.directory).resolve()))
+                    ][module_name]["patch"] = str(patch_path.relative_to(self.directory.resolve()))
                 modules_json.dump()
 
     def check_if_in_include_stmts(self, component_path: str) -> Dict[str, List[Dict[str, Union[int, str]]]]:
diff --git a/nf_core/components/components_test.py b/nf_core/components/components_test.py
index f9b891004a..57c0034ba4 100644
--- a/nf_core/components/components_test.py
+++ b/nf_core/components/components_test.py
@@ -93,7 +93,7 @@ def run(self) -> None:
         os.environ["NFT_DIFF_ARGS"] = (
             "--line-numbers --expand-tabs=2"  # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences
         )
-        with nf_core.utils.set_wd(Path(self.directory)):
+        with nf_core.utils.set_wd(self.directory):
             self.check_snapshot_stability()
         if len(self.errors) > 0:
             errors = "\n - ".join(self.errors)
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index ddf5e1e165..be6b225a0a 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -104,7 +104,7 @@ def __init__(
                             repo_url,
                             Path(self.directory, self.component_type, org, comp),
                             self.repo_type,
-                            Path(self.directory),
+                            self.directory,
                             self.component_type,
                         )
                     )
@@ -121,20 +121,20 @@ def __init__(
                         None,
                         Path(local_component_dir, comp),
                         self.repo_type,
-                        Path(self.directory),
+                        self.directory,
                         self.component_type,
                         remote_component=False,
                     )
                     for comp in self.get_local_components()
                 ]
-            self.config = nf_core.utils.fetch_wf_config(Path(self.directory), cache_config=True)
+            self.config = nf_core.utils.fetch_wf_config(self.directory, cache_config=True)
         elif self.repo_type == "modules":
             component_dir = Path(
                 self.directory,
                 self.default_modules_path if self.component_type == "modules" else self.default_subworkflows_path,
             )
             self.all_remote_components = [
-                NFCoreComponent(m, None, component_dir / m, self.repo_type, Path(self.directory), self.component_type)
+                NFCoreComponent(m, None, component_dir / m, self.repo_type, self.directory, self.component_type)
                 for m in self.get_components_clone_modules()
             ]
             self.all_local_components = []
@@ -142,9 +142,7 @@ def __init__(
                 raise LookupError(f"No {self.component_type} in '{self.component_type}' directory")
 
             # This could be better, perhaps glob for all nextflow.config files in?
-            self.config = nf_core.utils.fetch_wf_config(
-                Path(self.directory).joinpath("tests", "config"), cache_config=True
-            )
+            self.config = nf_core.utils.fetch_wf_config(self.directory / "tests" / "config", cache_config=True)
 
             if registry is None:
                 self.registry = self.config.get("docker.registry", "quay.io")
diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
index 6546cccc9a..2d8854e3c0 100644
--- a/nf_core/modules/bump_versions.py
+++ b/nf_core/modules/bump_versions.py
@@ -76,7 +76,7 @@ def bump_versions(
             )
 
         # Get list of all modules
-        _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(Path(self.directory))
+        _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.directory)
 
         # Load the .nf-core.yml config
         _, self.tools_config = nf_core.utils.load_tools_config(self.directory)

From fa00b1b61e0315177bee09c3d2e8f486cd4ae86e Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 14:42:13 +0200
Subject: [PATCH 148/414] fix types for 3.8

---
 nf_core/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/utils.py b/nf_core/utils.py
index 80324fc9a8..86ed09555c 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -905,7 +905,7 @@ def prompt_remote_pipeline_name(wfs):
 
 def prompt_pipeline_release_branch(
     wf_releases: List[Dict[str, Any]], wf_branches: Dict[str, Any], multiple: bool = False
-) -> tuple[Any, list[str]]:
+) -> Tuple[Any, List[str]]:
     """Prompt for pipeline release / branch
 
     Args:

From e7f06bea17e9c29bb40a1b7f8e54818ab308a264 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 14:46:10 +0200
Subject: [PATCH 149/414] limit `component` to type string

---
 nf_core/components/install.py   |  9 +++++----
 nf_core/modules/modules_json.py | 14 ++++++--------
 2 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/nf_core/components/install.py b/nf_core/components/install.py
index f2849f85bc..9b42ba77db 100644
--- a/nf_core/components/install.py
+++ b/nf_core/components/install.py
@@ -1,7 +1,10 @@
 import logging
 import os
 from pathlib import Path
-from typing import List, Optional, Union
+from typing import TYPE_CHECKING, List, Optional, Union
+
+if TYPE_CHECKING:
+    from nf_core.modules.modules_repo import ModulesRepo
 
 import questionary
 from rich.console import Console
@@ -180,9 +183,7 @@ def install_included_components(self, subworkflow_dir):
             self.component_type = original_component_type
             self.installed_by = original_installed
 
-    def collect_and_verify_name(
-        self, component: Optional[str], modules_repo: "nf_core.modules.modules_repo.ModulesRepo"
-    ) -> str:
+    def collect_and_verify_name(self, component: Optional[str], modules_repo: ModulesRepo) -> str:
         """
         Collect component name.
         Check that the supplied name is an available module/subworkflow.
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 39d70b7d78..ff4922dc02 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -355,7 +355,7 @@ def determine_branches_and_shas(
 
         # Clean up the modules/subworkflows we were unable to find the sha for
         for component in sb_local:
-            log.debug(f"Moving {component_type[:-1]} '{Path(install_dir, str(component))}' to 'local' directory")
+            log.debug(f"Moving {component_type[:-1]} '{Path(install_dir, component)}' to 'local' directory")
             self.move_component_to_local(component_type, component, str(install_dir))
 
         for component in dead_components:
@@ -398,13 +398,13 @@ def find_correct_commit_sha(
                 return commit_sha
         return None
 
-    def move_component_to_local(self, component_type: str, component: Union[str, Path], repo_name: str):
+    def move_component_to_local(self, component_type: str, component: str, repo_name: str):
         """
         Move a module/subworkflow to the 'local' directory
 
         Args:
             component_type (str): The type of component, either 'modules' or 'subworkflows'
-            component (Union[str,Path]): The name of the module/subworkflow
+            component (str): The name of the module/subworkflow
             repo_name (str): The name of the repository the module resides in
         """
         if component_type == "modules":
@@ -418,7 +418,7 @@ def move_component_to_local(self, component_type: str, component: Union[str, Pat
         if not local_dir.exists():
             local_dir.mkdir()
 
-        to_name = str(component)
+        to_name = component
         # Check if there is already a subdirectory with the name
         while (local_dir / to_name).exists():
             # Add a time suffix to the path to make it unique
@@ -1086,9 +1086,7 @@ def get_installed_by_entries(self, component_type, name):
 
         return installed_by_entries
 
-    def get_component_branch(
-        self, component_type: str, component: Union[str, Path], repo_url: str, install_dir: str
-    ) -> str:
+    def get_component_branch(self, component_type: str, component: str, repo_url: str, install_dir: str) -> str:
         """
         Gets the branch from which the module/subworkflow was installed
 
@@ -1101,7 +1099,7 @@ def get_component_branch(
             self.load()
             assert self.modules_json is not None  # mypy
         try:
-            branch = self.modules_json["repos"][repo_url][component_type][install_dir][str(component)]["branch"]
+            branch = self.modules_json["repos"][repo_url][component_type][install_dir][component]["branch"]
         except (KeyError, TypeError):
             branch = None
         if branch is None:

From ae7d912369630daaf2e43ddcd636bdb8d8cfb2d4 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 14:59:04 +0200
Subject: [PATCH 150/414] handle more type warnings

---
 nf_core/modules/modules_json.py | 10 ++++++++--
 nf_core/modules/modules_repo.py |  2 +-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index ff4922dc02..19649a57cd 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -42,7 +42,7 @@ class ModulesJson:
     An object for handling a 'modules.json' file in a pipeline
     """
 
-    def __init__(self, pipeline_dir: Union[str, Path]):
+    def __init__(self, pipeline_dir: Union[str, Path]) -> None:
         """
         Initialise the object.
 
@@ -130,6 +130,10 @@ def get_component_names_from_repo(
         names = []
         for repo_url in repos:
             modules_repo = ModulesRepo(repo_url)
+            if modules_repo is None:
+                raise UserWarning(f"Could not find module repository for '{repo_url}' in '{directory}'")
+            if modules_repo.repo_path is None:
+                raise UserWarning(f"Could not find module repository path for '{repo_url}' in '{directory}'")
             components = (
                 repo_url,
                 [
@@ -195,6 +199,8 @@ def get_pipeline_module_repositories(
 
                 # Verify that there is a directory corresponding the remote
                 nrepo_name = ModulesRepo(nrepo_remote).repo_path
+                if nrepo_name is None:
+                    raise UserWarning(f"Could not find the repository name for '{nrepo_remote}'")
                 if not (directory / nrepo_name).exists():
                     log.info(
                         "The provided remote does not seem to correspond to a local directory. "
@@ -416,7 +422,7 @@ def move_component_to_local(self, component_type: str, component: str, repo_name
         current_path = directory / repo_name / component
         local_dir = directory / "local"
         if not local_dir.exists():
-            local_dir.mkdir()
+            local_dir.mkdir(parents=True)
 
         to_name = component
         # Check if there is already a subdirectory with the name
diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py
index 5b50205484..357fc49cc5 100644
--- a/nf_core/modules/modules_repo.py
+++ b/nf_core/modules/modules_repo.py
@@ -40,7 +40,7 @@ def __init__(
         branch: Optional[str] = None,
         no_pull: bool = False,
         hide_progress: bool = False,
-    ):
+    ) -> None:
         """
         Initializes the object and clones the git repository if it is not already present
         """

From d7587dc1577602ab26d53dd34a438aedfb4c8a1e Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 16:18:32 +0200
Subject: [PATCH 151/414] fix import errors, handle outdir as string

---
 nf_core/components/info.py         | 17 +++++++++--------
 nf_core/components/install.py      | 10 +++++-----
 nf_core/pipelines/create/create.py |  3 +--
 nf_core/utils.py                   | 12 ++++++++++--
 4 files changed, 25 insertions(+), 17 deletions(-)

diff --git a/nf_core/components/info.py b/nf_core/components/info.py
index 726586b5b7..98f8be5272 100644
--- a/nf_core/components/info.py
+++ b/nf_core/components/info.py
@@ -1,7 +1,7 @@
 import logging
 import os
 from pathlib import Path
-from typing import Dict, Optional, Union
+from typing import Dict, List, Optional, Tuple, Union
 
 import questionary
 import yaml
@@ -83,14 +83,14 @@ def __init__(
             self.modules_json = None
         self.component = self.init_mod_name(component_name)
 
-    def _configure_repo_and_paths(self, nf_dir_req=False):
+    def _configure_repo_and_paths(self, nf_dir_req=False) -> None:
         """
         Override the default with nf_dir_req set to False to allow
         info to be run from anywhere and still return remote info
         """
         return super()._configure_repo_and_paths(nf_dir_req)
 
-    def init_mod_name(self, component):
+    def init_mod_name(self, component: Optional[str]) -> str:
         """
         Makes sure that we have a module/subworkflow name before proceeding.
 
@@ -106,9 +106,10 @@ def init_mod_name(self, component):
                     components = self.get_components_clone_modules()
                 elif self.repo_type == "pipeline":
                     assert self.modules_json is not None  # mypy
-                    all_components = self.modules_json.get_all_components(self.component_type).get(
-                        self.modules_repo.remote_url, {}
-                    )
+                    all_components: List[Tuple[str, str]] = self.modules_json.get_all_components(
+                        self.component_type
+                    ).get(self.modules_repo.remote_url, [])
+
                     components = [
                         component if directory == self.modules_repo.repo_path else f"{directory}/{component}"
                         for directory, component in all_components
@@ -169,7 +170,7 @@ def get_component_info(self):
 
         return self.generate_component_info_help()
 
-    def get_local_yaml(self):
+    def get_local_yaml(self) -> Optional[Dict]:
         """Attempt to get the meta.yml file from a locally installed module/subworkflow.
 
         Returns:
@@ -316,7 +317,7 @@ def generate_component_info_help(self):
             )
 
         # Print include statement
-        if self.local_path:
+        if self.local_path and self.modules_repo.repo_path is not None:
             install_folder = Path(self.directory, self.component_type, self.modules_repo.repo_path)
             component_name = "_".join(self.component.upper().split("/"))
             renderables.append(
diff --git a/nf_core/components/install.py b/nf_core/components/install.py
index 9b42ba77db..a7be737bf9 100644
--- a/nf_core/components/install.py
+++ b/nf_core/components/install.py
@@ -1,16 +1,14 @@
 import logging
 import os
 from pathlib import Path
-from typing import TYPE_CHECKING, List, Optional, Union
-
-if TYPE_CHECKING:
-    from nf_core.modules.modules_repo import ModulesRepo
+from typing import List, Optional, Union
 
 import questionary
 from rich.console import Console
 from rich.syntax import Syntax
 
 import nf_core.components
+import nf_core.modules.modules_repo
 import nf_core.modules.modules_utils
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
@@ -183,7 +181,9 @@ def install_included_components(self, subworkflow_dir):
             self.component_type = original_component_type
             self.installed_by = original_installed
 
-    def collect_and_verify_name(self, component: Optional[str], modules_repo: ModulesRepo) -> str:
+    def collect_and_verify_name(
+        self, component: Optional[str], modules_repo: "nf_core.modules.modules_repo.ModulesRepo"
+    ) -> str:
         """
         Collect component name.
         Check that the supplied name is an available module/subworkflow.
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index d5c230e048..899507847e 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -83,9 +83,8 @@ def __init__(
 
         if self.config.outdir is None:
             self.config.outdir = str(Path.cwd())
-
         self.jinja_params, skip_paths = self.obtain_jinja_params_dict(
-            self.config.skip_features or [], Path(self.config.outdir)
+            self.config.skip_features or [], str(self.config.outdir)
         )
 
         skippable_paths = {
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 86ed09555c..c1cc7c1301 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -30,7 +30,7 @@
 import rich.markup
 import yaml
 from packaging.version import Version
-from pydantic import BaseModel, ValidationError
+from pydantic import BaseModel, ValidationError, field_validator
 from rich.live import Live
 from rich.spinner import Spinner
 
@@ -1050,10 +1050,18 @@ class NFCoreTemplateConfig(BaseModel):
     author: Optional[str] = None
     version: Optional[str] = None
     force: Optional[bool] = None
-    outdir: Optional[str] = None
+    outdir: Optional[Union[str, Path]] = None
     skip_features: Optional[list] = None
     is_nfcore: Optional[bool] = None
 
+    # convert outdir to str
+    @field_validator("outdir")
+    @classmethod
+    def outdir_to_str(cls, v: Optional[Union[str, Path]]) -> Optional[str]:
+        if v is not None:
+            v = str(v)
+        return v
+
     def __getitem__(self, item: str) -> Any:
         if self is None:
             return None

From a4cf066e3a041be2b05fa67c661f408644bd5327 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Mon, 29 Jul 2024 16:41:19 +0200
Subject: [PATCH 152/414] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 nf_core/pipelines/create/custompipeline.py | 4 ++--
 tests/test_create.py                       | 1 -
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py
index 7a94ab228a..0925fb5bab 100644
--- a/nf_core/pipelines/create/custompipeline.py
+++ b/nf_core/pipelines/create/custompipeline.py
@@ -42,8 +42,8 @@
 """
 
 markdown_code_linters = """
-Pipelines include code linters, these linters will check the formatting of your code.
-Linters will check JSON, YAML, Python and others.
+Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers.
+Linters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository.
 The available code linters are:
 
 - pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository.
diff --git a/tests/test_create.py b/tests/test_create.py
index 896a8e7ad6..b4ac89c7de 100644
--- a/tests/test_create.py
+++ b/tests/test_create.py
@@ -118,4 +118,3 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path):
         assert not os.path.exists(Path(pipeline.outdir / ".github"))
         assert not os.path.exists(Path(pipeline.outdir / "conf" / "igenomes.config"))
         assert not os.path.exists(Path(pipeline.outdir / ".editorconfig"))
-        assert not os.path.exists(Path(pipeline.outdir / ".editorconfig"))

From 419242b931ff228fee0babf63d50313b2fbd6ee9 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 29 Jul 2024 16:46:46 +0200
Subject: [PATCH 153/414] use pathlib instead of os.path

---
 tests/test_create.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tests/test_create.py b/tests/test_create.py
index b4ac89c7de..920a0f4750 100644
--- a/tests/test_create.py
+++ b/tests/test_create.py
@@ -106,15 +106,15 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path):
         pipeline.init_pipeline()
 
         # Check pipeline template yml has been dumped to `.nf-core.yml` and matches input
-        assert not os.path.exists(Path(pipeline.outdir / "pipeline_template.yml"))
-        assert os.path.exists(Path(pipeline.outdir / ".nf-core.yml"))
-        with open(Path(pipeline.outdir / ".nf-core.yml")) as fh:
+        assert not (pipeline.outdir / "pipeline_template.yml").exists()
+        assert (pipeline.outdir / ".nf-core.yml").exists()
+        with open(pipeline.outdir / ".nf-core.yml") as fh:
             nfcore_yml = yaml.safe_load(fh)
             assert "template" in nfcore_yml
             assert yaml.safe_load(PIPELINE_TEMPLATE_YML.read_text()).items() <= nfcore_yml["template"].items()
 
         # Check that some of the skipped files are not present
-        assert not os.path.exists(Path(pipeline.outdir / "CODE_OF_CONDUCT.md"))
-        assert not os.path.exists(Path(pipeline.outdir / ".github"))
-        assert not os.path.exists(Path(pipeline.outdir / "conf" / "igenomes.config"))
-        assert not os.path.exists(Path(pipeline.outdir / ".editorconfig"))
+        assert not (pipeline.outdir / "CODE_OF_CONDUCT.md").exists()
+        assert not (pipeline.outdir / ".github").exists()
+        assert not (pipeline.outdir / "conf" / "igenomes.config").exists()
+        assert not (pipeline.outdir / ".editorconfig").exists()

From f5e865086bda88e28523f0757bf4e71366b228ad Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 29 Jul 2024 16:48:44 +0200
Subject: [PATCH 154/414] update chagelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b27dce4b5c..8eae70a311 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@
 - Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046))
 - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055))
 - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072))
+- add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084))
 
 ### Linting
 

From 5979b9d1f4ee8fa157eb1798ec3a7226238f00cb Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 17:24:52 +0200
Subject: [PATCH 155/414] add error message and resolve circular import

---
 nf_core/components/components_utils.py |  2 +-
 nf_core/components/install.py          | 13 +++++++++----
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py
index 632ae7b2aa..9289d90004 100644
--- a/nf_core/components/components_utils.py
+++ b/nf_core/components/components_utils.py
@@ -63,7 +63,7 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P
 
     # Check if it's a valid answer
     if repo_type not in ["pipeline", "modules"]:
-        raise UserWarning(f"Invalid repository type: '{repo_type}'")
+        raise UserWarning(f"Invalid repository type: '{repo_type}', must be 'pipeline' or 'modules'")
     org: str = ""
     # Check for org if modules repo
     if repo_type == "modules":
diff --git a/nf_core/components/install.py b/nf_core/components/install.py
index a7be737bf9..6130a4cf72 100644
--- a/nf_core/components/install.py
+++ b/nf_core/components/install.py
@@ -8,7 +8,6 @@
 from rich.syntax import Syntax
 
 import nf_core.components
-import nf_core.modules.modules_repo
 import nf_core.modules.modules_utils
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
@@ -69,12 +68,18 @@ def install(self, component: str, silent: bool = False) -> bool:
 
         # Verify SHA
         if not self.modules_repo.verify_sha(self.prompt, self.sha):
+            err_msg = f"SHA '{self.sha}' is not a valid commit SHA for the repository '{self.modules_repo.remote_url}'"
+            log.error(err_msg)
             return False
 
         # verify self.modules_repo entries:
         if self.modules_repo is None:
+            err_msg = "Could not find a valid modules repository."
+            log.error(err_msg)
             return False
         if self.modules_repo.repo_path is None:
+            err_msg = "Could not find a valid modules repository path."
+            log.error(err_msg)
             return False
 
         # Check and verify component name
@@ -200,10 +205,10 @@ def collect_and_verify_name(
 
         # Check that the supplied name is an available module/subworkflow
         if component and component not in modules_repo.get_avail_components(self.component_type, commit=self.sha):
-            log.error(
-                f"{self.component_type[:-1].title()} '{component}' not found in list of available {self.component_type}."
-            )
             log.info(f"Use the command 'nf-core {self.component_type} list' to view available software")
+            raise SystemError(
+                f"{self.component_type[:-1].title()} '{component}' not found in available {self.component_type}"
+            )
 
         if not modules_repo.component_exists(component, self.component_type, commit=self.sha):
             warn_msg = f"{self.component_type[:-1].title()} '{component}' not found in remote '{modules_repo.remote_url}' ({modules_repo.branch})"

From 24a3ece90f28b9efe1336a5768b55dc6dc62b184 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 17:45:45 +0200
Subject: [PATCH 156/414] actually test installation with a correct subworkflow

---
 tests/subworkflows/test_install.py | 46 ++++++++++++++++--------------
 1 file changed, 25 insertions(+), 21 deletions(-)

diff --git a/tests/subworkflows/test_install.py b/tests/subworkflows/test_install.py
index af1ad92415..e6ba9439a4 100644
--- a/tests/subworkflows/test_install.py
+++ b/tests/subworkflows/test_install.py
@@ -17,26 +17,6 @@
 
 
 class TestSubworkflowsInstall(TestSubworkflows):
-    def test_subworkflow_install_nopipeline(self):
-        """Test installing a subworkflow - no pipeline given"""
-        assert self.subworkflow_install.directory is not None
-        self.subworkflow_install.directory = Path("non_existent_dir")
-        assert self.subworkflow_install.install("foo") is False
-
-    @with_temporary_folder
-    def test_subworkflows_install_emptypipeline(self, tmpdir):
-        """Test installing a subworkflow - empty dir given"""
-
-        Path(tmpdir, "nf-core-pipe").mkdir(exist_ok=True)
-        self.subworkflow_install.directory = Path(tmpdir, "nf-core-pipe")
-        with pytest.raises(UserWarning) as excinfo:
-            self.subworkflow_install.install("foo")
-        assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
-
-    def test_subworkflows_install_nosubworkflow(self):
-        """Test installing a subworkflow - unrecognised subworkflow given"""
-        assert self.subworkflow_install.install("foo") is False
-
     def test_subworkflows_install_bam_sort_stats_samtools(self):
         """Test installing a subworkflow - bam_sort_stats_samtools"""
         assert self.subworkflow_install.install("bam_sort_stats_samtools") is not False
@@ -57,6 +37,28 @@ def test_subworkflows_install_bam_sort_stats_samtools(self):
         assert samtools_idxstats_path.exists()
         assert samtools_flagstat_path.exists()
 
+    def test_subworkflow_install_nopipeline(self):
+        """Test installing a subworkflow - no pipeline given"""
+        assert self.subworkflow_install.directory is not None
+        self.subworkflow_install.directory = Path("non_existent_dir")
+        assert self.subworkflow_install.install("bam_stats_samtools") is False
+
+    @with_temporary_folder
+    def test_subworkflows_install_emptypipeline(self, tmpdir):
+        """Test installing a subworkflow - empty dir given"""
+
+        Path(tmpdir, "nf-core-pipe").mkdir(exist_ok=True)
+        self.subworkflow_install.directory = Path(tmpdir, "nf-core-pipe")
+        with pytest.raises(UserWarning) as excinfo:
+            self.subworkflow_install.install("bam_stats_samtools")
+        assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
+
+    def test_subworkflows_install_nosubworkflow(self):
+        """Test installing a subworkflow - unrecognised subworkflow given"""
+        with pytest.raises(SystemError) as excinfo:
+            self.subworkflow_install.install("foo")
+        assert "Subworkflow 'foo' not found in available subworkflows" in str(excinfo.value)
+
     def test_subworkflows_install_bam_sort_stats_samtools_twice(self):
         """Test installing a subworkflow - bam_sort_stats_samtools already there"""
         self.subworkflow_install.install("bam_sort_stats_samtools")
@@ -76,7 +78,9 @@ def test_subworkflows_install_different_branch_fail(self):
         """Test installing a subworkflow from a different branch"""
         install_obj = SubworkflowInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH)
         # The bam_stats_samtools subworkflow does not exists in the branch-test branch
-        assert install_obj.install("bam_stats_samtools") is False
+        with pytest.raises(Exception) as excinfo:
+            install_obj.install("bam_stats_samtools")
+            assert "Subworkflow 'bam_stats_samtools' not found in available subworkflows" in str(excinfo.value)
 
     def test_subworkflows_install_tracking(self):
         """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json"""

From 05def5932e12de9aa8fa2d07d763a54cd552038c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 22:21:13 +0200
Subject: [PATCH 157/414] fix list and info command

---
 nf_core/components/components_command.py | 10 ++++------
 nf_core/components/lint/__init__.py      | 21 +++++++++++++++------
 nf_core/components/list.py               |  2 +-
 nf_core/modules/bump_versions.py         | 13 ++++++++-----
 nf_core/subworkflows/list.py             |  2 +-
 nf_core/utils.py                         |  2 ++
 tests/subworkflows/test_list.py          |  2 +-
 7 files changed, 32 insertions(+), 20 deletions(-)

diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 4e739fd6b8..bff2467383 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -37,6 +37,8 @@ def __init__(
         self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)
         self.hide_progress: bool = hide_progress
         self.no_prompts: bool = no_prompts
+        self.repo_type: Optional[str] = None
+        self.org: str = ""
         self._configure_repo_and_paths()
 
     def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
@@ -50,15 +52,11 @@ def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
         try:
             if self.directory:
                 self.directory, self.repo_type, self.org = get_repo_info(self.directory, use_prompt=not self.no_prompts)
-            else:
-                self.repo_type = None
-                self.org = ""
-
         except UserWarning:
             if nf_dir_req:
                 raise
-            self.repo_type = None
-            self.org = ""
+        except FileNotFoundError:
+            raise
 
         self.default_modules_path = Path("modules", self.org)
         self.default_tests_path = Path("tests", "modules", self.org)
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index be6b225a0a..d0f6685365 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -86,6 +86,11 @@ def __init__(
         else:
             self.lint_tests = self.get_all_subworkflow_lint_tests(self.repo_type == "pipeline")
 
+        if self.repo_type is None:
+            raise LookupError(
+                "Could not determine repository type. Please check the repository type in the nf-core.yml"
+            )
+
         if self.repo_type == "pipeline":
             modules_json = ModulesJson(self.directory)
             modules_json.check_up_to_date()
@@ -128,6 +133,8 @@ def __init__(
                     for comp in self.get_local_components()
                 ]
             self.config = nf_core.utils.fetch_wf_config(self.directory, cache_config=True)
+            self._set_registry(registry)
+
         elif self.repo_type == "modules":
             component_dir = Path(
                 self.directory,
@@ -143,16 +150,18 @@ def __init__(
 
             # This could be better, perhaps glob for all nextflow.config files in?
             self.config = nf_core.utils.fetch_wf_config(self.directory / "tests" / "config", cache_config=True)
-
-            if registry is None:
-                self.registry = self.config.get("docker.registry", "quay.io")
-            else:
-                self.registry = registry
-            log.debug(f"Registry set to {self.registry}")
+            self._set_registry(registry)
 
     def __repr__(self) -> str:
         return f"ComponentLint({self.component_type}, {self.directory})"
 
+    def _set_registry(self, registry) -> None:
+        if registry is None:
+            self.registry = self.config.get("docker.registry", "quay.io")
+        else:
+            self.registry = registry
+        log.debug(f"Registry set to {self.registry}")
+
     @staticmethod
     def get_all_module_lint_tests(is_pipeline):
         if is_pipeline:
diff --git a/nf_core/components/list.py b/nf_core/components/list.py
index ded035c897..65a28db716 100644
--- a/nf_core/components/list.py
+++ b/nf_core/components/list.py
@@ -16,7 +16,7 @@ class ComponentList(ComponentCommand):
     def __init__(
         self,
         component_type: str,
-        pipeline_dir: Union[str, Path],
+        pipeline_dir: Union[str, Path] = ".",
         remote: bool = True,
         remote_url: Optional[str] = None,
         branch: Optional[str] = None,
diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
index 2d8854e3c0..d98eac7cd6 100644
--- a/nf_core/modules/bump_versions.py
+++ b/nf_core/modules/bump_versions.py
@@ -245,12 +245,15 @@ def bump_module_version(self, module: NFCoreComponent) -> bool:
                 fh.write(content)
 
             # change version in environment.yml
-            with open(str(module.environment_yml)) as fh:
+            if not module.environment_yml:
+                log.error(f"Could not read `environment.yml` of {module.component_name} module.")
+                return False
+            with open(module.environment_yml) as fh:
                 env_yml = yaml.safe_load(fh)
             env_yml["dependencies"][0] = re.sub(
                 bioconda_packages[0], f"bioconda::{bioconda_tool_name}={last_ver}", env_yml["dependencies"][0]
             )
-            with open(str(module.environment_yml), "w") as fh:
+            with open(module.environment_yml, "w") as fh:
                 yaml.dump(env_yml, fh, default_flow_style=False, Dumper=custom_yaml_dumper())
 
             self.updated.append(
@@ -271,11 +274,11 @@ def get_bioconda_version(self, module: NFCoreComponent) -> List[str]:
         """
         # Check whether file exists and load it
         bioconda_packages = []
-        try:
-            with open(str(module.environment_yml)) as fh:
+        if module.environment_yml is not None and module.environment_yml.exists():
+            with open(module.environment_yml) as fh:
                 env_yml = yaml.safe_load(fh)
             bioconda_packages = env_yml.get("dependencies", [])
-        except FileNotFoundError:
+        else:
             log.error(f"Could not read `environment.yml` of {module.component_name} module.")
 
         return bioconda_packages
diff --git a/nf_core/subworkflows/list.py b/nf_core/subworkflows/list.py
index 9e84d6cbe0..5f849a1f9c 100644
--- a/nf_core/subworkflows/list.py
+++ b/nf_core/subworkflows/list.py
@@ -10,7 +10,7 @@
 class SubworkflowList(ComponentList):
     def __init__(
         self,
-        pipeline_dir: Union[str, Path] = ".",
+        pipeline_dir: Union[str, Path],
         remote: bool = True,
         remote_url: Optional[str] = None,
         branch: Optional[str] = None,
diff --git a/nf_core/utils.py b/nf_core/utils.py
index c1cc7c1301..a95eea4b69 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -1113,6 +1113,8 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path]
         else:
             log.debug(f"Could not find a config file in the directory '{directory}'")
             return Path(directory, CONFIG_PATHS[0]), None
+    if not Path(config_fn).is_file():
+        raise FileNotFoundError(f"No `.nf-core.yml` file found in the directory '{directory}'")
     with open(str(config_fn)) as fh:
         tools_config = yaml.safe_load(fh)
 
diff --git a/tests/subworkflows/test_list.py b/tests/subworkflows/test_list.py
index aa1c4de7af..1ae8f5fff6 100644
--- a/tests/subworkflows/test_list.py
+++ b/tests/subworkflows/test_list.py
@@ -19,7 +19,7 @@ def test_subworkflows_list_remote(self):
     def test_subworkflows_list_remote_gitlab(self):
         """Test listing the subworkflows in the remote gitlab repo"""
         subworkflows_list = nf_core.subworkflows.SubworkflowList(
-            None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
+            remote=True, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH
         )
         listed_subworkflows = subworkflows_list.list_components()
         console = Console(record=True)

From cce51e3cb06c2e9fbb320ffde026572327eac052 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 29 Jul 2024 22:35:58 +0200
Subject: [PATCH 158/414] add migrate_pytest option to `nf-core test` command

---
 nf_core/__main__.py              | 20 ++++++++++---
 nf_core/commands_modules.py      | 50 +++++++++++++++++++++-----------
 nf_core/commands_subworkflows.py | 39 +++++++++++++------------
 3 files changed, 70 insertions(+), 39 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 3da153ee1f..00ae8e2a1f 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1154,11 +1154,17 @@ def command_modules_create(
     default=None,
     help="Run tests with a specific profile",
 )
-def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile):
+@click.option(
+    "--migrate-pytest",
+    is_flag=True,
+    default=False,
+    help="Migrate a module with pytest tests to nf-test",
+)
+def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile, migrate_pytest):
     """
     Run nf-test for a module.
     """
-    modules_test(ctx, tool, dir, no_prompts, update, once, profile)
+    modules_test(ctx, tool, dir, no_prompts, update, once, profile, migrate_pytest)
 
 
 # nf-core modules lint
@@ -1352,11 +1358,17 @@ def command_subworkflows_create(ctx, subworkflow, dir, author, force, migrate_py
     default=None,
     help="Run tests with a specific profile",
 )
-def command_subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile):
+@click.option(
+    "--migrate-pytest",
+    is_flag=True,
+    default=False,
+    help="Migrate a subworkflow with pytest tests to nf-test",
+)
+def command_subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile, migrate_pytest):
     """
     Run nf-test for a subworkflow.
     """
-    subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile)
+    subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile, migrate_pytest)
 
 
 # nf-core subworkflows list subcommands
diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py
index 3d96d332b0..c65c42d41a 100644
--- a/nf_core/commands_modules.py
+++ b/nf_core/commands_modules.py
@@ -219,7 +219,7 @@ def modules_create(
         sys.exit(1)
 
 
-def modules_test(ctx, tool, dir, no_prompts, update, once, profile):
+def modules_test(ctx, tool, dir, no_prompts, update, once, profile, migrate_pytest):
     """
     Run nf-test for a module.
 
@@ -227,23 +227,39 @@ def modules_test(ctx, tool, dir, no_prompts, update, once, profile):
     """
     from nf_core.components.components_test import ComponentsTest
 
-    try:
-        module_tester = ComponentsTest(
-            component_type="modules",
-            component_name=tool,
-            directory=dir,
-            no_prompts=no_prompts,
-            update=update,
-            once=once,
-            remote_url=ctx.obj["modules_repo_url"],
-            branch=ctx.obj["modules_repo_branch"],
-            verbose=ctx.obj["verbose"],
-            profile=profile,
+    if migrate_pytest:
+        modules_create(
+            ctx,
+            tool,
+            dir,
+            author="",
+            label="",
+            meta=True,
+            no_meta=False,
+            force=False,
+            conda_name=None,
+            conda_package_version=None,
+            empty_template=False,
+            migrate_pytest=migrate_pytest,
         )
-        module_tester.run()
-    except (UserWarning, LookupError) as e:
-        log.critical(e)
-        sys.exit(1)
+    else:
+        try:
+            module_tester = ComponentsTest(
+                component_type="modules",
+                component_name=tool,
+                directory=dir,
+                no_prompts=no_prompts,
+                update=update,
+                once=once,
+                remote_url=ctx.obj["modules_repo_url"],
+                branch=ctx.obj["modules_repo_branch"],
+                verbose=ctx.obj["verbose"],
+                profile=profile,
+            )
+            module_tester.run()
+        except (UserWarning, LookupError) as e:
+            log.critical(e)
+            sys.exit(1)
 
 
 def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version):
diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py
index a3abce3f85..8c3be2bb46 100644
--- a/nf_core/commands_subworkflows.py
+++ b/nf_core/commands_subworkflows.py
@@ -34,7 +34,7 @@ def subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest):
         sys.exit(1)
 
 
-def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile):
+def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile, migrate_pytest):
     """
     Run nf-test for a subworkflow.
 
@@ -42,23 +42,26 @@ def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile):
     """
     from nf_core.components.components_test import ComponentsTest
 
-    try:
-        sw_tester = ComponentsTest(
-            component_type="subworkflows",
-            component_name=subworkflow,
-            directory=dir,
-            no_prompts=no_prompts,
-            update=update,
-            once=once,
-            remote_url=ctx.obj["modules_repo_url"],
-            branch=ctx.obj["modules_repo_branch"],
-            verbose=ctx.obj["verbose"],
-            profile=profile,
-        )
-        sw_tester.run()
-    except (UserWarning, LookupError) as e:
-        log.critical(e)
-        sys.exit(1)
+    if migrate_pytest:
+        subworkflows_create(ctx, subworkflow, dir, None, False, True)
+    else:
+        try:
+            sw_tester = ComponentsTest(
+                component_type="subworkflows",
+                component_name=subworkflow,
+                directory=dir,
+                no_prompts=no_prompts,
+                update=update,
+                once=once,
+                remote_url=ctx.obj["modules_repo_url"],
+                branch=ctx.obj["modules_repo_branch"],
+                verbose=ctx.obj["verbose"],
+                profile=profile,
+            )
+            sw_tester.run()
+        except (UserWarning, LookupError) as e:
+            log.critical(e)
+            sys.exit(1)
 
 
 def subworkflows_list_remote(ctx, keywords, json):

From 640ce03ab4f687e744f2631ba11971db576d7135 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 29 Jul 2024 20:39:02 +0000
Subject: [PATCH 159/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b27dce4b5c..49a58ff6bf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -54,6 +54,7 @@
 - Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071))
 - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074))
 - Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079))
+- Add `--migrate_pytest` option to `nf-core test` command ([#3085](https://github.com/nf-core/tools/pull/3085))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From 2d4d0799d9827797c82059d187a16932f08c8af2 Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Tue, 30 Jul 2024 18:43:15 +1200
Subject: [PATCH 160/414] Added process_high_memory to create/lint list

---
 nf_core/components/create.py    | 1 +
 nf_core/modules/lint/main_nf.py | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/nf_core/components/create.py b/nf_core/components/create.py
index 5d6c411bdc..bae6487925 100644
--- a/nf_core/components/create.py
+++ b/nf_core/components/create.py
@@ -236,6 +236,7 @@ def _get_module_structure_components(self):
             "process_medium",
             "process_high",
             "process_long",
+            "process_high_memory",
         ]
         if self.process_label is None:
             log.info(
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 81308ba5c5..5477ee9db9 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -423,7 +423,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
 
 
 def check_process_labels(self, lines):
-    correct_process_labels = ["process_single", "process_low", "process_medium", "process_high", "process_long"]
+    correct_process_labels = ["process_single", "process_low", "process_medium", "process_high", "process_long", "process_high_memory"]
     all_labels = [line.strip() for line in lines if line.lstrip().startswith("label ")]
     bad_labels = []
     good_labels = []

From 423af01f9bd41b644280668a31b229cace850406 Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Tue, 30 Jul 2024 18:48:51 +1200
Subject: [PATCH 161/414] Updated changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b27dce4b5c..a56abe0acb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@
 
 - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976))
 - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014))
+- Fix module linting warning for process_high_memory ([#3086](https://github.com/nf-core/tools/issues/3086))
 
 ### Download
 

From c18d9cdbb3071dad0c221bd07e299f0909263149 Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Tue, 30 Jul 2024 18:51:48 +1200
Subject: [PATCH 162/414] Fixed linting

---
 nf_core/modules/lint/main_nf.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 5477ee9db9..883d2bb3e0 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -423,7 +423,14 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
 
 
 def check_process_labels(self, lines):
-    correct_process_labels = ["process_single", "process_low", "process_medium", "process_high", "process_long", "process_high_memory"]
+    correct_process_labels = [
+        "process_single",
+        "process_low",
+        "process_medium",
+        "process_high",
+        "process_long",
+        "process_high_memory",
+    ]
     all_labels = [line.strip() for line in lines if line.lstrip().startswith("label ")]
     bad_labels = []
     good_labels = []

From 8de38715468b084a00a9627c89c5e1ec77bf52f4 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 30 Jul 2024 09:21:01 +0200
Subject: [PATCH 163/414] exclude click from rich traceback

---
 nf_core/pipelines/create/__init__.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nf_core/pipelines/create/__init__.py b/nf_core/pipelines/create/__init__.py
index 56e25bf1d5..1dd9902fb1 100644
--- a/nf_core/pipelines/create/__init__.py
+++ b/nf_core/pipelines/create/__init__.py
@@ -2,6 +2,7 @@
 
 import logging
 
+import click
 from textual.app import App
 from textual.widgets import Button
 
@@ -23,6 +24,7 @@
     show_time=False,
     show_path=False,
     markup=True,
+    tracebacks_suppress=[click],
 )
 logging.basicConfig(
     level="INFO",

From 8fe4be6520995812a8d819b3cfe213055d8f6864 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 30 Jul 2024 10:16:43 +0200
Subject: [PATCH 164/414] give nicer message on install failure, fix install
 test

---
 nf_core/__main__.py           |  2 +-
 nf_core/components/install.py | 21 +++++++++++++++++----
 tests/modules/test_install.py |  4 +++-
 3 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 11ab574ccc..1e5cb210a5 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -126,7 +126,7 @@
 # because they are actually preliminary, but intended program terminations.
 # (Custom exceptions are cleaner than `sys.exit(1)`, which we used before)
 def selective_traceback_hook(exctype, value, traceback):
-    if exctype in {DownloadError, UserWarning}:  # extend set as needed
+    if exctype in {DownloadError, UserWarning, ValueError}:  # extend set as needed
         log.error(value)
     else:
         # print the colored traceback for all other exceptions with rich as usual
diff --git a/nf_core/components/install.py b/nf_core/components/install.py
index 6130a4cf72..5bdcd1ebd6 100644
--- a/nf_core/components/install.py
+++ b/nf_core/components/install.py
@@ -4,7 +4,10 @@
 from typing import List, Optional, Union
 
 import questionary
+from rich import print
 from rich.console import Console
+from rich.markdown import Markdown
+from rich.panel import Panel
 from rich.syntax import Syntax
 
 import nf_core.components
@@ -160,7 +163,7 @@ def install(self, component: str, silent: bool = False) -> bool:
             )
             if self.component_type == "subworkflows":
                 subworkflow_config = Path(install_folder, component, "nextflow.config").relative_to(self.directory)
-                if os.path.isfile(subworkflow_config):
+                if subworkflow_config.is_file():
                     log.info("Add the following config statement to use this subworkflow:")
                     Console().print(
                         Syntax(f"includeConfig '{subworkflow_config}'", "groovy", theme="ansi_dark", padding=1)
@@ -205,11 +208,21 @@ def collect_and_verify_name(
 
         # Check that the supplied name is an available module/subworkflow
         if component and component not in modules_repo.get_avail_components(self.component_type, commit=self.sha):
-            log.info(f"Use the command 'nf-core {self.component_type} list' to view available software")
-            raise SystemError(
-                f"{self.component_type[:-1].title()} '{component}' not found in available {self.component_type}"
+            log.error(f"{self.component_type[:-1].title()} '{component}' not found in available {self.component_type}")
+            print(
+                Panel(
+                    Markdown(
+                        f"Use the command `nf-core {self.component_type} list` to view available {self.component_type}."
+                    ),
+                    title="info",
+                    title_align="left",
+                    style="blue",
+                    padding=1,
+                )
             )
 
+            raise ValueError
+
         if not modules_repo.component_exists(component, self.component_type, commit=self.sha):
             warn_msg = f"{self.component_type[:-1].title()} '{component}' not found in remote '{modules_repo.remote_url}' ({modules_repo.branch})"
             log.warning(warn_msg)
diff --git a/tests/modules/test_install.py b/tests/modules/test_install.py
index 8f7ac0a1dc..5f45d1b5b4 100644
--- a/tests/modules/test_install.py
+++ b/tests/modules/test_install.py
@@ -55,7 +55,9 @@ def test_modules_install_different_branch_fail(self):
         """Test installing a module from a different branch"""
         install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH)
         # The FastQC module does not exists in the branch-test branch
-        assert install_obj.install("fastqc") is False
+        with pytest.raises(Exception) as excinfo:
+            install_obj.install("fastqc")
+            assert "Module 'fastqc' not found in available module" in str(excinfo.value)
 
     def test_modules_install_different_branch_succeed(self):
         """Test installing a module from a different branch"""

From 6bc7361043ffe2e34685383a8b5af6fef6f4b36f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 30 Jul 2024 10:48:56 +0200
Subject: [PATCH 165/414] use self.registry

---
 nf_core/modules/lint/__init__.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index fcf2d7d066..b75f7e7570 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -200,13 +200,12 @@ def lint_modules(
 
             for mod in modules:
                 progress_bar.update(lint_progress, advance=1, test_name=mod.component_name)
-                self.lint_module(mod, progress_bar, registry=registry, local=local, fix_version=fix_version)
+                self.lint_module(mod, progress_bar, local=local, fix_version=fix_version)
 
     def lint_module(
         self,
         mod: NFCoreComponent,
         progress_bar: rich.progress.Progress,
-        registry: str,
         local: bool = False,
         fix_version: bool = False,
     ):
@@ -228,7 +227,7 @@ def lint_module(
         # TODO: consider unifying modules and subworkflows lint_module() function and add it to the ComponentLint class
         # Only check the main script in case of a local module
         if local:
-            self.main_nf(mod, fix_version, registry, progress_bar)
+            self.main_nf(mod, fix_version, self.registry, progress_bar)
             self.passed += [LintResult(mod, *m) for m in mod.passed]
             warned = [LintResult(mod, *m) for m in (mod.warned + mod.failed)]
             if not self.fail_warned:
@@ -245,7 +244,7 @@ def lint_module(
 
             for test_name in self.lint_tests:
                 if test_name == "main_nf":
-                    getattr(self, test_name)(mod, fix_version, registry, progress_bar)
+                    getattr(self, test_name)(mod, fix_version, self.registry, progress_bar)
                 else:
                     getattr(self, test_name)(mod)
 

From e4717cccccce91402535bd9ff49a619ee81ff323 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 30 Jul 2024 10:53:39 +0200
Subject: [PATCH 166/414] move subworkflows main_nf linting closer to the
 modules version

---
 nf_core/subworkflows/lint/main_nf.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/nf_core/subworkflows/lint/main_nf.py b/nf_core/subworkflows/lint/main_nf.py
index edca32bf30..3ad3f34864 100644
--- a/nf_core/subworkflows/lint/main_nf.py
+++ b/nf_core/subworkflows/lint/main_nf.py
@@ -31,8 +31,9 @@ def main_nf(_, subworkflow: NFCoreComponent) -> Tuple[List[str], List[str]]:
     outputs: List[str] = []
 
     # Read the lines directly from the subworkflow
-    lines = None
-    if lines is None:
+    lines: List[str] = []
+
+    if len(lines) == 0:
         try:
             # Check whether file exists and load it
             with open(subworkflow.main_nf) as fh:

From b022862f0c1bce3dbc0188f4aa3135e2b8a71812 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 30 Jul 2024 14:49:54 +0200
Subject: [PATCH 167/414] fix handling of missing dir in list command

---
 nf_core/components/components_command.py |  2 ++
 nf_core/components/list.py               | 11 ++++++++++-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index bff2467383..f25fb33a6f 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -51,6 +51,8 @@ def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
         """
         try:
             if self.directory:
+                if self.directory == Path(".") and not nf_dir_req:
+                    self.no_prompts = True
                 self.directory, self.repo_type, self.org = get_repo_info(self.directory, use_prompt=not self.no_prompts)
         except UserWarning:
             if nf_dir_req:
diff --git a/nf_core/components/list.py b/nf_core/components/list.py
index 65a28db716..05a8f71120 100644
--- a/nf_core/components/list.py
+++ b/nf_core/components/list.py
@@ -22,8 +22,17 @@ def __init__(
         branch: Optional[str] = None,
         no_pull: bool = False,
     ) -> None:
-        super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
         self.remote = remote
+        super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
+
+    def _configure_repo_and_paths(self, nf_dir_req=True) -> None:
+        """
+        Override the default with nf_dir_req set to False to allow
+        info to be run from anywhere and still return remote info
+        """
+        if self.remote:
+            nf_dir_req = False
+        return super()._configure_repo_and_paths(nf_dir_req)
 
     def list_components(
         self, keywords: Optional[List[str]] = None, print_json: bool = False

From e9bf654aec84fc749b915e5e834e45ec2d035deb Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 30 Jul 2024 14:50:52 +0200
Subject: [PATCH 168/414] remove unnecessary string conversion

---
 nf_core/components/create.py            | 2 +-
 nf_core/components/nfcore_component.py  | 4 ++--
 nf_core/modules/lint/environment_yml.py | 2 +-
 nf_core/modules/lint/meta_yml.py        | 4 ++--
 nf_core/modules/lint/module_tests.py    | 1 +
 nf_core/modules/modules_differ.py       | 2 +-
 nf_core/pipelines/create_logo.py        | 4 ++--
 nf_core/utils.py                        | 2 +-
 8 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/nf_core/components/create.py b/nf_core/components/create.py
index fdcf402b47..c9af6d1adb 100644
--- a/nf_core/components/create.py
+++ b/nf_core/components/create.py
@@ -290,7 +290,7 @@ def _render_template(self) -> Optional[bool]:
             # Write output to the target file
             log.debug(f"Writing output to: '{dest_fn}'")
             dest_fn.parent.mkdir(exist_ok=True, parents=True)
-            with open(str(dest_fn), "w") as fh:
+            with open(dest_fn, "w") as fh:
                 log.debug(f"Writing output to: '{dest_fn}'")
                 fh.write(rendered_output)
 
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 129871d68c..db3196be91 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -163,7 +163,7 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st
     def get_inputs_from_main_nf(self) -> None:
         """Collect all inputs from the main.nf file."""
         inputs: List[str] = []
-        with open(str(self.main_nf)) as f:
+        with open(self.main_nf) as f:
             data = f.read()
         # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo
         # regex matches:
@@ -191,7 +191,7 @@ def get_inputs_from_main_nf(self) -> None:
 
     def get_outputs_from_main_nf(self):
         outputs = []
-        with open(str(self.main_nf)) as f:
+        with open(self.main_nf) as f:
             data = f.read()
         # get output values from main.nf after "output:". the names are always after "emit:"
         if "output:" not in data:
diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py
index e34b9d5856..341b9cd730 100644
--- a/nf_core/modules/lint/environment_yml.py
+++ b/nf_core/modules/lint/environment_yml.py
@@ -25,7 +25,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
     if module.environment_yml is None:
         raise LintExceptionError("Module does not have an `environment.yml` file")
     try:
-        with open(str(module.environment_yml)) as fh:
+        with open(module.environment_yml) as fh:
             env_yml = yaml.safe_load(fh)
 
         module.passed.append(("environment_yml_exists", "Module's `environment.yml` exists", module.environment_yml))
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 32110b7131..4a0ef6e01e 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -43,7 +43,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
     module.get_outputs_from_main_nf()
     # Check if we have a patch file, get original file in that case
     meta_yaml = None
-    if module.is_patched:
+    if module.is_patched and module_lint_object.modules_repo.repo_path is not None:
         lines = ModulesDiffer.try_apply_patch(
             module.component_name,
             module_lint_object.modules_repo.repo_path,
@@ -57,7 +57,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
         raise LintExceptionError("Module does not have a `meta.yml` file")
     if meta_yaml is None:
         try:
-            with open(str(module.meta_yml)) as fh:
+            with open(module.meta_yml) as fh:
                 meta_yaml = yaml.safe_load(fh)
             module.passed.append(("meta_yml_exists", "Module `meta.yml` exists", module.meta_yml))
         except FileNotFoundError:
diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py
index 9301db81ee..6722c12129 100644
--- a/nf_core/modules/lint/module_tests.py
+++ b/nf_core/modules/lint/module_tests.py
@@ -73,6 +73,7 @@ def module_tests(_, module: NFCoreComponent):
         with open(module.nftest_main_nf) as fh:
             if "snapshot(" in fh.read():
                 snap_file = module.nftest_testdir / "main.nf.test.snap"
+
                 if snap_file.is_file():
                     module.passed.append(
                         (
diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py
index e310b3bf8b..f6b334eb6d 100644
--- a/nf_core/modules/modules_differ.py
+++ b/nf_core/modules/modules_differ.py
@@ -307,7 +307,7 @@ def per_file_patch(patch_fn: Union[str, Path]) -> Dict[str, List[str]]:
             dict[str, str]: A dictionary indexed by the filenames with the
                             file patches as values
         """
-        with open(str(patch_fn)) as fh:
+        with open(patch_fn) as fh:
             lines = fh.readlines()
 
         patches = {}
diff --git a/nf_core/pipelines/create_logo.py b/nf_core/pipelines/create_logo.py
index 6619b910b5..c54d8f2085 100644
--- a/nf_core/pipelines/create_logo.py
+++ b/nf_core/pipelines/create_logo.py
@@ -62,7 +62,7 @@ def create_logo(
         img: Optional[Image.Image] = None
         if cache_path.is_file():
             log.debug(f"Logo already exists in cache at: {cache_path}. Reusing this file.")
-            img = Image.open(str(cache_path))
+            img = Image.open(cache_path)
         if img is None:
             log.debug(f"Creating logo for {text}")
 
@@ -81,7 +81,7 @@ def create_logo(
                 template_fn = "nf-core-repo-logo-base-darkbg.png"
 
             template_path = assets / template_fn
-            img = Image.open(str(template_path))
+            img = Image.open(template_path)
             # get the height of the template image
             height = img.size[1]
 
diff --git a/nf_core/utils.py b/nf_core/utils.py
index a95eea4b69..c12ec191fb 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -1115,7 +1115,7 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path]
             return Path(directory, CONFIG_PATHS[0]), None
     if not Path(config_fn).is_file():
         raise FileNotFoundError(f"No `.nf-core.yml` file found in the directory '{directory}'")
-    with open(str(config_fn)) as fh:
+    with open(config_fn) as fh:
         tools_config = yaml.safe_load(fh)
 
     # If the file is empty

From d4c06cb17fce07eedf00b2104e5be6fc5fc5548c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 30 Jul 2024 14:51:05 +0200
Subject: [PATCH 169/414] fix tests

---
 nf_core/modules/lint/main_nf.py     |  9 +++++----
 nf_core/pipelines/refgenie.py       | 14 +++++++++-----
 tests/modules/test_install.py       | 15 ++++++---------
 tests/modules/test_list.py          |  6 +++---
 tests/pipelines/test_params_file.py | 18 +++++++++---------
 tests/subworkflows/test_install.py  |  5 +++--
 6 files changed, 35 insertions(+), 32 deletions(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 985a92fa1f..358d6a75a4 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -43,8 +43,8 @@ def main_nf(
       of ``software`` and ``prefix``
     """
 
-    inputs = []
-    outputs = []
+    inputs: List[str] = []
+    outputs: List[str] = []
 
     # Check if we have a patch file affecting the 'main.nf' file
     # otherwise read the lines directly from the module
@@ -58,7 +58,7 @@ def main_nf(
             reverse=True,
         ).get("main.nf", [""])
 
-    if not lines:
+    if len(lines) == 0:
         try:
             # Check whether file exists and load it
             with open(module.main_nf) as fh:
@@ -66,9 +66,10 @@ def main_nf(
             module.passed.append(("main_nf_exists", "Module file exists", module.main_nf))
         except FileNotFoundError:
             module.failed.append(("main_nf_exists", "Module file does not exist", module.main_nf))
+            raise FileNotFoundError(f"Module file does not exist: {module.main_nf}")
 
     deprecated_i = ["initOptions", "saveFiles", "getSoftwareName", "getProcessName", "publishDir"]
-    if lines is not None:
+    if len(lines) > 0:
         lines_j = "\n".join(lines)
     else:
         lines_j = ""
diff --git a/nf_core/pipelines/refgenie.py b/nf_core/pipelines/refgenie.py
index 19ef4b5121..f2eb09f330 100644
--- a/nf_core/pipelines/refgenie.py
+++ b/nf_core/pipelines/refgenie.py
@@ -181,14 +181,18 @@ def update_config(rgc):
         log.info("Could not determine path to 'refgenie_genomes.config' file.")
         return False
 
+    if refgenie_genomes_config_file is None:
+        log.info("Could not determine path to 'refgenie_genomes.config' file.")
+        return False
+
     # Save the updated genome config
-    try:
-        with open(str(refgenie_genomes_config_file), "w+") as fh:
-            fh.write(refgenie_genomes)
-        log.info(f"Updated nf-core genomes config: {refgenie_genomes_config_file}")
-    except FileNotFoundError:
+    if not Path(refgenie_genomes_config_file).is_file():
         log.warning(f"Could not write to {refgenie_genomes_config_file}")
         return False
+    else:
+        with open(refgenie_genomes_config_file, "w+") as fh:
+            fh.write(refgenie_genomes)
+        log.info(f"Updated nf-core genomes config: {refgenie_genomes_config_file}")
 
     # Add include statement to NXF_HOME/config
     if nxf_home:
diff --git a/tests/modules/test_install.py b/tests/modules/test_install.py
index 5f45d1b5b4..92d30a494f 100644
--- a/tests/modules/test_install.py
+++ b/tests/modules/test_install.py
@@ -1,4 +1,3 @@
-import os
 from pathlib import Path
 
 import pytest
@@ -17,30 +16,28 @@
 
 
 class TestModulesCreate(TestModules):
-    def test_modules_install_nopipeline(self):
-        """Test installing a module - no pipeline given"""
-        self.pipeline_dir = None
-        assert self.mods_install.install("foo") is False
-
     @with_temporary_folder
     def test_modules_install_emptypipeline(self, tmpdir):
         """Test installing a module - empty dir given"""
         Path(tmpdir, "nf-core-pipe").mkdir()
         self.mods_install.directory = Path(tmpdir, "nf-core-pipe")
         with pytest.raises(UserWarning) as excinfo:
-            self.mods_install.install("foo")
+            self.mods_install.install("fastp")
         assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
 
     def test_modules_install_nomodule(self):
         """Test installing a module - unrecognised module given"""
-        assert self.mods_install.install("foo") is False
+        with pytest.raises(ValueError) as excinfo:
+            self.mods_install.install("foo")
+        assert excinfo.typename == "ValueError"
+        assert "Module 'foo' not found in available modules" in self.caplog.text
 
     def test_modules_install_trimgalore(self):
         """Test installing a module - TrimGalore!"""
         assert self.mods_install.install("trimgalore") is not False
         assert self.mods_install.directory is not None
         module_path = Path(self.mods_install.directory, "modules", "nf-core", "trimgalore")
-        assert os.path.exists(module_path)
+        assert module_path.exists()
 
     def test_modules_install_trimgalore_twice(self):
         """Test installing a module - TrimGalore! already there"""
diff --git a/tests/modules/test_list.py b/tests/modules/test_list.py
index a170f6d6fc..282f044c1b 100644
--- a/tests/modules/test_list.py
+++ b/tests/modules/test_list.py
@@ -10,10 +10,10 @@
 from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL
 
 
-class TestModulesCreate(TestModules):
+class TestModulesList(TestModules):
     def test_modules_list_remote(self):
         """Test listing available modules"""
-        mods_list = nf_core.modules.list.ModuleList(remote=True)
+        mods_list = nf_core.modules.list.ModuleList()
         listed_mods = mods_list.list_components()
         console = Console(record=True)
         console.print(listed_mods)
@@ -22,7 +22,7 @@ def test_modules_list_remote(self):
 
     def test_modules_list_remote_gitlab(self):
         """Test listing the modules in the remote gitlab repo"""
-        mods_list = nf_core.modules.list.ModuleList(remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH)
+        mods_list = nf_core.modules.list.ModuleList(remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH)
         listed_mods = mods_list.list_components()
         console = Console(record=True)
         console.print(listed_mods)
diff --git a/tests/pipelines/test_params_file.py b/tests/pipelines/test_params_file.py
index 7e3e4b4f42..22a6182acd 100644
--- a/tests/pipelines/test_params_file.py
+++ b/tests/pipelines/test_params_file.py
@@ -20,15 +20,15 @@ def setup_class(cls):
 
         # Create a test pipeline in temp directory
         cls.tmp_dir = tempfile.mkdtemp()
-        cls.template_dir = os.path.join(cls.tmp_dir, "wf")
+        cls.template_dir = Path(cls.tmp_dir, "wf")
         create_obj = nf_core.pipelines.create.create.PipelineCreate(
             "testpipeline", "a description", "Me", outdir=cls.template_dir, no_git=True
         )
         create_obj.init_pipeline()
 
-        cls.template_schema = os.path.join(cls.template_dir, "nextflow_schema.json")
+        cls.template_schema = Path(cls.template_dir, "nextflow_schema.json")
         cls.params_template_builder = ParamsFileBuilder(cls.template_dir)
-        cls.invalid_template_schema = os.path.join(cls.template_dir, "nextflow_schema_invalid.json")
+        cls.invalid_template_schema = Path(cls.template_dir, "nextflow_schema_invalid.json")
 
         # Remove the allOf section to make the schema invalid
         with open(cls.template_schema) as fh:
@@ -40,14 +40,14 @@ def setup_class(cls):
 
     @classmethod
     def teardown_class(cls):
-        if os.path.exists(cls.tmp_dir):
+        if Path(cls.tmp_dir).exists():
             shutil.rmtree(cls.tmp_dir)
 
     def test_build_template(self):
-        outfile = os.path.join(self.tmp_dir, "params-file.yml")
-        self.params_template_builder.write_params_file(outfile)
+        outfile = Path(self.tmp_dir, "params-file.yml")
+        self.params_template_builder.write_params_file(str(outfile))
 
-        assert os.path.exists(outfile)
+        assert outfile.exists()
 
         with open(outfile) as fh:
             out = fh.read()
@@ -56,9 +56,9 @@ def test_build_template(self):
 
     def test_build_template_invalid_schema(self, caplog):
         """Build a schema from a template"""
-        outfile = os.path.join(self.tmp_dir, "params-file-invalid.yml")
+        outfile = Path(self.tmp_dir, "params-file-invalid.yml")
         builder = ParamsFileBuilder(self.invalid_template_schema)
-        res = builder.write_params_file(outfile)
+        res = builder.write_params_file(str(outfile))
 
         assert res is False
         assert "Pipeline schema file is invalid" in caplog.text
diff --git a/tests/subworkflows/test_install.py b/tests/subworkflows/test_install.py
index e6ba9439a4..00ba888414 100644
--- a/tests/subworkflows/test_install.py
+++ b/tests/subworkflows/test_install.py
@@ -55,9 +55,10 @@ def test_subworkflows_install_emptypipeline(self, tmpdir):
 
     def test_subworkflows_install_nosubworkflow(self):
         """Test installing a subworkflow - unrecognised subworkflow given"""
-        with pytest.raises(SystemError) as excinfo:
+        with pytest.raises(ValueError) as excinfo:
             self.subworkflow_install.install("foo")
-        assert "Subworkflow 'foo' not found in available subworkflows" in str(excinfo.value)
+        assert excinfo.typename == "ValueError"
+        assert "Subworkflow 'foo' not found in available subworkflows" in self.caplog.text
 
     def test_subworkflows_install_bam_sort_stats_samtools_twice(self):
         """Test installing a subworkflow - bam_sort_stats_samtools already there"""

From d57c815b83213154179be3b3e390557a6404d3b5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 30 Jul 2024 15:30:46 +0200
Subject: [PATCH 170/414] add type hints to utils functions

---
 nf_core/components/update.py    |  4 +--
 nf_core/modules/modules_json.py |  2 +-
 nf_core/pipelines/download.py   |  2 +-
 nf_core/utils.py                | 48 ++++++++++++++++-----------------
 tests/modules/test_list.py      |  2 +-
 5 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index eb15f976bf..3e4694adc8 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -755,7 +755,7 @@ def move_files_from_tmp_dir(self, component: str, install_folder: str, repo_path
             config_files = [f for f in pipeline_files if str(f).endswith(".config")]
             for config_file in config_files:
                 log.debug(f"Moving '{component}/{config_file}' to updated component")
-                shutil.move(pipeline_path / config_file, temp_component_dir / config_file)
+                shutil.move(str(pipeline_path / config_file), temp_component_dir / config_file)
                 files.append(temp_component_dir / config_file)
 
         else:
@@ -772,7 +772,7 @@ def move_files_from_tmp_dir(self, component: str, install_folder: str, repo_path
                 log.debug(f"Moving '{file}' to updated component")
                 dest = Path(pipeline_path, file)
                 dest.parent.mkdir(parents=True, exist_ok=True)
-                shutil.move(path, dest)
+                shutil.move(str(path), dest)
 
         log.info(f"Updating '{repo_path}/{component}'")
         log.debug(f"Updating {self.component_type[:-1]} '{component}' to {new_version} from {repo_path}")
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 19649a57cd..536589d81e 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -430,7 +430,7 @@ def move_component_to_local(self, component_type: str, component: str, repo_name
             # Add a time suffix to the path to make it unique
             # (do it again and again if it didn't work out...)
             to_name += f"-{datetime.datetime.now().strftime('%y%m%d%H%M%S')}"
-        shutil.move(current_path, local_dir / to_name)
+        shutil.move(str(current_path), local_dir / to_name)
 
     def unsynced_components(self) -> Tuple[List[str], List[str], dict]:
         """
diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py
index 704fe91b2f..97453b127e 100644
--- a/nf_core/pipelines/download.py
+++ b/nf_core/pipelines/download.py
@@ -1388,7 +1388,7 @@ def singularity_pull_image(
         # where the output of 'singularity pull' is first generated before being copied to the NXF_SINGULARITY_CACHDIR.
         # if not defined by the Singularity administrators, then use the temporary directory to avoid storing the images in the work directory.
         if os.environ.get("SINGULARITY_CACHEDIR") is None:
-            os.environ["SINGULARITY_CACHEDIR"] = NFCORE_CACHE_DIR
+            os.environ["SINGULARITY_CACHEDIR"] = str(NFCORE_CACHE_DIR)
 
         # Sometimes, container still contain an explicit library specification, which
         # resulted in attempted pulls e.g. from docker://quay.io/quay.io/qiime2/core:2022.11
diff --git a/nf_core/utils.py b/nf_core/utils.py
index c12ec191fb..ea850a5d24 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -19,7 +19,7 @@
 import time
 from contextlib import contextmanager
 from pathlib import Path
-from typing import Any, Dict, Generator, List, Optional, Tuple, Union
+from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, Union
 
 import git
 import prompt_toolkit.styles
@@ -66,11 +66,11 @@
     ]
 )
 
-NFCORE_CACHE_DIR = os.path.join(
-    os.environ.get("XDG_CACHE_HOME", os.path.join(os.getenv("HOME") or "", ".cache")),
+NFCORE_CACHE_DIR = Path(
+    os.environ.get("XDG_CACHE_HOME", Path(os.getenv("HOME") or "", ".cache")),
     "nfcore",
 )
-NFCORE_DIR = os.path.join(os.environ.get("XDG_CONFIG_HOME", os.path.join(os.getenv("HOME") or "", ".config")), "nfcore")
+NFCORE_DIR = Path(os.environ.get("XDG_CONFIG_HOME", os.path.join(os.getenv("HOME") or "", ".config")), "nfcore")
 
 
 def fetch_remote_version(source_url):
@@ -358,17 +358,17 @@ def run_cmd(executable: str, cmd: str) -> Union[Tuple[bytes, bytes], None]:
             )
 
 
-def setup_nfcore_dir():
+def setup_nfcore_dir() -> bool:
     """Creates a directory for files that need to be kept between sessions
 
     Currently only used for keeping local copies of modules repos
     """
-    if not os.path.exists(NFCORE_DIR):
-        os.makedirs(NFCORE_DIR)
-        return True
+    if not NFCORE_DIR.exists():
+        NFCORE_DIR.mkdir(parents=True)
+    return True
 
 
-def setup_requests_cachedir() -> dict:
+def setup_requests_cachedir() -> Dict[str, Union[Path, datetime.timedelta, str]]:
     """Sets up local caching for faster remote HTTP requests.
 
     Caching directory will be set up in the user's home directory under
@@ -377,10 +377,10 @@ def setup_requests_cachedir() -> dict:
     Uses requests_cache monkey patching.
     Also returns the config dict so that we can use the same setup with a Session.
     """
-    pyversion = ".".join(str(v) for v in sys.version_info[0:3])
-    cachedir = setup_nfcore_cachedir(f"cache_{pyversion}")
-    config = {
-        "cache_name": os.path.join(cachedir, "github_info"),
+    pyversion: str = ".".join(str(v) for v in sys.version_info[0:3])
+    cachedir: Path = setup_nfcore_cachedir(f"cache_{pyversion}")
+    config: Dict[str, Union[Path, datetime.timedelta, str]] = {
+        "cache_name": Path(cachedir, "github_info"),
         "expire_after": datetime.timedelta(hours=1),
         "backend": "sqlite",
     }
@@ -403,7 +403,7 @@ def setup_nfcore_cachedir(cache_fn: Union[str, Path]) -> Path:
     return cachedir
 
 
-def wait_cli_function(poll_func, refresh_per_second=20):
+def wait_cli_function(poll_func: Callable[[], bool], refresh_per_second: int = 20) -> None:
     """
     Display a command-line spinner while calling a function repeatedly.
 
@@ -427,7 +427,7 @@ def wait_cli_function(poll_func, refresh_per_second=20):
         raise AssertionError("Cancelled!")
 
 
-def poll_nfcore_web_api(api_url, post_data=None):
+def poll_nfcore_web_api(api_url: str, post_data: Optional[Dict] = None) -> Dict:
     """
     Poll the nf-core website API
 
@@ -448,7 +448,7 @@ def poll_nfcore_web_api(api_url, post_data=None):
             raise AssertionError(f"Could not connect to URL: {api_url}")
         else:
             if response.status_code != 200 and response.status_code != 301:
-                log.debug(f"Response content:\n{response.content}")
+                log.debug(f"Response content:\n{response.content.decode()}")
                 raise AssertionError(
                     f"Could not access remote API results: {api_url} (HTML {response.status_code} Error)"
                 )
@@ -460,7 +460,7 @@ def poll_nfcore_web_api(api_url, post_data=None):
                 if "status" not in web_response:
                     raise AssertionError()
             except (json.decoder.JSONDecodeError, AssertionError, TypeError):
-                log.debug(f"Response content:\n{response.content}")
+                log.debug(f"Response content:\n{response.content.decode()}")
                 raise AssertionError(
                     f"nf-core website API results response not recognised: {api_url}\n "
                     "See verbose log for full response"
@@ -476,14 +476,14 @@ class GitHubAPISession(requests_cache.CachedSession):
     such as automatically setting up GitHub authentication if we can.
     """
 
-    def __init__(self):  # pylint: disable=super-init-not-called
-        self.auth_mode = None
-        self.return_ok = [200, 201]
-        self.return_retry = [403]
-        self.return_unauthorised = [401]
-        self.has_init = False
+    def __init__(self) -> None:
+        self.auth_mode: Optional[str] = None
+        self.return_ok: List[int] = [200, 201]
+        self.return_retry: List[int] = [403]
+        self.return_unauthorised: List[int] = [401]
+        self.has_init: bool = False
 
-    def lazy_init(self):
+    def lazy_init(self) -> None:
         """
         Initialise the object.
 
diff --git a/tests/modules/test_list.py b/tests/modules/test_list.py
index 282f044c1b..3e92a33ab4 100644
--- a/tests/modules/test_list.py
+++ b/tests/modules/test_list.py
@@ -67,7 +67,7 @@ def test_modules_list_local_json(self):
         assert "fastqc" in listed_mods
         assert "multiqc" in listed_mods
 
-    def test_modules_list_remote_json(self):
+    def test_modules_list_remote_json(self) -> None:
         """Test listing available modules as JSON"""
         mods_list = nf_core.modules.list.ModuleList(remote=True)
         listed_mods: str = str(mods_list.list_components(print_json=True))

From 495e05acc406b64e1d21e008aed92b443c5fb40e Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 30 Jul 2024 15:46:39 +0200
Subject: [PATCH 171/414] fix refgenie tests

---
 nf_core/pipelines/refgenie.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipelines/refgenie.py b/nf_core/pipelines/refgenie.py
index f2eb09f330..426ca5eb7d 100644
--- a/nf_core/pipelines/refgenie.py
+++ b/nf_core/pipelines/refgenie.py
@@ -186,13 +186,13 @@ def update_config(rgc):
         return False
 
     # Save the updated genome config
-    if not Path(refgenie_genomes_config_file).is_file():
-        log.warning(f"Could not write to {refgenie_genomes_config_file}")
-        return False
-    else:
+    try:
         with open(refgenie_genomes_config_file, "w+") as fh:
             fh.write(refgenie_genomes)
         log.info(f"Updated nf-core genomes config: {refgenie_genomes_config_file}")
+    except FileNotFoundError:
+        log.info(f"Could not write to {refgenie_genomes_config_file}")
+        return False
 
     # Add include statement to NXF_HOME/config
     if nxf_home:

From 4c07bdfef5542de71954dbaedba6293e71bfcc9d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 30 Jul 2024 15:57:15 +0200
Subject: [PATCH 172/414] fix tests

---
 nf_core/subworkflows/list.py |  2 +-
 nf_core/utils.py             | 10 ++++++++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/nf_core/subworkflows/list.py b/nf_core/subworkflows/list.py
index 5f849a1f9c..9e84d6cbe0 100644
--- a/nf_core/subworkflows/list.py
+++ b/nf_core/subworkflows/list.py
@@ -10,7 +10,7 @@
 class SubworkflowList(ComponentList):
     def __init__(
         self,
-        pipeline_dir: Union[str, Path],
+        pipeline_dir: Union[str, Path] = ".",
         remote: bool = True,
         remote_url: Optional[str] = None,
         branch: Optional[str] = None,
diff --git a/nf_core/utils.py b/nf_core/utils.py
index ea850a5d24..48b7eae294 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -448,7 +448,10 @@ def poll_nfcore_web_api(api_url: str, post_data: Optional[Dict] = None) -> Dict:
             raise AssertionError(f"Could not connect to URL: {api_url}")
         else:
             if response.status_code != 200 and response.status_code != 301:
-                log.debug(f"Response content:\n{response.content.decode()}")
+                response_content = response.content
+                if isinstance(response_content, bytes):
+                    response_content = response_content.decode()
+                log.debug(f"Response content:\n{response_content}")
                 raise AssertionError(
                     f"Could not access remote API results: {api_url} (HTML {response.status_code} Error)"
                 )
@@ -460,7 +463,10 @@ def poll_nfcore_web_api(api_url: str, post_data: Optional[Dict] = None) -> Dict:
                 if "status" not in web_response:
                     raise AssertionError()
             except (json.decoder.JSONDecodeError, AssertionError, TypeError):
-                log.debug(f"Response content:\n{response.content.decode()}")
+                response_content = response.content
+                if isinstance(response_content, bytes):
+                    response_content = response_content.decode()
+                log.debug(f"Response content:\n{response_content}")
                 raise AssertionError(
                     f"nf-core website API results response not recognised: {api_url}\n "
                     "See verbose log for full response"

From c9f86ca5e841cdda6660803ade89919b538efc92 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Thu, 1 Aug 2024 00:15:29 +0000
Subject: [PATCH 173/414] Update pre-commit hook pre-commit/mirrors-mypy to
 v1.11.1

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 63202e5178..879bc15c01 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -19,7 +19,7 @@ repos:
         alias: ec
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.11.0"
+    rev: "v1.11.1"
     hooks:
       - id: mypy
         additional_dependencies:

From 6f0345f445e97ade328b32b1c059788898ec208a Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 1 Aug 2024 00:16:33 +0000
Subject: [PATCH 174/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a56abe0acb..ec033ff1ee 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -55,6 +55,7 @@
 - Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071))
 - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074))
 - Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079))
+- Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From 38ea56804aad6a0bd4492b55e164af42f1bac758 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 2 Aug 2024 10:10:19 +0200
Subject: [PATCH 175/414] allow numbers in custom pipeline name

---
 nf_core/pipelines/create/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
index c15d61e266..a360b5f3a9 100644
--- a/nf_core/pipelines/create/utils.py
+++ b/nf_core/pipelines/create/utils.py
@@ -65,7 +65,7 @@ def name_nospecialchars(cls, v: str, info: ValidationInfo) -> str:
             if not re.match(r"^[a-z]+$", v):
                 raise ValueError("Must be lowercase without punctuation.")
         else:
-            if not re.match(r"^[a-zA-Z-_]+$", v):
+            if not re.match(r"^[a-zA-Z-_0-9]+$", v):
                 raise ValueError("Must not contain special characters. Only '-' or '_' are allowed.")
         return v
 

From 8a781b8bcb3f5bc40e67819ee3e03fe774e14a9a Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Fri, 2 Aug 2024 08:12:16 +0000
Subject: [PATCH 176/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ec033ff1ee..b6cd12d551 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -56,6 +56,7 @@
 - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074))
 - Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079))
 - Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091))
+- Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From 7ea871858fbcb263c65de4527fa4644f0ee007fb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?=
 <mashehu@users.noreply.github.com>
Date: Fri, 2 Aug 2024 10:24:58 +0200
Subject: [PATCH 177/414] Update CHANGELOG.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 49a58ff6bf..12001d56ef 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -54,7 +54,7 @@
 - Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071))
 - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074))
 - Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079))
-- Add `--migrate_pytest` option to `nf-core test` command ([#3085](https://github.com/nf-core/tools/pull/3085))
+- Add `--migrate_pytest` option to `nf-core <modules|subworkflows> test` command ([#3085](https://github.com/nf-core/tools/pull/3085))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From cbee6d06bb0fbaa2a76d6e7f7c2a842e0a81ec54 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 2 Aug 2024 12:03:07 +0200
Subject: [PATCH 178/414] allow module lables between double quotes

---
 nf_core/modules/lint/main_nf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 883d2bb3e0..2762dd22d5 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -437,7 +437,7 @@ def check_process_labels(self, lines):
     if len(all_labels) > 0:
         for label in all_labels:
             try:
-                label = re.match(r"^label\s+'?([a-zA-Z0-9_-]+)'?$", label).group(1)
+                label = re.match(r"^label\s+'?\"?([a-zA-Z0-9_-]+)'?\"?$", label).group(1)
             except AttributeError:
                 self.warned.append(
                     (

From 086302e209fa56fd869aae3590e7d1bae780c3fa Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 2 Aug 2024 12:48:00 +0200
Subject: [PATCH 179/414] allow multiline module input tuple

---
 nf_core/modules/lint/main_nf.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 883d2bb3e0..ed3d93e2ca 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -81,6 +81,7 @@ def main_nf(module_lint_object, module, fix_version, registry, progress_bar):
     script_lines = []
     shell_lines = []
     when_lines = []
+    lines = iter(lines)
     for line in lines:
         if re.search(r"^\s*process\s*\w*\s*{", line) and state == "module":
             state = "process"
@@ -104,6 +105,13 @@ def main_nf(module_lint_object, module, fix_version, registry, progress_bar):
         if state == "process" and not _is_empty(line):
             process_lines.append(line)
         if state == "input" and not _is_empty(line):
+            # allow multiline tuples
+            if "tuple" in line and line.count("(") <= 1:
+                joint_tuple = line
+                while re.sub(r"\s", "", line) != ")":
+                    joint_tuple = joint_tuple + line
+                    line = next(lines)
+                line = joint_tuple
             inputs.extend(_parse_input(module, line))
         if state == "output" and not _is_empty(line):
             outputs += _parse_output(module, line)

From 5b7425368135301c53f664262133bf84981cbdd9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Fri, 2 Aug 2024 15:34:20 +0200
Subject: [PATCH 180/414] Update nf_core/pipelines/create/utils.py

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 nf_core/pipelines/create/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
index a360b5f3a9..c387960c39 100644
--- a/nf_core/pipelines/create/utils.py
+++ b/nf_core/pipelines/create/utils.py
@@ -65,7 +65,7 @@ def name_nospecialchars(cls, v: str, info: ValidationInfo) -> str:
             if not re.match(r"^[a-z]+$", v):
                 raise ValueError("Must be lowercase without punctuation.")
         else:
-            if not re.match(r"^[a-zA-Z-_0-9]+$", v):
+            if not re.match(r"^[-\w]+$", v):
                 raise ValueError("Must not contain special characters. Only '-' or '_' are allowed.")
         return v
 

From 4f755380032ce01d6b1222036ae68172976e40f5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 5 Aug 2024 08:27:26 +0200
Subject: [PATCH 181/414] update ruff

---
 .github/workflows/changelog.py    | 9 +++++----
 .pre-commit-config.yaml           | 2 +-
 nf_core/modules/modules_differ.py | 2 +-
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/changelog.py b/.github/workflows/changelog.py
index 471665e4b1..24130e65c4 100644
--- a/.github/workflows/changelog.py
+++ b/.github/workflows/changelog.py
@@ -1,3 +1,4 @@
+#! /usr/bin/env python3
 """
 Taken from https://github.com/MultiQC/MultiQC/blob/main/.github/workflows/changelog.py and updated for nf-core
 
@@ -18,7 +19,7 @@
 import re
 import sys
 from pathlib import Path
-from typing import List
+from typing import List, Tuple
 
 REPO_URL = "https://github.com/nf-core/tools"
 
@@ -32,7 +33,7 @@
 assert pr_number, pr_number
 
 # Trim the PR number added when GitHub squashes commits, e.g. "Template: Updated (#2026)"
-pr_title = pr_title.removesuffix(f" (#{pr_number})")
+pr_title = pr_title.removesuffix(f" (#{pr_number})")  # type: ignore
 
 changelog_path = workspace_path / "CHANGELOG.md"
 
@@ -50,7 +51,7 @@
     sys.exit(0)
 
 
-def _determine_change_type(pr_title) -> tuple[str, str]:
+def _determine_change_type(pr_title) -> Tuple[str, str]:
     """
     Determine the type of the PR: Template, Download, Linting, Modules, Subworkflows, or General
     Returns a tuple of the section name and the module info.
@@ -85,7 +86,7 @@ def _determine_change_type(pr_title) -> tuple[str, str]:
 pr_link = f"([#{pr_number}]({REPO_URL}/pull/{pr_number}))"
 
 # Handle manual changelog entries through comments.
-if comment := comment.removeprefix("@nf-core-bot changelog").strip():
+if comment := comment.removeprefix("@nf-core-bot changelog").strip():  # type: ignore
     print(f"Adding manual changelog entry: {comment}")
     pr_title = comment
 new_lines = [
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f763fa6658..c83cb5a4b7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.1
+    rev: v0.5.6
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py
index f6b334eb6d..b6d7f0d0fa 100644
--- a/nf_core/modules/modules_differ.py
+++ b/nf_core/modules/modules_differ.py
@@ -312,7 +312,7 @@ def per_file_patch(patch_fn: Union[str, Path]) -> Dict[str, List[str]]:
 
         patches = {}
         i = 0
-        patch_lines: list[str] = []
+        patch_lines: List[str] = []
         key = "preamble"
         while i < len(lines):
             line = lines[i]

From f4323602f8481460aea48c973c22e6b79dde6fae Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 5 Aug 2024 13:13:33 +0200
Subject: [PATCH 182/414] add option to exclude gitpod for custom pipeline
 template

---
 .github/workflows/create-test-lint-wf-template.yml |  5 +++++
 nf_core/pipeline-template/nextflow.config          |  2 ++
 nf_core/pipelines/create/create.py                 |  2 ++
 nf_core/pipelines/create/custompipeline.py         | 13 +++++++++++++
 tests/data/pipeline_create_template_skip.yml       |  1 +
 5 files changed, 23 insertions(+)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index cfa0a50079..8a893ce9f0 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -42,6 +42,7 @@ jobs:
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
           - "template_skip_code_linters.yml"
+          - "template_skip_gitpod.yml"
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
@@ -107,6 +108,10 @@ jobs:
         run: |
           printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml
 
+      - name: Create template skip gitpod
+        run: |
+          printf "org: my-prefix\nskip: gitpod" > create-test-lint-wf/template_skip_gitpod.yml
+
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 2e6a56b001..8a6ca6b327 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -178,11 +178,13 @@ profiles {
         wave.freeze             = true
         wave.strategy           = 'conda,container'
     }
+    {%- if gitpod %}
     gitpod {
         executor.name           = 'local'
         executor.cpus           = 4
         executor.memory         = 8.GB
     }
+    {%- endif %}
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
 }
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 42e4a6ad7b..8f279df190 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -101,6 +101,7 @@ def __init__(
                 ".prettierrc.yml",
                 ".github/workflows/fix-linting.yml",
             ],
+            "gitpod": [".gitpod.yml"],
         }
         # Get list of files we're skipping with the supplied skip keys
         self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k])
@@ -210,6 +211,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
             "igenomes": {"file": True, "content": True},
             "nf_core_configs": {"file": False, "content": True},
             "code_linters": {"file": True, "content": True},
+            "gitpod": {"file": True, "content": True},
         }
 
         # Set the parameters for the jinja template
diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py
index 0925fb5bab..e839042187 100644
--- a/nf_core/pipelines/create/custompipeline.py
+++ b/nf_core/pipelines/create/custompipeline.py
@@ -51,6 +51,13 @@
 - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc).
 """
 
+markdown_gitpod = """
+Gitpod (https://www.gitpod.io/) provides standardized and automated development environments.
+
+Including this to your pipeline will provide an environment with the latest version of nf-core/tools installed and all its requirements.
+This is useful to have all the tools ready for pipeline development.
+"""
+
 
 class CustomPipeline(Screen):
     """Select if the pipeline will use genomic data."""
@@ -96,6 +103,12 @@ def compose(self) -> ComposeResult:
                 "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.",
                 "code_linters",
             ),
+            PipelineFeature(
+                markdown_gitpod,
+                "Include a gitpod environment",
+                "Include the configuration required to use Gitpod.",
+                "gitpod",
+            ),
             classes="features-container",
         )
         yield Center(
diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml
index d9ef405c51..c18d810cd9 100644
--- a/tests/data/pipeline_create_template_skip.yml
+++ b/tests/data/pipeline_create_template_skip.yml
@@ -12,3 +12,4 @@ skip_features:
   - igenomes
   - nf_core_configs
   - code_linters
+  - gitpod

From 997468d81855989fdd95c04e38955ee594bf6335 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 5 Aug 2024 11:15:26 +0000
Subject: [PATCH 183/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index aea91cb51a..df11c64169 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@
 - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055))
 - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072))
 - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084))
+- add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100))
 
 ### Linting
 

From 51f37561bf9555202803c23494959f8cec7e1ae3 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 5 Aug 2024 15:27:13 +0200
Subject: [PATCH 184/414] add option to exclude citations for custom pipeline
 template

---
 .../create-test-lint-wf-template.yml          |   5 +
 nf_core/pipeline-template/nextflow.config     |   3 +-
 .../pipeline-template/nextflow_schema.json    |   4 +-
 .../pipeline-template/workflows/pipeline.nf   |   4 +
 nf_core/pipelines/create/create.py            |   2 +
 nf_core/pipelines/create/custompipeline.py    |  13 +
 tests/__snapshots__/test_create_app.ambr      | 511 +++++++++---------
 tests/data/pipeline_create_template_skip.yml  |   1 +
 8 files changed, 284 insertions(+), 259 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index cfa0a50079..818c206167 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -42,6 +42,7 @@ jobs:
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
           - "template_skip_code_linters.yml"
+          - "template_skip_citations.yml"
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
@@ -107,6 +108,10 @@ jobs:
         run: |
           printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml
 
+      - name: Create template skip citations
+        run: |
+          printf "org: my-prefix\nskip: citations" > create-test-lint-wf/template_skip_citations.yml
+
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 2e6a56b001..f622205a12 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -25,7 +25,8 @@ params {
     multiqc_title              = null
     multiqc_logo               = null
     max_multiqc_email_size     = '25.MB'
-    multiqc_methods_description = null
+    {%- if citations %}
+    multiqc_methods_description = null{% endif %}
 
     // Boilerplate options
     outdir                       = null
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 18bad71b76..0bd4443675 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -234,12 +234,12 @@
                     "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
                     "fa_icon": "fas fa-image",
                     "hidden": true
-                },
+                },{% if citations %}
                 "multiqc_methods_description": {
                     "type": "string",
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog"
-                },
+                },{% endif %}
                 "validate_params": {
                     "type": "boolean",
                     "description": "Boolean whether to validate parameters against the schema at runtime",
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index de0f21fe38..765b97c68e 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -63,21 +63,25 @@ workflow {{ short_name|upper }} {
         workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
 
+    {%- if citations %}
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
     ch_methods_description                = Channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
+    {%- endif %}
 
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
+    {%- if citations %}
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_methods_description.collectFile(
             name: 'methods_description_mqc.yaml',
             sort: true
         )
     )
+    {%- endif %}
 
     MULTIQC (
         ch_multiqc_files.collect(),
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 42e4a6ad7b..86ca1763fc 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -101,6 +101,7 @@ def __init__(
                 ".prettierrc.yml",
                 ".github/workflows/fix-linting.yml",
             ],
+            "citations": ["CITATIONS.md", "assets/methods_description_template.yml"],
         }
         # Get list of files we're skipping with the supplied skip keys
         self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k])
@@ -210,6 +211,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
             "igenomes": {"file": True, "content": True},
             "nf_core_configs": {"file": False, "content": True},
             "code_linters": {"file": True, "content": True},
+            "citations": {"file": True, "content": True},
         }
 
         # Set the parameters for the jinja template
diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py
index 0925fb5bab..1dd6134848 100644
--- a/nf_core/pipelines/create/custompipeline.py
+++ b/nf_core/pipelines/create/custompipeline.py
@@ -51,6 +51,13 @@
 - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc).
 """
 
+markdown_citations = """
+If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline.
+
+Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to describe a Materials & Methods section describing the tools used in the pieline,
+and the logics to add this section to the output MultiQC report (if the report is generated).
+"""
+
 
 class CustomPipeline(Screen):
     """Select if the pipeline will use genomic data."""
@@ -96,6 +103,12 @@ def compose(self) -> ComposeResult:
                 "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.",
                 "code_linters",
             ),
+            PipelineFeature(
+                markdown_citations,
+                "Include citations",
+                "Include a CITATIONS.md file to add pipeline tools citations.",
+                "citations",
+            ),
             classes="features-container",
         )
         yield Center(
diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr
index 5e5b005de0..531ea098bf 100644
--- a/tests/__snapshots__/test_create_app.ambr
+++ b/tests/__snapshots__/test_create_app.ambr
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diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml
index d9ef405c51..06e01cc7f2 100644
--- a/tests/data/pipeline_create_template_skip.yml
+++ b/tests/data/pipeline_create_template_skip.yml
@@ -12,3 +12,4 @@ skip_features:
   - igenomes
   - nf_core_configs
   - code_linters
+  - citations

From 74bd318ef0785108f122bc1f14f4d9d668f57b35 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 5 Aug 2024 13:29:41 +0000
Subject: [PATCH 185/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index aea91cb51a..a723bd3283 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@
 - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055))
 - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072))
 - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084))
+- add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101))
 
 ### Linting
 

From ed4554d7c4a37341a034bb227c4a02953a88ce05 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 5 Aug 2024 15:32:04 +0200
Subject: [PATCH 186/414] update snapshots

---
 tests/__snapshots__/test_create_app.ambr | 511 +++++++++++------------
 1 file changed, 255 insertions(+), 256 deletions(-)

diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr
index 5e5b005de0..531ea098bf 100644
--- a/tests/__snapshots__/test_create_app.ambr
+++ b/tests/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
           font-weight: 700;
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+      .terminal-4194849765-matrix {
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           font-family: arial;
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From 9182530d2a4356fa2924798b5aa2025fed793dd0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Mon, 5 Aug 2024 16:13:37 +0200
Subject: [PATCH 187/414] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 nf_core/pipelines/create/custompipeline.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py
index 1dd6134848..d5bcf04bc7 100644
--- a/nf_core/pipelines/create/custompipeline.py
+++ b/nf_core/pipelines/create/custompipeline.py
@@ -54,7 +54,7 @@
 markdown_citations = """
 If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline.
 
-Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to describe a Materials & Methods section describing the tools used in the pieline,
+Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline,
 and the logics to add this section to the output MultiQC report (if the report is generated).
 """
 
@@ -106,7 +106,7 @@ def compose(self) -> ComposeResult:
             PipelineFeature(
                 markdown_citations,
                 "Include citations",
-                "Include a CITATIONS.md file to add pipeline tools citations.",
+                "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled).",
                 "citations",
             ),
             classes="features-container",

From b0d07609507ef60ba79179e810b0cac1f308108a Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 5 Aug 2024 16:23:54 +0200
Subject: [PATCH 188/414] exclude content of CITATIONS.md instead of the whole
 file

---
 nf_core/pipeline-template/CITATIONS.md                        | 3 +++
 nf_core/pipeline-template/README.md                           | 4 ++--
 .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf | 2 ++
 nf_core/pipeline-template/workflows/pipeline.nf               | 2 +-
 nf_core/pipelines/create/create.py                            | 2 +-
 5 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md
index 6edf8f620c..c0c0729277 100644
--- a/nf_core/pipeline-template/CITATIONS.md
+++ b/nf_core/pipeline-template/CITATIONS.md
@@ -8,6 +8,8 @@
 
 > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
 
+{%- if citations %}
+
 ## Pipeline tools
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
@@ -39,3 +41,4 @@
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
 
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
+  > {%- endif %}
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index feece399b5..4efa88d5f6 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -116,10 +116,10 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use {{ name }} for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+{% if citations %}<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
-
+{% endif %}
 {% if is_nfcore -%}
 You can cite the `nf-core` publication as follows:
 
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index a4bfb9f8be..0c2e1d8b0a 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -207,6 +207,7 @@ def genomeExistsError() {
 }
 {%- endif %}
 
+{%- if citations %}
 //
 // Generate methods description for MultiQC
 //
@@ -270,3 +271,4 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     return description_html.toString()
 }
+{% endif %}
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 765b97c68e..8ce3637e4e 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -9,7 +9,7 @@ include { MULTIQC                } from '../modules/nf-core/multiqc/main'
 include { paramsSummaryMap       } from 'plugin/nf-validation'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
+{% if citations %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 86ca1763fc..3adeec60b7 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -101,7 +101,7 @@ def __init__(
                 ".prettierrc.yml",
                 ".github/workflows/fix-linting.yml",
             ],
-            "citations": ["CITATIONS.md", "assets/methods_description_template.yml"],
+            "citations": ["assets/methods_description_template.yml"],
         }
         # Get list of files we're skipping with the supplied skip keys
         self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k])

From 138ecb793ab57f34b7fb124a81df04512f0b36fd Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 5 Aug 2024 16:58:50 +0200
Subject: [PATCH 189/414] update snapshot

---
 tests/__snapshots__/test_create_app.ambr | 511 ++++++++++++-----------
 1 file changed, 256 insertions(+), 255 deletions(-)

diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr
index 531ea098bf..940a875839 100644
--- a/tests/__snapshots__/test_create_app.ambr
+++ b/tests/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
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From d94d1d065001885e2a4b58bf55d1cd5fb352f5b9 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 6 Aug 2024 10:28:23 +0200
Subject: [PATCH 190/414] add bot action to update textual snapshots

---
 .github/workflows/regenerate-snapshots.yml | 92 ++++++++++++++++++++++
 CONTRIBUTING.md                            | 21 +++++
 2 files changed, 113 insertions(+)
 create mode 100644 .github/workflows/regenerate-snapshots.yml

diff --git a/.github/workflows/regenerate-snapshots.yml b/.github/workflows/regenerate-snapshots.yml
new file mode 100644
index 0000000000..d05505a953
--- /dev/null
+++ b/.github/workflows/regenerate-snapshots.yml
@@ -0,0 +1,92 @@
+name: Regenerate Textual snapshots from a comment
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  regenerate-snapshots:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, '@nf-core-bot regenerate snapshots') &&
+      github.repository == 'nf-core/tools'
+    runs-on: ubuntu-latest
+    steps:
+      # Use the @nf-core-bot token to check out so we can push later
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          token: ${{ secrets.nf_core_bot_auth_token }}
+
+      # indication that the command is running
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+
+      # Install dependencies and run pytest
+      - name: Set up Python
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip -r requirements-dev.txt
+          pip install -e .
+
+      - name: Run pytest to regenerate snapshots
+        id: pytest
+        run: |
+          python3 -m pytest tests/test_create_app.py --snapshot-update --color=yes --cov --durations=0
+        continue-on-error: true
+
+      # indication that the run has finished
+      - name: react if finished succesfully
+        if: steps.pytest.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: "+1"
+
+      - name: Commit & push changes
+        id: commit-and-push
+        if: steps.pytest.outcome == 'failure'
+        run: |
+          git config user.email "core@nf-co.re"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "[automated] Update Textual snapshots"
+          git push
+
+      - name: react if snapshots were updated
+        id: react-if-updated
+        if: steps.commit-and-push.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: hooray
+
+      - name: react if snapshots were not updated
+        if: steps.commit-and-push.outcome == 'failure'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: confused
+
+      - name: react if snapshots were not updated
+        if: steps.commit-and-push.outcome  == 'failure'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          issue-number: ${{ github.event.issue.number }}
+          body: |
+            @${{ github.actor }} I tried to update the snapshots, but it didn't work. Please update them manually.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 2b2dfc1bed..cc81fa3f48 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -125,3 +125,24 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
+
+## nf-core-bot
+
+nf-core has a bot which you can use to perform certain actions on a PR.
+
+- Fix linting:
+
+If the linting tests is failing on a PR to nf-core/tools, you can post a comment with the magic words `@nf-core-bot fix linting`. The bot will try to fix the linting, push to your branch, and react to the comment if the fix was successful or not.
+
+- Update the `CHANGELOG.md`:
+
+The nf-core-bot runs automatically on every PR updating the `CHANGELOG.md` if it was not updated. It will add the new change using the title of your PR.
+If the action didn't run automatically, or you want to provide a different title, you can post a comment with `@nf-core-bot changelog`, optionally followed by the description that you want to add to the changelog.
+
+- Update Textual snapshots:
+
+If the Textual snapshots (run by `tests/test_crate_app.py`) fail, an HTML report is generated and uploaded as an artifact.
+If you are sure that these changes are correct, you can automatically update the snapshots form the PR by posting a comment with the magic words `@nf-core-bot regenerate snapshots`.
+
+> [!WARNING]
+> Please always check this report to make sure that the changes are expected.

From c76a2ba95adef683e8fa197258472cf6deb36b8d Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 6 Aug 2024 08:31:24 +0000
Subject: [PATCH 191/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index aea91cb51a..013e8a5d45 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -58,6 +58,7 @@
 - Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079))
 - Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091))
 - Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094))
+- Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From d07f3ffbc0a490a7813897ab14f969a079cef70d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Tue, 6 Aug 2024 10:49:42 +0200
Subject: [PATCH 192/414] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 .github/workflows/regenerate-snapshots.yml | 5 +++--
 CONTRIBUTING.md                            | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/regenerate-snapshots.yml b/.github/workflows/regenerate-snapshots.yml
index d05505a953..8fcc9b6f1b 100644
--- a/.github/workflows/regenerate-snapshots.yml
+++ b/.github/workflows/regenerate-snapshots.yml
@@ -8,7 +8,7 @@ jobs:
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
-      contains(github.event.comment.body, '@nf-core-bot regenerate snapshots') &&
+      contains(github.event.comment.body, '@nf-core-bot update snapshots') &&
       github.repository == 'nf-core/tools'
     runs-on: ubuntu-latest
     steps:
@@ -36,6 +36,7 @@ jobs:
         uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
+          cache: "pip"
 
       - name: Install dependencies
         run: |
@@ -45,7 +46,7 @@ jobs:
       - name: Run pytest to regenerate snapshots
         id: pytest
         run: |
-          python3 -m pytest tests/test_create_app.py --snapshot-update --color=yes --cov --durations=0
+          python3 -m pytest tests/test_create_app.py --snapshot-update --color=yes  --durations=0
         continue-on-error: true
 
       # indication that the run has finished
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index cc81fa3f48..3ad9e57243 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -145,4 +145,4 @@ If the Textual snapshots (run by `tests/test_crate_app.py`) fail, an HTML report
 If you are sure that these changes are correct, you can automatically update the snapshots form the PR by posting a comment with the magic words `@nf-core-bot regenerate snapshots`.
 
 > [!WARNING]
-> Please always check this report to make sure that the changes are expected.
+> Please always check the HTML report to make sure that the changes are expected.

From 346344f55d47d8bd20fd7344eaff799079f6b3cc Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 6 Aug 2024 10:54:39 +0200
Subject: [PATCH 193/414] rename regenerae-snapshots to
 update-textual-snapshots

---
 ...shots.yml => update-textual-snapshots.yml} |  6 ++---
 CONTRIBUTING.md                               | 22 ++++++++++++++++---
 2 files changed, 22 insertions(+), 6 deletions(-)
 rename .github/workflows/{regenerate-snapshots.yml => update-textual-snapshots.yml} (96%)

diff --git a/.github/workflows/regenerate-snapshots.yml b/.github/workflows/update-textual-snapshots.yml
similarity index 96%
rename from .github/workflows/regenerate-snapshots.yml
rename to .github/workflows/update-textual-snapshots.yml
index 8fcc9b6f1b..fb936762f8 100644
--- a/.github/workflows/regenerate-snapshots.yml
+++ b/.github/workflows/update-textual-snapshots.yml
@@ -1,10 +1,10 @@
-name: Regenerate Textual snapshots from a comment
+name: Update Textual snapshots from a comment
 on:
   issue_comment:
     types: [created]
 
 jobs:
-  regenerate-snapshots:
+  update-snapshots:
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
@@ -43,7 +43,7 @@ jobs:
           python -m pip install --upgrade pip -r requirements-dev.txt
           pip install -e .
 
-      - name: Run pytest to regenerate snapshots
+      - name: Run pytest to update snapshots
         id: pytest
         run: |
           python3 -m pytest tests/test_create_app.py --snapshot-update --color=yes  --durations=0
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 3ad9e57243..f9773296c1 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -132,17 +132,33 @@ nf-core has a bot which you can use to perform certain actions on a PR.
 
 - Fix linting:
 
-If the linting tests is failing on a PR to nf-core/tools, you can post a comment with the magic words `@nf-core-bot fix linting`. The bot will try to fix the linting, push to your branch, and react to the comment if the fix was successful or not.
+If the linting tests is failing on a PR to nf-core/tools, you can post a comment with the magic words:
+
+```
+@nf-core-bot fix linting
+```
+
+The bot will try to fix the linting, push to your branch, and react to the comment when it starts running (👀) and if the fix was successful (👍🏻) or not (😕).
 
 - Update the `CHANGELOG.md`:
 
 The nf-core-bot runs automatically on every PR updating the `CHANGELOG.md` if it was not updated. It will add the new change using the title of your PR.
-If the action didn't run automatically, or you want to provide a different title, you can post a comment with `@nf-core-bot changelog`, optionally followed by the description that you want to add to the changelog.
+If the action didn't run automatically, or you want to provide a different title, you can post a comment with:
+
+```
+@nf-core-bot changelog
+```
+
+Optionally followed by the description that you want to add to the changelog.
 
 - Update Textual snapshots:
 
 If the Textual snapshots (run by `tests/test_crate_app.py`) fail, an HTML report is generated and uploaded as an artifact.
-If you are sure that these changes are correct, you can automatically update the snapshots form the PR by posting a comment with the magic words `@nf-core-bot regenerate snapshots`.
+If you are sure that these changes are correct, you can automatically update the snapshots form the PR by posting a comment with the magic words:
+
+```
+@nf-core-bot update snapshots
+```
 
 > [!WARNING]
 > Please always check the HTML report to make sure that the changes are expected.

From 6144d0f1ab8b9440623bfa586de61c75ee240569 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 6 Aug 2024 14:48:57 +0200
Subject: [PATCH 194/414] add option to exclude multiqc from pipeline template

---
 .../create-test-lint-wf-template.yml          |  5 ++
 .prettierignore                               |  2 +
 .../pipeline-template/.github/CONTRIBUTING.md |  2 +
 nf_core/pipeline-template/CITATIONS.md        |  5 +-
 nf_core/pipeline-template/README.md           |  2 +-
 .../assets/sendmail_template.txt              |  2 +
 nf_core/pipeline-template/conf/modules.config |  2 +
 nf_core/pipeline-template/docs/output.md      |  8 ++-
 nf_core/pipeline-template/docs/usage.md       |  2 +-
 nf_core/pipeline-template/main.nf             |  6 +-
 nf_core/pipeline-template/modules.json        |  3 +-
 nf_core/pipeline-template/nextflow.config     |  2 +
 .../pipeline-template/nextflow_schema.json    |  7 ++-
 .../utils_nfcore_pipeline_pipeline/main.nf    |  9 ++-
 nf_core/pipeline-template/tower.yml           |  2 +
 .../pipeline-template/workflows/pipeline.nf   | 15 ++---
 nf_core/pipelines/create/create.py            | 62 ++++++++++++-------
 nf_core/pipelines/create/custompipeline.py    |  8 ++-
 nf_core/pipelines/create/nfcorepipeline.py    |  8 ++-
 nf_core/pipelines/create/utils.py             |  6 ++
 20 files changed, 111 insertions(+), 47 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index cfa0a50079..0bc32d8e41 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -42,6 +42,7 @@ jobs:
           - "template_skip_igenomes.yml"
           - "template_skip_ci.yml"
           - "template_skip_code_linters.yml"
+          - "template_skip_multiqc.yml"
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
@@ -107,6 +108,10 @@ jobs:
         run: |
           printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml
 
+      - name: Create template skip multiqc
+        run: |
+          printf "org: my-prefix\nskip: multiqc" > create-test-lint-wf/template_skip_multiqc.yml
+
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |
diff --git a/.prettierignore b/.prettierignore
index 2a445d487f..059007ab03 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -5,6 +5,8 @@ docs/api/_build
 testing
 nf_core/module-template/meta.yml
 nf_core/pipeline-template/nextflow_schema.json
+nf_core/pipeline-template/modules.json
+nf_core/pipeline-template/tower.yml
 # don't run on things handled by ruff
 *.py
 *.pyc
diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md
index e22a664250..2d6ecc174a 100644
--- a/nf_core/pipeline-template/.github/CONTRIBUTING.md
+++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md
@@ -87,8 +87,10 @@ If you wish to contribute a new step, please use the following coding standards:
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+   {%- if multiqc %}
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
+    {% endif %}
 
 ### Default values
 
diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md
index 6edf8f620c..22f5da4e70 100644
--- a/nf_core/pipeline-template/CITATIONS.md
+++ b/nf_core/pipeline-template/CITATIONS.md
@@ -14,9 +14,10 @@
 
   > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
-- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+{% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
-  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+> {%- endif %}
 
 ## Software packaging/containerisation tools
 
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index feece399b5..a9c913d6e2 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -45,7 +45,7 @@
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+   {% if multiqc %}2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)){% endif %}
 
 ## Usage
 
diff --git a/nf_core/pipeline-template/assets/sendmail_template.txt b/nf_core/pipeline-template/assets/sendmail_template.txt
index 3e59cd2d6d..5257815f7c 100644
--- a/nf_core/pipeline-template/assets/sendmail_template.txt
+++ b/nf_core/pipeline-template/assets/sendmail_template.txt
@@ -26,6 +26,7 @@ Content-Disposition: inline; filename="{{ name_noslash }}_logo_light.png"
     join( '\n' ) %>
 
 <%
+{%- if multiqc %}
 if (mqcFile){
 def mqcFileObj = new File("$mqcFile")
 if (mqcFileObj.length() < mqcMaxSize){
@@ -48,6 +49,7 @@ ${mqcFileObj.
     join( '\n' )}
 """
 }}
+{%- endif %}
 %>
 
 --nfcoremimeboundary--
diff --git a/nf_core/pipeline-template/conf/modules.config b/nf_core/pipeline-template/conf/modules.config
index d203d2b6e6..84972d8e24 100644
--- a/nf_core/pipeline-template/conf/modules.config
+++ b/nf_core/pipeline-template/conf/modules.config
@@ -22,6 +22,7 @@ process {
         ext.args = '--quiet'
     }
 
+    {%- if multiqc %}
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
@@ -30,5 +31,6 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+    {%- endif %}
 
 }
diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md
index 53b0e242e5..e27ff99598 100644
--- a/nf_core/pipeline-template/docs/output.md
+++ b/nf_core/pipeline-template/docs/output.md
@@ -2,7 +2,7 @@
 
 ## Introduction
 
-This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
+This document describes the output produced by the pipeline. {% if multiqc %}Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.{% endif %}
 
 The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
@@ -13,7 +13,7 @@ The directories listed below will be created in the results directory after the
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
 - [FastQC](#fastqc) - Raw read QC
-- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+  {% if multiqc %}- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline{% endif %}
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### FastQC
@@ -36,8 +36,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 ![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
 
 :::note
-The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
+The FastQC plots {% if multiqc %}displayed in the MultiQC report{% endif %} shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
 :::
+{% if multiqc %}
 
 ### MultiQC
 
@@ -54,6 +55,7 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
 [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
 
 Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
+{% endif %}
 
 ### Pipeline information
 
diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md
index bf637219f8..1dc033eea5 100644
--- a/nf_core/pipeline-template/docs/usage.md
+++ b/nf_core/pipeline-template/docs/usage.md
@@ -114,7 +114,7 @@ It is a good idea to specify a pipeline version when running the pipeline on you
 
 First, go to the [{{ name }} releases page](https://github.com/{{ name }}/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
 
-This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
+This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. {% if multiqc %}For example, at the bottom of the MultiQC reports.{% endif %}
 
 To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index c13a0d24e1..fddfc5489e 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -56,10 +56,10 @@ workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
     {{ short_name|upper }} (
         samplesheet
     )
-
+{%- if multiqc %}
     emit:
     multiqc_report = {{ short_name|upper }}.out.multiqc_report // channel: /path/to/multiqc_report.html
-
+{%- endif %}
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -101,7 +101,7 @@ workflow {
         params.outdir,
         params.monochrome_logs,
         params.hook_url,
-        {{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report
+        {%- if multiqc %}{{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %}
     )
 }
 
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 9137c59675..eb9391b29a 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -9,12 +9,13 @@
                         "branch": "master",
                         "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["modules"]
-                    },
+                    }{%- if multiqc %},
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
                     }
+                    {%- endif %}
                 }
             },
             "subworkflows": {
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 2e6a56b001..07c04d7b4c 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -20,12 +20,14 @@ params {
     igenomes_ignore            = false
     {%- endif %}
 
+    {%- if multiqc %}
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
     multiqc_logo               = null
     max_multiqc_email_size     = '25.MB'
     multiqc_methods_description = null
+    {%- endif %}
 
     // Boilerplate options
     outdir                       = null
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 18bad71b76..1815f57ef0 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -35,12 +35,13 @@
                     "fa_icon": "fas fa-envelope",
                     "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                     "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
-                },
+                }{% if multiqc %},
                 "multiqc_title": {
                     "type": "string",
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                     "fa_icon": "fas fa-file-signature"
                 }
+                {% endif %}
             }
         },
         {%- if igenomes %}
@@ -201,6 +202,7 @@
                     "fa_icon": "fas fa-remove-format",
                     "hidden": true
                 },
+                {%- if multiqc %}
                 "max_multiqc_email_size": {
                     "type": "string",
                     "description": "File size limit when attaching MultiQC reports to summary emails.",
@@ -209,6 +211,7 @@
                     "fa_icon": "fas fa-file-upload",
                     "hidden": true
                 },
+                {% endif %}
                 "monochrome_logs": {
                     "type": "boolean",
                     "description": "Do not use coloured log outputs.",
@@ -222,6 +225,7 @@
                     "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                     "hidden": true
                 },
+                {%- if multiqc %}
                 "multiqc_config": {
                     "type": "string",
                     "format": "file-path",
@@ -240,6 +244,7 @@
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog"
                 },
+                {%- endif %}
                 "validate_params": {
                     "type": "boolean",
                     "description": "Boolean whether to validate parameters against the schema at runtime",
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index a4bfb9f8be..7c5b7b2213 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -123,7 +123,7 @@ workflow PIPELINE_COMPLETION {
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
-    multiqc_report  //  string: Path to MultiQC report
+    {% if multiqc %}multiqc_report  //  string: Path to MultiQC report{% endif %}
 
     main:
 
@@ -134,7 +134,11 @@ workflow PIPELINE_COMPLETION {
     //
     workflow.onComplete {
         if (email || email_on_fail) {
+            {%- if multiqc %}
             completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
+            {%- else %}
+            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, [])
+            {%- endif %}
         }
 
         completionSummary(monochrome_logs)
@@ -206,7 +210,7 @@ def genomeExistsError() {
     }
 }
 {%- endif %}
-
+{%- if multiqc %}
 //
 // Generate methods description for MultiQC
 //
@@ -270,3 +274,4 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     return description_html.toString()
 }
+{% endif %}
diff --git a/nf_core/pipeline-template/tower.yml b/nf_core/pipeline-template/tower.yml
index 787aedfe92..2ddbef770e 100644
--- a/nf_core/pipeline-template/tower.yml
+++ b/nf_core/pipeline-template/tower.yml
@@ -1,5 +1,7 @@
 reports:
+  {%- if multiqc %}
   multiqc_report.html:
     display: "MultiQC HTML report"
+  {%- endif %}
   samplesheet.csv:
     display: "Auto-created samplesheet with collated metadata and FASTQ paths"
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index de0f21fe38..eb56cb9235 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -5,11 +5,11 @@
 */
 
 include { FASTQC                 } from '../modules/nf-core/fastqc/main'
-include { MULTIQC                } from '../modules/nf-core/multiqc/main'
+{% if multiqc %}include { MULTIQC                } from '../modules/nf-core/multiqc/main'{% endif %}
 include { paramsSummaryMap       } from 'plugin/nf-validation'
-include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+{% if multiqc %}include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
+{% if multiqc %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -25,7 +25,7 @@ workflow {{ short_name|upper }} {
     main:
 
     ch_versions = Channel.empty()
-    ch_multiqc_files = Channel.empty()
+    {% if multiqc %}ch_multiqc_files = Channel.empty(){% endif %}
 
     //
     // MODULE: Run FastQC
@@ -33,7 +33,7 @@ workflow {{ short_name|upper }} {
     FASTQC (
         ch_samplesheet
     )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
+    {% if multiqc %}ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}){% endif %}
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     //
@@ -47,6 +47,7 @@ workflow {{ short_name|upper }} {
             newLine: true
         ).set { ch_collated_versions }
 
+{% if multiqc %}
     //
     // MODULE: MultiQC
     //
@@ -85,9 +86,9 @@ workflow {{ short_name|upper }} {
         ch_multiqc_custom_config.toList(),
         ch_multiqc_logo.toList()
     )
-
+{% endif %}
     emit:
-    multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    {%- if multiqc %}multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html{% endif %}
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
 }
 
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 42e4a6ad7b..386ddd3bd9 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -101,6 +101,11 @@ def __init__(
                 ".prettierrc.yml",
                 ".github/workflows/fix-linting.yml",
             ],
+            "multiqc": [
+                "assets/multiqc_config.yml",
+                "assets/methods_description_template.yml",
+                "modules/nf-core/multiqc/",
+            ],
         }
         # Get list of files we're skipping with the supplied skip keys
         self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k])
@@ -210,6 +215,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
             "igenomes": {"file": True, "content": True},
             "nf_core_configs": {"file": False, "content": True},
             "code_linters": {"file": True, "content": True},
+            "multiqc": {"file": True, "content": True},
         }
 
         # Set the parameters for the jinja template
@@ -374,8 +380,8 @@ def render_template(self):
                 # in the github bug report template
                 self.remove_nf_core_in_bug_report_template()
 
-            # Update the .nf-core.yml with linting configurations
-            self.fix_linting()
+        # Update the .nf-core.yml with linting configurations
+        self.fix_linting()
 
         if self.config:
             config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir)
@@ -425,28 +431,31 @@ def fix_linting(self):
         """
         # Create a lint config
         short_name = self.jinja_params["short_name"]
-        lint_config = {
-            "files_exist": [
-                "CODE_OF_CONDUCT.md",
-                f"assets/nf-core-{short_name}_logo_light.png",
-                f"docs/images/nf-core-{short_name}_logo_light.png",
-                f"docs/images/nf-core-{short_name}_logo_dark.png",
-                ".github/ISSUE_TEMPLATE/config.yml",
-                ".github/workflows/awstest.yml",
-                ".github/workflows/awsfulltest.yml",
-            ],
-            "files_unchanged": [
-                "CODE_OF_CONDUCT.md",
-                f"assets/nf-core-{short_name}_logo_light.png",
-                f"docs/images/nf-core-{short_name}_logo_light.png",
-                f"docs/images/nf-core-{short_name}_logo_dark.png",
-            ],
-            "nextflow_config": [
-                "manifest.name",
-                "manifest.homePage",
-            ],
-            "multiqc_config": ["report_comment"],
-        }
+        if not self.config.is_nfcore:
+            lint_config = {
+                "files_exist": [
+                    "CODE_OF_CONDUCT.md",
+                    f"assets/nf-core-{short_name}_logo_light.png",
+                    f"docs/images/nf-core-{short_name}_logo_light.png",
+                    f"docs/images/nf-core-{short_name}_logo_dark.png",
+                    ".github/ISSUE_TEMPLATE/config.yml",
+                    ".github/workflows/awstest.yml",
+                    ".github/workflows/awsfulltest.yml",
+                ],
+                "files_unchanged": [
+                    "CODE_OF_CONDUCT.md",
+                    f"assets/nf-core-{short_name}_logo_light.png",
+                    f"docs/images/nf-core-{short_name}_logo_light.png",
+                    f"docs/images/nf-core-{short_name}_logo_dark.png",
+                ],
+                "nextflow_config": [
+                    "manifest.name",
+                    "manifest.homePage",
+                ],
+                "multiqc_config": ["report_comment"],
+            }
+        else:
+            lint_config = {"files_exist": [], "files_unchanged": []}
 
         # Add GitHub hosting specific configurations
         if not self.jinja_params["github"]:
@@ -505,6 +514,11 @@ def fix_linting(self):
         if not self.jinja_params["github_badges"] or not self.jinja_params["github"]:
             lint_config["readme"] = ["nextflow_badge"]
 
+        # Add multiqc specific configurations
+        if not self.jinja_params["multiqc"]:
+            lint_config["files_unchanged"].extend([".github/CONTRIBUTING.md", "assets/sendmail_template.txt"])
+            lint_config["multiqc_config"] = ["report_comment"]
+
         # If the pipeline is not nf-core
         if not self.config.is_nfcore:
             lint_config["files_unchanged"].extend([".github/ISSUE_TEMPLATE/bug_report.yml"])
diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py
index 0925fb5bab..0ddd6533b1 100644
--- a/nf_core/pipelines/create/custompipeline.py
+++ b/nf_core/pipelines/create/custompipeline.py
@@ -6,7 +6,7 @@
 from textual.screen import Screen
 from textual.widgets import Button, Footer, Header, Markdown, Switch
 
-from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes
+from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes, markdown_multiqc
 
 markdown_ci = """
 Nf-core provides a set of Continuous Integration (CI) tests for Github.
@@ -96,6 +96,12 @@ def compose(self) -> ComposeResult:
                 "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.",
                 "code_linters",
             ),
+            PipelineFeature(
+                markdown_multiqc,
+                "Use multiqc",
+                "The pipeline will include the MultiQC module which generates an HTML report for quality control.",
+                "multiqc",
+            ),
             classes="features-container",
         )
         yield Center(
diff --git a/nf_core/pipelines/create/nfcorepipeline.py b/nf_core/pipelines/create/nfcorepipeline.py
index 49cc1f8f86..8319cb044c 100644
--- a/nf_core/pipelines/create/nfcorepipeline.py
+++ b/nf_core/pipelines/create/nfcorepipeline.py
@@ -6,7 +6,7 @@
 from textual.screen import Screen
 from textual.widgets import Button, Footer, Header, Markdown, Switch
 
-from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes
+from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes, markdown_multiqc
 
 
 class NfcorePipeline(Screen):
@@ -29,6 +29,12 @@ def compose(self) -> ComposeResult:
                 "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes",
                 "igenomes",
             ),
+            PipelineFeature(
+                markdown_multiqc,
+                "Use multiqc",
+                "The pipeline will include the MultiQC module which generates an HTML report for quality control.",
+                "multiqc",
+            ),
             classes="features-container",
         )
         yield Center(
diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
index c387960c39..43094ab531 100644
--- a/nf_core/pipelines/create/utils.py
+++ b/nf_core/pipelines/create/utils.py
@@ -259,3 +259,9 @@ def remove_hide_class(app, widget_id: str) -> None:
 For more information about reference genomes in nf-core pipelines,
 see the [nf-core docs](https://nf-co.re/docs/usage/reference_genomes).
 """
+
+markdown_multiqc = """
+MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory.
+
+The pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info.
+"""

From dcc4214f65009f9a94a6a3dd70543567d7016ccd Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 6 Aug 2024 12:50:57 +0000
Subject: [PATCH 195/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index aea91cb51a..5256acf3de 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@
 - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055))
 - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072))
 - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084))
+- add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103))
 
 ### Linting
 

From a2d6b447f4bb0f11d184d576602dcaf964ccd9b9 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 7 Aug 2024 08:31:00 +0200
Subject: [PATCH 196/414] fix tests

---
 nf_core/pipelines/create/create.py       |  13 +-
 tests/__snapshots__/test_create_app.ambr | 764 +++++++++++------------
 2 files changed, 392 insertions(+), 385 deletions(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 386ddd3bd9..86e104aa55 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -455,7 +455,7 @@ def fix_linting(self):
                 "multiqc_config": ["report_comment"],
             }
         else:
-            lint_config = {"files_exist": [], "files_unchanged": []}
+            lint_config = {}
 
         # Add GitHub hosting specific configurations
         if not self.jinja_params["github"]:
@@ -516,8 +516,15 @@ def fix_linting(self):
 
         # Add multiqc specific configurations
         if not self.jinja_params["multiqc"]:
-            lint_config["files_unchanged"].extend([".github/CONTRIBUTING.md", "assets/sendmail_template.txt"])
-            lint_config["multiqc_config"] = ["report_comment"]
+            try:
+                lint_config["files_unchanged"].extend([".github/CONTRIBUTING.md", "assets/sendmail_template.txt"])
+            except KeyError:
+                lint_config["files_unchanged"] = [".github/CONTRIBUTING.md", "assets/sendmail_template.txt"]
+            try:
+                lint_config["files_exist"].extend(["assets/multiqc_config.yml"])
+            except KeyError:
+                lint_config["files_exist"] = ["assets/multiqc_config.yml"]
+            lint_config["multiqc_config"] = False
 
         # If the pipeline is not nf-core
         if not self.config.is_nfcore:
diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr
index 5e5b005de0..6c93216bea 100644
--- a/tests/__snapshots__/test_create_app.ambr
+++ b/tests/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
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From 88a354fa73a657570496fd9cc6343d7e75aeaba7 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 7 Aug 2024 09:29:48 +0200
Subject: [PATCH 197/414] update textual snapshots

---
 tests/__snapshots__/test_create_app.ambr | 511 ++++++++++++-----------
 1 file changed, 256 insertions(+), 255 deletions(-)

diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr
index ed597e46b6..57e4258ef8 100644
--- a/tests/__snapshots__/test_create_app.ambr
+++ b/tests/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
           font-weight: 700;
       }
   
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+      .terminal-3843971496-matrix {
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           font-size: 20px;
           line-height: 24.4px;
           font-variant-east-asian: full-width;
       }
   
-      .terminal-4194849765-title {
+      .terminal-3843971496-title {
           font-size: 18px;
           font-weight: bold;
           font-family: arial;
       }
   
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-  .terminal-4194849765-r3 { fill: #989898 }
-  .terminal-4194849765-r4 { fill: #e1e1e1 }
-  .terminal-4194849765-r5 { fill: #4ebf71;font-weight: bold }
-  .terminal-4194849765-r6 { fill: #1e1e1e }
-  .terminal-4194849765-r7 { fill: #0178d4 }
-  .terminal-4194849765-r8 { fill: #454a50 }
-  .terminal-4194849765-r9 { fill: #e2e2e2 }
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-  .terminal-4194849765-r11 { fill: #e2e3e3;font-weight: bold }
-  .terminal-4194849765-r12 { fill: #000000 }
-  .terminal-4194849765-r13 { fill: #e4e4e4 }
-  .terminal-4194849765-r14 { fill: #14191f }
-  .terminal-4194849765-r15 { fill: #507bb3 }
-  .terminal-4194849765-r16 { fill: #dde6ed;font-weight: bold }
-  .terminal-4194849765-r17 { fill: #001541 }
-  .terminal-4194849765-r18 { fill: #7ae998 }
-  .terminal-4194849765-r19 { fill: #0a180e;font-weight: bold }
-  .terminal-4194849765-r20 { fill: #008139 }
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-  .terminal-4194849765-r22 { fill: #a7a9ab }
-  .terminal-4194849765-r23 { fill: #e2e3e3 }
+      .terminal-3843971496-r1 { fill: #c5c8c6 }
+  .terminal-3843971496-r2 { fill: #e3e3e3 }
+  .terminal-3843971496-r3 { fill: #989898 }
+  .terminal-3843971496-r4 { fill: #e1e1e1 }
+  .terminal-3843971496-r5 { fill: #4ebf71;font-weight: bold }
+  .terminal-3843971496-r6 { fill: #1e1e1e }
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+  .terminal-3843971496-r8 { fill: #454a50 }
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+  .terminal-3843971496-r11 { fill: #e2e3e3;font-weight: bold }
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+  .terminal-3843971496-r13 { fill: #e4e4e4 }
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+  .terminal-3843971496-r15 { fill: #507bb3 }
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+  .terminal-3843971496-r18 { fill: #7ae998 }
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+  .terminal-3843971496-r20 { fill: #008139 }
+  .terminal-3843971496-r21 { fill: #fea62b;font-weight: bold }
+  .terminal-3843971496-r22 { fill: #a7a9ab }
+  .terminal-3843971496-r23 { fill: #e2e3e3 }
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+      <clipPath id="terminal-3843971496-clip-terminal">
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From 3c1b1b07bf57aa5ab36fc60d0deb96859053057e Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 7 Aug 2024 10:01:49 +0200
Subject: [PATCH 198/414] add multiqc potion to test data

---
 tests/data/pipeline_create_template_skip.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml
index 1431114c08..7ae5bba8c4 100644
--- a/tests/data/pipeline_create_template_skip.yml
+++ b/tests/data/pipeline_create_template_skip.yml
@@ -14,3 +14,4 @@ skip_features:
   - code_linters
   - citations
   - gitpod
+  - multiqc

From 2fcfd0e7237ce6c624ce538d902c2c14c6d0dcab Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 7 Aug 2024 10:12:23 +0200
Subject: [PATCH 199/414] update textual snapshots

---
 tests/__snapshots__/test_create_app.ambr | 512 +++++++++++------------
 1 file changed, 256 insertions(+), 256 deletions(-)

diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr
index 51ff46d68d..9aad37cc96 100644
--- a/tests/__snapshots__/test_create_app.ambr
+++ b/tests/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
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From 57ed19ae36e40e74dda75f18c008a606f79073af Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 7 Aug 2024 10:46:27 +0200
Subject: [PATCH 200/414] run tests also after pytest-migrate

---
 nf_core/commands_modules.py | 35 +++++++++++++++++------------------
 1 file changed, 17 insertions(+), 18 deletions(-)

diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py
index c65c42d41a..a34e9a519e 100644
--- a/nf_core/commands_modules.py
+++ b/nf_core/commands_modules.py
@@ -242,24 +242,23 @@ def modules_test(ctx, tool, dir, no_prompts, update, once, profile, migrate_pyte
             empty_template=False,
             migrate_pytest=migrate_pytest,
         )
-    else:
-        try:
-            module_tester = ComponentsTest(
-                component_type="modules",
-                component_name=tool,
-                directory=dir,
-                no_prompts=no_prompts,
-                update=update,
-                once=once,
-                remote_url=ctx.obj["modules_repo_url"],
-                branch=ctx.obj["modules_repo_branch"],
-                verbose=ctx.obj["verbose"],
-                profile=profile,
-            )
-            module_tester.run()
-        except (UserWarning, LookupError) as e:
-            log.critical(e)
-            sys.exit(1)
+    try:
+        module_tester = ComponentsTest(
+            component_type="modules",
+            component_name=tool,
+            directory=dir,
+            no_prompts=no_prompts,
+            update=update,
+            once=once,
+            remote_url=ctx.obj["modules_repo_url"],
+            branch=ctx.obj["modules_repo_branch"],
+            verbose=ctx.obj["verbose"],
+            profile=profile,
+        )
+        module_tester.run()
+    except (UserWarning, LookupError) as e:
+        log.critical(e)
+        sys.exit(1)
 
 
 def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version):

From baae14c03e4feec6ef77caf32c610079dcad419f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 7 Aug 2024 10:47:39 +0200
Subject: [PATCH 201/414] and the same for subworkflows

---
 nf_core/commands_subworkflows.py | 35 ++++++++++++++++----------------
 1 file changed, 17 insertions(+), 18 deletions(-)

diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py
index 8c3be2bb46..8b2db3578a 100644
--- a/nf_core/commands_subworkflows.py
+++ b/nf_core/commands_subworkflows.py
@@ -44,24 +44,23 @@ def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile,
 
     if migrate_pytest:
         subworkflows_create(ctx, subworkflow, dir, None, False, True)
-    else:
-        try:
-            sw_tester = ComponentsTest(
-                component_type="subworkflows",
-                component_name=subworkflow,
-                directory=dir,
-                no_prompts=no_prompts,
-                update=update,
-                once=once,
-                remote_url=ctx.obj["modules_repo_url"],
-                branch=ctx.obj["modules_repo_branch"],
-                verbose=ctx.obj["verbose"],
-                profile=profile,
-            )
-            sw_tester.run()
-        except (UserWarning, LookupError) as e:
-            log.critical(e)
-            sys.exit(1)
+    try:
+        sw_tester = ComponentsTest(
+            component_type="subworkflows",
+            component_name=subworkflow,
+            directory=dir,
+            no_prompts=no_prompts,
+            update=update,
+            once=once,
+            remote_url=ctx.obj["modules_repo_url"],
+            branch=ctx.obj["modules_repo_branch"],
+            verbose=ctx.obj["verbose"],
+            profile=profile,
+        )
+        sw_tester.run()
+    except (UserWarning, LookupError) as e:
+        log.critical(e)
+        sys.exit(1)
 
 
 def subworkflows_list_remote(ctx, keywords, json):

From f9eb2a58d7ad231cd14f971d86b57558d3e67912 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 7 Aug 2024 11:15:59 +0200
Subject: [PATCH 202/414] remove multiqc images from the template docs

---
 .../docs/images/mqc_fastqc_adapter.png          | Bin 23458 -> 0 bytes
 .../docs/images/mqc_fastqc_counts.png           | Bin 33918 -> 0 bytes
 .../docs/images/mqc_fastqc_quality.png          | Bin 55769 -> 0 bytes
 nf_core/pipeline-template/docs/output.md        |  11 +----------
 4 files changed, 1 insertion(+), 10 deletions(-)
 delete mode 100755 nf_core/pipeline-template/docs/images/mqc_fastqc_adapter.png
 delete mode 100755 nf_core/pipeline-template/docs/images/mqc_fastqc_counts.png
 delete mode 100755 nf_core/pipeline-template/docs/images/mqc_fastqc_quality.png

diff --git a/nf_core/pipeline-template/docs/images/mqc_fastqc_adapter.png b/nf_core/pipeline-template/docs/images/mqc_fastqc_adapter.png
deleted file mode 100755
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z|35^;Kh!RoxxS?J`m4pp#<kIp4=<bPx9h7FczEo=vJHPHHtw6eUT0c~ZS9Ajr&m9*
z`}N@5O!K(h`!&DL_*^N!e(IyE^5Y*DCo$)GyWLfp8#Bu`UQgWq)X7u){jMJqCqH=_
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zf8?K(wPoXyS8o@W$5vFox|;I$(pzi0s`OQXOUiElVXy!Acx4*r?Z$TYbN>GWtNM@K
zJIlPYRkyg-+HUWTOwXxzj%?fcDqiMhz>ljx949-=-i-Kh_1KBUKX&esw4a``^RJ>*
zXwhtT%ei{n#FzEH|C;yZ>+$!u_x#*<oPG9wkK6iN-=6!te*Y)0KPh^(uV3!_e(CX&
z(4zOZW$gX7ezX9ZzT#~hKX0Dpr$gLlufO`RGPnD)O@4L7hPSG-{#87fxzK(3zcTI2
zrP{Gyt8D*WoFxdFy?78-T(K!|TiWx>+`=L8{b9SH^9&27u3G_Gxqxe`L2UJtdxghk
z&-wzDFvLvW{chK5u3{n6GSKKy!P&C6w^IFpbD0bcp^A{{2lcLh_DXj@ybtYvc^;(2
M)78&qol`;+0Fu7JivR!s

diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md
index e27ff99598..edd48b83f4 100644
--- a/nf_core/pipeline-template/docs/output.md
+++ b/nf_core/pipeline-template/docs/output.md
@@ -29,16 +29,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
-![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
-
-![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png)
-
-![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
-
-:::note
-The FastQC plots {% if multiqc %}displayed in the MultiQC report{% endif %} shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
-:::
-{% if multiqc %}
+{%- if multiqc %}
 
 ### MultiQC
 

From 3507b15ee40383a7cccce3975e2d9e9a96266985 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 7 Aug 2024 11:56:01 +0200
Subject: [PATCH 203/414] add option to exclude codespaces from pipeline
 template

---
 .github/workflows/create-test-lint-wf-template.yml |  7 +++----
 nf_core/pipeline-template/.github/CONTRIBUTING.md  |  2 ++
 nf_core/pipelines/create/create.py                 |  6 ++++++
 nf_core/pipelines/create/custompipeline.py         | 13 +++++++++++++
 tests/data/pipeline_create_template_skip.yml       |  1 +
 5 files changed, 25 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index c4eca40fa6..79c2ba6c89 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -44,6 +44,7 @@ jobs:
           - "template_skip_code_linters.yml"
           - "template_skip_citations.yml"
           - "template_skip_gitpod.yml"
+          - "template_skip_codespaces.yml"
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
@@ -117,11 +118,9 @@ jobs:
         run: |
           printf "org: my-prefix\nskip: gitpod" > create-test-lint-wf/template_skip_gitpod.yml
 
-      # Create a pipeline from the template
-      - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
+      - name: Create template skip codespaces
         run: |
-          cd create-test-lint-wf
-          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
+          printf "org: my-prefix\nskip: codespaces" > create-test-lint-wf/template_skip_codespaces.yml
 
       - name: run the pipeline
         run: |
diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md
index e22a664250..3a9cd3bcba 100644
--- a/nf_core/pipeline-template/.github/CONTRIBUTING.md
+++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md
@@ -116,6 +116,7 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
+{%- if codespaces %}
 
 ## GitHub Codespaces
 
@@ -131,3 +132,4 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
+  {% endif %}
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 05a5804ee3..225565dbaf 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -103,6 +103,7 @@ def __init__(
             ],
             "citations": ["assets/methods_description_template.yml"],
             "gitpod": [".gitpod.yml"],
+            "codespaces": [".devcontainer/devcontainer.json"],
         }
         # Get list of files we're skipping with the supplied skip keys
         self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k])
@@ -214,6 +215,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
             "code_linters": {"file": True, "content": True},
             "citations": {"file": True, "content": True},
             "gitpod": {"file": True, "content": True},
+            "codespaces": {"file": True, "content": True},
         }
 
         # Set the parameters for the jinja template
@@ -509,6 +511,10 @@ def fix_linting(self):
         if not self.jinja_params["github_badges"] or not self.jinja_params["github"]:
             lint_config["readme"] = ["nextflow_badge"]
 
+        # Add codespaces specific configurations
+        if not self.jinja_params["codespaces"]:
+            lint_config["files_unchanged"].extend([".github/CONTRIBUTING.md"])
+
         # If the pipeline is not nf-core
         if not self.config.is_nfcore:
             lint_config["files_unchanged"].extend([".github/ISSUE_TEMPLATE/bug_report.yml"])
diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py
index 5f131a7d84..4c75ff2795 100644
--- a/nf_core/pipelines/create/custompipeline.py
+++ b/nf_core/pipelines/create/custompipeline.py
@@ -65,6 +65,13 @@
 This is useful to have all the tools ready for pipeline development.
 """
 
+markdown_codespaces = """
+The pipeline will include a devcontainer configuration.
+The devcontainer will create a GitHub Codespaces for Nextflow development with nf-core/tools and Nextflow installed.
+
+Github Codespaces (https://github.com/features/codespaces) is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+"""
+
 
 class CustomPipeline(Screen):
     """Select if the pipeline will use genomic data."""
@@ -122,6 +129,12 @@ def compose(self) -> ComposeResult:
                 "Include the configuration required to use Gitpod.",
                 "gitpod",
             ),
+            PipelineFeature(
+                markdown_codespaces,
+                "Include GitHub Codespaces",
+                "The pipeline will include a devcontainer configuration for GitHub Codespaces, providing a development environment with nf-core/tools and Nextflow installed.",
+                "codespaces",
+            ),
             classes="features-container",
         )
         yield Center(
diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml
index 1431114c08..29a336069f 100644
--- a/tests/data/pipeline_create_template_skip.yml
+++ b/tests/data/pipeline_create_template_skip.yml
@@ -14,3 +14,4 @@ skip_features:
   - code_linters
   - citations
   - gitpod
+  - codespaces

From 26769f2eb5568d56977023a88f142e0d28da7e0f Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 7 Aug 2024 12:44:24 +0200
Subject: [PATCH 204/414] add option to exclude changelog from custom pipeline
 template

---
 .github/workflows/create-test-lint-wf-template.yml |  5 +++++
 nf_core/pipelines/create/create.py                 |  6 ++++++
 nf_core/pipelines/create/custompipeline.py         | 11 +++++++++++
 tests/data/pipeline_create_template_skip.yml       |  1 +
 4 files changed, 23 insertions(+)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index c4eca40fa6..b4022d780a 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -44,6 +44,7 @@ jobs:
           - "template_skip_code_linters.yml"
           - "template_skip_citations.yml"
           - "template_skip_gitpod.yml"
+          - "template_skip_changelog.yml"
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
@@ -117,6 +118,10 @@ jobs:
         run: |
           printf "org: my-prefix\nskip: gitpod" > create-test-lint-wf/template_skip_gitpod.yml
 
+      - name: Create template skip changelog
+        run: |
+          printf "org: my-prefix\nskip: changelog" > create-test-lint-wf/template_skip_changelog.yml
+
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 05a5804ee3..27dc729439 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -103,6 +103,7 @@ def __init__(
             ],
             "citations": ["assets/methods_description_template.yml"],
             "gitpod": [".gitpod.yml"],
+            "changelog": ["CHANGELOG.md"],
         }
         # Get list of files we're skipping with the supplied skip keys
         self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k])
@@ -214,6 +215,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
             "code_linters": {"file": True, "content": True},
             "citations": {"file": True, "content": True},
             "gitpod": {"file": True, "content": True},
+            "changelog": {"file": True, "content": False},
         }
 
         # Set the parameters for the jinja template
@@ -509,6 +511,10 @@ def fix_linting(self):
         if not self.jinja_params["github_badges"] or not self.jinja_params["github"]:
             lint_config["readme"] = ["nextflow_badge"]
 
+        # Add changelog specific configurations
+        if not self.jinja_params["changelog"]:
+            lint_config["files_exist"].extend(["CHANGELOG.md"])
+
         # If the pipeline is not nf-core
         if not self.config.is_nfcore:
             lint_config["files_unchanged"].extend([".github/ISSUE_TEMPLATE/bug_report.yml"])
diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py
index 5f131a7d84..c39c26507e 100644
--- a/nf_core/pipelines/create/custompipeline.py
+++ b/nf_core/pipelines/create/custompipeline.py
@@ -65,6 +65,11 @@
 This is useful to have all the tools ready for pipeline development.
 """
 
+markdown_changelog = """
+Having a `CHANGELOG.md` file in the pipeline root directory is useful to track the changes added to each version.
+You can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/
+"""
+
 
 class CustomPipeline(Screen):
     """Select if the pipeline will use genomic data."""
@@ -122,6 +127,12 @@ def compose(self) -> ComposeResult:
                 "Include the configuration required to use Gitpod.",
                 "gitpod",
             ),
+            PipelineFeature(
+                markdown_changelog,
+                "Add a changelog",
+                "Add a CHANGELOG.md file.",
+                "changelog",
+            ),
             classes="features-container",
         )
         yield Center(
diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml
index 1431114c08..ed0b5ef2ad 100644
--- a/tests/data/pipeline_create_template_skip.yml
+++ b/tests/data/pipeline_create_template_skip.yml
@@ -14,3 +14,4 @@ skip_features:
   - code_linters
   - citations
   - gitpod
+  - changelog

From 4d55d7a3382e85efc8be610a8ed3211969626206 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 7 Aug 2024 11:16:38 +0000
Subject: [PATCH 205/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 765507c4e1..52654b5dee 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@
 - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084))
 - add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101))
 - add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100))
+- add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104))
 
 ### Linting
 

From c0bbca287e39709b35457aa1970f9c745c206c0a Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 7 Aug 2024 11:17:25 +0000
Subject: [PATCH 206/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 765507c4e1..8e3dfdda55 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@
 - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084))
 - add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101))
 - add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100))
+- add option to exclude codespaces from pipeline template ([#3105](https://github.com/nf-core/tools/pull/3105))
 
 ### Linting
 

From 4cf16be72aa114b5062a82abc0fe0dafcc4f1b61 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Wed, 7 Aug 2024 15:09:55 +0200
Subject: [PATCH 207/414] Update nf_core/pipelines/create/create.py
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 nf_core/pipelines/create/create.py | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 908dd962d0..d9051f4165 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -520,14 +520,8 @@ def fix_linting(self):
 
         # Add multiqc specific configurations
         if not self.jinja_params["multiqc"]:
-            try:
-                lint_config["files_unchanged"].extend([".github/CONTRIBUTING.md", "assets/sendmail_template.txt"])
-            except KeyError:
-                lint_config["files_unchanged"] = [".github/CONTRIBUTING.md", "assets/sendmail_template.txt"]
-            try:
-                lint_config["files_exist"].extend(["assets/multiqc_config.yml"])
-            except KeyError:
-                lint_config["files_exist"] = ["assets/multiqc_config.yml"]
+            lint_config.setdefault("files_unchanged", []).extend([".github/CONTRIBUTING.md", "assets/sendmail_template.txt"])
+lint_config.setdefault("files_exist", []).extend(["assets/multiqc_config.yml"])
             lint_config["multiqc_config"] = False
 
         # If the pipeline is not nf-core

From f8d54635e853ecdd948a79d134bdea62c2dbb07a Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 7 Aug 2024 15:38:59 +0200
Subject: [PATCH 208/414] fix indentation

---
 nf_core/pipelines/create/create.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index d9051f4165..684b13f83a 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -520,8 +520,10 @@ def fix_linting(self):
 
         # Add multiqc specific configurations
         if not self.jinja_params["multiqc"]:
-            lint_config.setdefault("files_unchanged", []).extend([".github/CONTRIBUTING.md", "assets/sendmail_template.txt"])
-lint_config.setdefault("files_exist", []).extend(["assets/multiqc_config.yml"])
+            lint_config.setdefault("files_unchanged", []).extend(
+                [".github/CONTRIBUTING.md", "assets/sendmail_template.txt"]
+            )
+            lint_config.setdefault("files_exist", []).extend(["assets/multiqc_config.yml"])
             lint_config["multiqc_config"] = False
 
         # If the pipeline is not nf-core

From 8b196cd9a2601e9f05270bbd4bac629cc0b8c823 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 7 Aug 2024 16:12:04 +0200
Subject: [PATCH 209/414] update textual snapshots

---
 tests/__snapshots__/test_create_app.ambr | 512 +++++++++++------------
 1 file changed, 256 insertions(+), 256 deletions(-)

diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr
index 9aad37cc96..231c038c66 100644
--- a/tests/__snapshots__/test_create_app.ambr
+++ b/tests/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
           font-weight: 700;
       }
   
-      .terminal-2285198722-matrix {
+      .terminal-1308777655-matrix {
           font-family: Fira Code, monospace;
           font-size: 20px;
           line-height: 24.4px;
           font-variant-east-asian: full-width;
       }
   
-      .terminal-2285198722-title {
+      .terminal-1308777655-title {
           font-size: 18px;
           font-weight: bold;
           font-family: arial;
       }
   
-      .terminal-2285198722-r1 { fill: #c5c8c6 }
-  .terminal-2285198722-r2 { fill: #e3e3e3 }
-  .terminal-2285198722-r3 { fill: #989898 }
-  .terminal-2285198722-r4 { fill: #e1e1e1 }
-  .terminal-2285198722-r5 { fill: #4ebf71;font-weight: bold }
-  .terminal-2285198722-r6 { fill: #1e1e1e }
-  .terminal-2285198722-r7 { fill: #0178d4 }
-  .terminal-2285198722-r8 { fill: #454a50 }
-  .terminal-2285198722-r9 { fill: #e2e2e2 }
-  .terminal-2285198722-r10 { fill: #808080 }
-  .terminal-2285198722-r11 { fill: #e2e3e3;font-weight: bold }
-  .terminal-2285198722-r12 { fill: #000000 }
-  .terminal-2285198722-r13 { fill: #e4e4e4 }
-  .terminal-2285198722-r14 { fill: #14191f }
-  .terminal-2285198722-r15 { fill: #507bb3 }
-  .terminal-2285198722-r16 { fill: #dde6ed;font-weight: bold }
-  .terminal-2285198722-r17 { fill: #001541 }
-  .terminal-2285198722-r18 { fill: #7ae998 }
-  .terminal-2285198722-r19 { fill: #0a180e;font-weight: bold }
-  .terminal-2285198722-r20 { fill: #008139 }
-  .terminal-2285198722-r21 { fill: #fea62b;font-weight: bold }
-  .terminal-2285198722-r22 { fill: #a7a9ab }
-  .terminal-2285198722-r23 { fill: #e2e3e3 }
+      .terminal-1308777655-r1 { fill: #c5c8c6 }
+  .terminal-1308777655-r2 { fill: #e3e3e3 }
+  .terminal-1308777655-r3 { fill: #989898 }
+  .terminal-1308777655-r4 { fill: #e1e1e1 }
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From 1aec52881d806646565b336ce663bcf8366cad9f Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 7 Aug 2024 16:31:46 +0200
Subject: [PATCH 210/414] update textual snapshots

---
 tests/__snapshots__/test_create_app.ambr | 512 +++++++++++------------
 1 file changed, 256 insertions(+), 256 deletions(-)

diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr
index 231c038c66..f2c1c45c45 100644
--- a/tests/__snapshots__/test_create_app.ambr
+++ b/tests/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
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From 19590c3b8aefea9943ba8380e6ece16e9ccf1c67 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 7 Aug 2024 16:52:04 +0200
Subject: [PATCH 211/414] don't remove creating a pipeline to test it
 :no_mouth:

---
 .github/workflows/create-test-lint-wf-template.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index f35016197a..dbe143fda6 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -132,6 +132,12 @@ jobs:
         run: |
           printf "org: my-prefix\nskip: codespaces" > create-test-lint-wf/template_skip_codespaces.yml
 
+      # Create a pipeline from the template
+      - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
+        run: |
+          cd create-test-lint-wf
+          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
+
       - name: run the pipeline
         run: |
           cd create-test-lint-wf

From 8acb9c4856cddac922536682a2873946ef8aa56b Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 8 Aug 2024 13:32:08 +0200
Subject: [PATCH 212/414] handle template features with a yaml file

---
 .../create-test-lint-wf-template.yml          |  78 +++----
 .prettierignore                               |   1 +
 nf_core/pipelines/create/create.py            | 200 ++++------------
 nf_core/pipelines/create/templatefeatures.yml | 213 ++++++++++++++++++
 tests/data/pipeline_create_template_skip.yml  |  13 +-
 tests/test_create.py                          |  18 +-
 6 files changed, 297 insertions(+), 226 deletions(-)
 create mode 100644 nf_core/pipelines/create/templatefeatures.yml

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index dbe143fda6..d4ff3fc557 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -31,31 +31,41 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
+  install-yq:
+    name: Install yq
+    runs-on: ubuntu-latest
+    steps:
+      - name: 🏗 Set up yq
+        uses: frenck/action-setup-yq@v1
+
+  prepare-matrix:
+    name: Retrieve all template features
+    runs-on: ubuntu-latest
+    outputs:
+      all_features: ${{ steps.create_matrix.outputs.matrix }}
+    steps:
+      - name: checkout
+        uses: actions/checkout@v3
+      - name: Create Matrix
+        id: create_matrix
+        run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
+
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}
     env:
       NXF_ANSI_LOG: false
     strategy:
       matrix:
-        TEMPLATE:
-          - "template_skip_github_badges.yml"
-          - "template_skip_igenomes.yml"
-          - "template_skip_ci.yml"
-          - "template_skip_code_linters.yml"
-          - "template_skip_citations.yml"
-          - "template_skip_gitpod.yml"
-          - "template_skip_codespaces.yml"
-          - "template_skip_multiqc.yml"
-          - "template_skip_changelog.yml"
+        TEMPLATE: ${{ fromJSON(needs.prepare-matrix.outputs.all_features) }}
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
         profile: ["self_hosted_runner"]
         include:
-          - TEMPLATE: "template_skip_all.yml"
+          - TEMPLATE: all
             runner: ubuntu-latest
             profile: "docker"
-          - TEMPLATE: "template_skip_nf_core_configs.yml"
+          - TEMPLATE: nf_core_configs
             runner: ubuntu-latest
             profile: "docker"
       fail-fast: false
@@ -90,53 +100,17 @@ jobs:
         run: |
           mkdir create-test-lint-wf
           export NXF_WORK=$(pwd)
-          printf "org: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > create-test-lint-wf/template_skip_all.yml
-
-      - name: Create template skip github_badges
-        run: |
-          printf "org: my-prefix\nskip: github_badges" > create-test-lint-wf/template_skip_github_badges.yml
-
-      - name: Create template skip igenomes
-        run: |
-          printf "org: my-prefix\nskip: igenomes" > create-test-lint-wf/template_skip_igenomes.yml
-
-      - name: Create template skip ci
-        run: |
-          printf "org: my-prefix\nskip: ci" > create-test-lint-wf/template_skip_ci.yml
-
-      - name: Create template skip nf_core_configs
-        run: |
-          printf "org: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml
-
-      - name: Create template skip code_linters
-        run: |
-          printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml
-
-      - name: Create template skip citations
-        run: |
-          printf "org: my-prefix\nskip: citations" > create-test-lint-wf/template_skip_citations.yml
-
-      - name: Create template skip gitpod
-        run: |
-          printf "org: my-prefix\nskip: gitpod" > create-test-lint-wf/template_skip_gitpod.yml
-
-      - name: Create template skip multiqc
-        run: |
-          printf "org: my-prefix\nskip: multiqc" > create-test-lint-wf/template_skip_multiqc.yml
-
-      - name: Create template skip changelog
-        run: |
-          printf "org: my-prefix\nskip: changelog" > create-test-lint-wf/template_skip_changelog.yml
+          printf "org: my-prefix\nskip: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml
 
-      - name: Create template skip codespaces
+      - name: Create template skip {{ matrix.TEMPLATE }}
         run: |
-          printf "org: my-prefix\nskip: codespaces" > create-test-lint-wf/template_skip_codespaces.yml
+          printf "org: my-prefix\nskip: {{ matrix.TEMPLATE }}" > create-test-lint-wf/template_skip_{{ matrix.TEMPLATE }}.yml
 
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |
           cd create-test-lint-wf
-          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
+          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml template_skip_${{ matrix.TEMPLATE }}.yml
 
       - name: run the pipeline
         run: |
diff --git a/.prettierignore b/.prettierignore
index 059007ab03..9387ee9509 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -7,6 +7,7 @@ nf_core/module-template/meta.yml
 nf_core/pipeline-template/nextflow_schema.json
 nf_core/pipeline-template/modules.json
 nf_core/pipeline-template/tower.yml
+tests/data/pipeline_create_template_skip.yml
 # don't run on things handled by ruff
 *.py
 *.pyc
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index b04b28c473..db0833c68e 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -76,43 +76,26 @@ def __init__(
         else:
             raise UserWarning("The template configuration was not provided.")
 
-        self.jinja_params, skip_paths = self.obtain_jinja_params_dict(
+        # Read features yaml file
+        features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml"
+        with open(features_yml_path) as fh:
+            self.template_features_yml = yaml.safe_load(fh)
+
+        self.jinja_params, self.skip_areas = self.obtain_jinja_params_dict(
             self.config.skip_features or [], self.config.outdir
         )
 
-        skippable_paths = {
-            "github": [
-                ".github/",
-                ".gitignore",
-            ],
-            "ci": [".github/workflows/"],
-            "igenomes": ["conf/igenomes.config"],
-            "is_nfcore": [
-                ".github/ISSUE_TEMPLATE/config",
-                "CODE_OF_CONDUCT.md",
-                ".github/workflows/awsfulltest.yml",
-                ".github/workflows/awstest.yml",
-                ".github/workflows/release-announcements.yml",
-            ],
-            "code_linters": [
-                ".editorconfig",
-                ".pre-commit-config.yaml",
-                ".prettierignore",
-                ".prettierrc.yml",
-                ".github/workflows/fix-linting.yml",
-            ],
-            "citations": ["assets/methods_description_template.yml"],
-            "gitpod": [".gitpod.yml"],
-            "codespaces": [".devcontainer/devcontainer.json"],
-            "multiqc": [
-                "assets/multiqc_config.yml",
-                "assets/methods_description_template.yml",
-                "modules/nf-core/multiqc/",
-            ],
-            "changelog": ["CHANGELOG.md"],
-        }
+        # format strings in features yaml
+        short_name = self.jinja_params["short_name"]
+        env = jinja2.Environment(loader=jinja2.PackageLoader("nf_core", "pipelines"), keep_trailing_newline=True)
+        features_template = env.get_template(
+            str(features_yml_path.relative_to(Path(nf_core.__file__).parent / "pipelines"))
+        )
+        rendered_features = features_template.render({"short_name": short_name})
+        self.template_features_yml = yaml.safe_load(rendered_features)
+
         # Get list of files we're skipping with the supplied skip keys
-        self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k])
+        self.skip_paths = set(sp for k in self.skip_areas for sp in self.template_features_yml[k]["skippable_paths"])
 
         # Set convenience variables
         self.name = self.config.name
@@ -205,43 +188,27 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
 
         Returns:
             jinja_params (dict): Dictionary of template areas to skip with values true/false.
-            skip_paths (list<str>): List of template areas which contain paths to skip.
+            skip_areas (list<str>): List of template areas which contain paths to skip.
         """
         # Try reading config file
         _, config_yml = nf_core.utils.load_tools_config(pipeline_dir)
 
-        # Define the different template areas, and what actions to take for each
-        # if they are skipped
-        template_areas = {
-            "github": {"file": True, "content": False},
-            "ci": {"file": True, "content": False},
-            "github_badges": {"file": False, "content": True},
-            "igenomes": {"file": True, "content": True},
-            "nf_core_configs": {"file": False, "content": True},
-            "code_linters": {"file": True, "content": True},
-            "citations": {"file": True, "content": True},
-            "gitpod": {"file": True, "content": True},
-            "codespaces": {"file": True, "content": True},
-            "multiqc": {"file": True, "content": True},
-            "changelog": {"file": True, "content": False},
-        }
-
         # Set the parameters for the jinja template
         jinja_params = self.config.model_dump()
 
         # Add template areas to jinja params and create list of areas with paths to skip
-        skip_paths = []
-        for t_area in template_areas:
+        skip_areas = []
+        for t_area in self.template_features_yml.keys():
             if t_area in features_to_skip:
-                if template_areas[t_area]["file"]:
-                    skip_paths.append(t_area)
+                if self.template_features_yml[t_area]["skippable_paths"]:
+                    skip_areas.append(t_area)
                 jinja_params[t_area] = False
             else:
                 jinja_params[t_area] = True
 
         # Add is_nfcore as an area to skip for non-nf-core pipelines, to skip all nf-core files
-        if not jinja_params["is_nfcore"]:
-            skip_paths.append("is_nfcore")
+        if not self.config.is_nfcore:
+            skip_areas.append("is_nfcore")
 
         # Set the last parameters based on the ones provided
         jinja_params["short_name"] = (
@@ -259,7 +226,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
             and "nextflow_config" in config_yml["lint"]
             and "manifest.name" in config_yml["lint"]["nextflow_config"]
         ):
-            return jinja_params, skip_paths
+            return jinja_params, skip_areas
 
         # Check that the pipeline name matches the requirements
         if not re.match(r"^[a-z]+$", jinja_params["short_name"]):
@@ -270,7 +237,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
                     "Your workflow name is not lowercase without punctuation. This may cause Nextflow errors.\nConsider changing the name to avoid special characters."
                 )
 
-        return jinja_params, skip_paths
+        return jinja_params, skip_areas
 
     def init_pipeline(self):
         """Creates the nf-core pipeline."""
@@ -438,109 +405,20 @@ def fix_linting(self):
         for a customized pipeline.
         """
         # Create a lint config
-        short_name = self.jinja_params["short_name"]
-        if not self.config.is_nfcore:
-            lint_config = {
-                "files_exist": [
-                    "CODE_OF_CONDUCT.md",
-                    f"assets/nf-core-{short_name}_logo_light.png",
-                    f"docs/images/nf-core-{short_name}_logo_light.png",
-                    f"docs/images/nf-core-{short_name}_logo_dark.png",
-                    ".github/ISSUE_TEMPLATE/config.yml",
-                    ".github/workflows/awstest.yml",
-                    ".github/workflows/awsfulltest.yml",
-                ],
-                "files_unchanged": [
-                    "CODE_OF_CONDUCT.md",
-                    f"assets/nf-core-{short_name}_logo_light.png",
-                    f"docs/images/nf-core-{short_name}_logo_light.png",
-                    f"docs/images/nf-core-{short_name}_logo_dark.png",
-                ],
-                "nextflow_config": [
-                    "manifest.name",
-                    "manifest.homePage",
-                ],
-                "multiqc_config": ["report_comment"],
-            }
-        else:
-            lint_config = {}
-
-        # Add GitHub hosting specific configurations
-        if not self.jinja_params["github"]:
-            lint_config["files_exist"].extend(
-                [
-                    ".github/ISSUE_TEMPLATE/bug_report.yml",
-                    ".github/ISSUE_TEMPLATE/feature_request.yml",
-                    ".github/PULL_REQUEST_TEMPLATE.md",
-                    ".github/CONTRIBUTING.md",
-                    ".github/.dockstore.yml",
-                    ".gitignore",
-                ]
-            )
-            lint_config["files_unchanged"].extend(
-                [
-                    ".github/ISSUE_TEMPLATE/bug_report.yml",
-                    ".github/ISSUE_TEMPLATE/config.yml",
-                    ".github/ISSUE_TEMPLATE/feature_request.yml",
-                    ".github/PULL_REQUEST_TEMPLATE.md",
-                    ".github/workflows/branch.yml",
-                    ".github/workflows/linting_comment.yml",
-                    ".github/workflows/linting.yml",
-                    ".github/CONTRIBUTING.md",
-                    ".github/.dockstore.yml",
-                ]
-            )
-
-        # Add CI specific configurations
-        if not self.jinja_params["ci"]:
-            lint_config["files_exist"].extend(
-                [
-                    ".github/workflows/branch.yml",
-                    ".github/workflows/ci.yml",
-                    ".github/workflows/linting_comment.yml",
-                    ".github/workflows/linting.yml",
-                ]
-            )
-
-        # Add custom config specific configurations
-        if not self.jinja_params["nf_core_configs"]:
-            lint_config["files_exist"].extend(["conf/igenomes.config"])
-            lint_config["nextflow_config"].extend(
-                [
-                    "process.cpus",
-                    "process.memory",
-                    "process.time",
-                    "custom_config",
-                ]
-            )
-
-        # Add igenomes specific configurations
-        if not self.jinja_params["igenomes"]:
-            lint_config["files_exist"].extend(["conf/igenomes.config"])
-
-        # Add github badges specific configurations
-        if not self.jinja_params["github_badges"] or not self.jinja_params["github"]:
-            lint_config["readme"] = ["nextflow_badge"]
-
-        # Add codespaces specific configurations
-        if not self.jinja_params["codespaces"]:
-            lint_config["files_unchanged"].extend([".github/CONTRIBUTING.md"])
-
-        # Add multiqc specific configurations
-        if not self.jinja_params["multiqc"]:
-            lint_config.setdefault("files_unchanged", []).extend(
-                [".github/CONTRIBUTING.md", "assets/sendmail_template.txt"]
-            )
-            lint_config.setdefault("files_exist", []).extend(["assets/multiqc_config.yml"])
-            lint_config["multiqc_config"] = False
-
-        # Add changelog specific configurations
-        if not self.jinja_params["changelog"]:
-            lint_config["files_exist"].extend(["CHANGELOG.md"])
-
-        # If the pipeline is not nf-core
-        if not self.config.is_nfcore:
-            lint_config["files_unchanged"].extend([".github/ISSUE_TEMPLATE/bug_report.yml"])
+        lint_config = {}
+        for area in self.skip_areas:
+            try:
+                for lint_test in self.template_features_yml[area]["linting"]:
+                    if not lint_config[lint_test]:
+                        pass
+                    if self.template_features_yml[area]["linting"][lint_test]:
+                        lint_config.setdefault(lint_test, []).extend(
+                            self.template_features_yml[area]["linting"][lint_test]
+                        )
+                    else:
+                        lint_config[lint_test] = False
+            except KeyError:
+                pass  # Areas without linting
 
         # Add the lint content to the preexisting nf-core config
         config_fn, nf_core_yml = nf_core.utils.load_tools_config(self.outdir)
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
new file mode 100644
index 0000000000..843203c7f8
--- /dev/null
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -0,0 +1,213 @@
+github:
+  skippable_paths:
+    - ".github/"
+    - ".gitignore"
+  short_description: ""
+  description: ""
+  help: ""
+  linting:
+    files_exist:
+      - ".github/ISSUE_TEMPLATE/bug_report.yml"
+      - ".github/ISSUE_TEMPLATE/feature_request.yml"
+      - ".github/PULL_REQUEST_TEMPLATE.md"
+      - ".github/CONTRIBUTING.md"
+      - ".github/.dockstore.yml"
+      - ".gitignore"
+    files_unchanged:
+      - ".github/ISSUE_TEMPLATE/bug_report.yml"
+      - ".github/ISSUE_TEMPLATE/config.yml"
+      - ".github/ISSUE_TEMPLATE/feature_request.yml"
+      - ".github/PULL_REQUEST_TEMPLATE.md"
+      - ".github/workflows/branch.yml"
+      - ".github/workflows/linting_comment.yml"
+      - ".github/workflows/linting.yml"
+      - ".github/CONTRIBUTING.md"
+      - ".github/.dockstore.yml"
+    readme:
+      - "nextflow_badge"
+ci:
+  skippable_paths:
+    - ".github/workflows/"
+  short_description: "Add Github CI tests"
+  description: "The pipeline will include several GitHub actions for Continuous Integration (CI) testing"
+  help: |
+    Nf-core provides a set of Continuous Integration (CI) tests for Github.
+    When you open a pull request (PR) on your pipeline repository, these tests will run automatically.
+
+    There are different types of tests:
+    * Linting tests check that your code is formatted correctly and that it adheres to nf-core standards
+        For code linting they will use [prettier](https://prettier.io/).
+    * Pipeline tests run your pipeline on a small dataset to check that it works
+        These tests are run with a small test dataset on GitHub and a larger test dataset on AWS
+    * Marking old issues as stale
+  linting:
+    files_exist:
+      - ".github/workflows/branch.yml"
+      - ".github/workflows/ci.yml"
+      - ".github/workflows/linting_comment.yml"
+      - ".github/workflows/linting.yml"
+igenomes:
+  skippable_paths:
+    - "conf/igenomes.config"
+  short_description: "Use reference genomes"
+  description: "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes"
+  help: |
+    Nf-core pipelines are configured to use a copy of the most common reference genome files.
+
+    By selecting this option, your pipeline will include a configuration file specifying the paths to these files.
+
+    The required code to use these files will also be included in the template.
+    When the pipeline user provides an appropriate genome key,
+    the pipeline will automatically download the required reference files.
+
+    For more information about reference genomes in nf-core pipelines,
+    see the [nf-core docs](https://nf-co.re/docs/usage/reference_genomes).
+  linting:
+    files_exist:
+      - "conf/igenomes.config"
+github_badges:
+  skippable_paths: False
+  short_description: "Add Github badges"
+  description: "The README.md file of the pipeline will include GitHub badges"
+  help: |
+    The pipeline `README.md` will include badges for:
+    * AWS CI Tests
+    * Zenodo DOI
+    * Nextflow
+    * Conda
+    * Docker
+    * Singularity
+    * Launching on Nextflow Tower
+  linting:
+    readme:
+      - "nextflow_badge"
+nf_core_configs:
+  skippable_paths: False
+  short_description: "Add configuration files"
+  description: "The pipeline will include configuration profiles containing custom parameters requried to run nf-core pipelines at different institutions"
+  help: |
+    Nf-core has a repository with a collection of configuration profiles.
+
+    Those config files define a set of parameters which are specific to compute environments at different Institutions.
+    They can be used within all nf-core pipelines.
+    If you are likely to be running nf-core pipelines regularly it is a good idea to use or create a custom config file for your organisation.
+
+    For more information about nf-core configuration profiles, see the [nf-core/configs repository](https://github.com/nf-core/configs)
+  linting:
+    files_exist:
+      - "conf/igenomes.config"
+    nextflow_config:
+      - "process.cpus"
+      - "process.memory"
+      - "process.time"
+      - "custom_config"
+is_nfcore:
+  skippable_paths:
+    - ".github/ISSUE_TEMPLATE/config"
+    - "CODE_OF_CONDUCT.md"
+    - ".github/workflows/awsfulltest.yml"
+    - ".github/workflows/awstest.yml"
+    - ".github/workflows/release-announcements.yml"
+  short_description: ""
+  description: ""
+  help: ""
+  linting:
+    files_exist:
+      - "CODE_OF_CONDUCT.md"
+      - "assets/nf-core-{{short_name}}_logo_light.png"
+      - "docs/images/nf-core-{{short_name}}_logo_light.png"
+      - "docs/images/nf-core-{{short_name}}_logo_dark.png"
+      - ".github/ISSUE_TEMPLATE/config.yml"
+      - ".github/workflows/awstest.yml"
+      - ".github/workflows/awsfulltest.yml"
+    files_unchanged:
+      - "CODE_OF_CONDUCT.md"
+      - "assets/nf-core-{{short_name}}_logo_light.png"
+      - "docs/images/nf-core-{{short_name}}_logo_light.png"
+      - "docs/images/nf-core-{{short_name}}_logo_dark.png"
+      - ".github/ISSUE_TEMPLATE/bug_report.yml"
+    nextflow_config:
+      - "manifest.name"
+      - "manifest.homePage"
+    multiqc_config:
+      - "report_comment"
+code_linters:
+  skippable_paths:
+    - ".editorconfig"
+    - ".pre-commit-config.yaml"
+    - ".prettierignore"
+    - ".prettierrc.yml"
+    - ".github/workflows/fix-linting.yml"
+  short_description: "Use code linters"
+  description: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier."
+  help: |
+    Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers.
+    Linters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository.
+    The available code linters are:
+
+    - pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository.
+    - editor-config (https://github.com/editorconfig-checker/editorconfig-checker): checks rules such as indentation or trailing spaces.
+    - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc).
+citations:
+  skippable_paths:
+    - "assets/methods_description_template.yml"
+  short_description: "Include citations"
+  description: "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled)."
+  help: |
+    If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline.
+
+    Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline,
+    and the logics to add this section to the output MultiQC report (if the report is generated).
+gitpod:
+  skippable_paths:
+    - ".gitpod.yml"
+  short_description: "Include a gitpod environment"
+  description: "Include the configuration required to use Gitpod."
+  help: |
+    Gitpod (https://www.gitpod.io/) provides standardized and automated development environments.
+
+    Including this to your pipeline will provide an environment with the latest version of nf-core/tools installed and all its requirements.
+    This is useful to have all the tools ready for pipeline development.
+codespaces:
+  skippable_paths:
+    - ".devcontainer/devcontainer.json"
+  short_description: "Include GitHub Codespaces"
+  description: "The pipeline will include a devcontainer configuration for GitHub Codespaces, providing a development environment with nf-core/tools and Nextflow installed."
+  help: |
+    The pipeline will include a devcontainer configuration.
+    The devcontainer will create a GitHub Codespaces for Nextflow development with nf-core/tools and Nextflow installed.
+
+    Github Codespaces (https://github.com/features/codespaces) is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+  linting:
+    files_unchanged:
+      - ".github/CONTRIBUTING.md"
+multiqc:
+  skippable_paths:
+    - "assets/multiqc_config.yml"
+    - "assets/methods_description_template.yml"
+    - "modules/nf-core/multiqc/"
+  short_description: "Use multiqc"
+  description: "The pipeline will include the MultiQC module which generates an HTML report for quality control."
+  help: |
+    MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory.
+
+    The pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info.
+  linting:
+    files_unchanged:
+      - ".github/CONTRIBUTING.md"
+      - "assets/sendmail_template.txt"
+    files_exist:
+      - "assets/multiqc_config.yml"
+    multiqc_config: False
+changelog:
+  skippable_paths:
+    - "CHANGELOG.md"
+  short_description: "Add a changelog"
+  description: "Add a CHANGELOG.md file."
+  help: |
+    Having a `CHANGELOG.md` file in the pipeline root directory is useful to track the changes added to each version.
+
+    You can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/
+  linting:
+    files_exist:
+      - "CHANGELOG.md"
diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml
index 21cdc0c3d5..3ab8f69eca 100644
--- a/tests/data/pipeline_create_template_skip.yml
+++ b/tests/data/pipeline_create_template_skip.yml
@@ -5,15 +5,4 @@ version: 1.0.0
 force: True
 org: testprefix
 is_nfcore: False
-skip_features:
-  - github
-  - ci
-  - github_badges
-  - igenomes
-  - nf_core_configs
-  - code_linters
-  - citations
-  - gitpod
-  - codespaces
-  - multiqc
-  - changelog
+skip_features: {{ all_features }}
diff --git a/tests/test_create.py b/tests/test_create.py
index 920a0f4750..92f7f2a9d9 100644
--- a/tests/test_create.py
+++ b/tests/test_create.py
@@ -5,6 +5,7 @@
 from pathlib import Path
 
 import git
+import jinja2
 import yaml
 
 import nf_core.pipelines.create.create
@@ -98,9 +99,24 @@ def test_pipeline_creation_initiation_customize_template(self, tmp_path):
 
     @with_temporary_folder
     def test_pipeline_creation_with_yml_skip(self, tmp_path):
+        # Update pipeline_create_template_skip.yml file
+        features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml"
+        with open(features_yml_path) as fh:
+            template_features_yml = yaml.safe_load(fh)
+        all_features = list(template_features_yml.keys())
+        all_features.remove("is_nfcore")
+        env = jinja2.Environment(loader=jinja2.PackageLoader("tests", "data"), keep_trailing_newline=True)
+        skip_template = env.get_template(
+            str(PIPELINE_TEMPLATE_YML_SKIP.relative_to(Path(nf_core.__file__).parent.parent / "tests" / "data"))
+        )
+        rendered_content = skip_template.render({"all_features": all_features})
+        rendered_yaml = Path(tmp_path) / "pipeline_create_template_skip.yml"
+        with open(rendered_yaml, "w") as fh:
+            fh.write(rendered_content)
+
         pipeline = nf_core.pipelines.create.create.PipelineCreate(
             outdir=tmp_path,
-            template_config=PIPELINE_TEMPLATE_YML_SKIP,
+            template_config=rendered_yaml,
             default_branch=self.default_branch,
         )
         pipeline.init_pipeline()

From 637317a3422f39d3f98fe2aafcc4efc6d0a88a80 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 8 Aug 2024 14:23:01 +0000
Subject: [PATCH 213/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 609c3aea06..c1e07f3bff 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@
 - add option to exclude codespaces from pipeline template ([#3105](https://github.com/nf-core/tools/pull/3105))
 - add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103))
 - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104))
+- handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108))
 
 ### Linting
 

From efff9eada0641bc4ee42cf73f2c6943182f00886 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 9 Aug 2024 10:30:55 +0200
Subject: [PATCH 214/414] use template features yaml file to generate textual
 layout

---
 nf_core/pipelines/create/__init__.py          |   8 +
 nf_core/pipelines/create/custompipeline.py    | 142 ++----------------
 nf_core/pipelines/create/nfcorepipeline.py    |  25 ++-
 nf_core/pipelines/create/templatefeatures.yml |  24 +++
 nf_core/pipelines/create/utils.py             |  21 ---
 5 files changed, 50 insertions(+), 170 deletions(-)

diff --git a/nf_core/pipelines/create/__init__.py b/nf_core/pipelines/create/__init__.py
index 56e25bf1d5..ae766b4e26 100644
--- a/nf_core/pipelines/create/__init__.py
+++ b/nf_core/pipelines/create/__init__.py
@@ -1,10 +1,13 @@
 """A Textual app to create a pipeline."""
 
 import logging
+from pathlib import Path
 
+import yaml
 from textual.app import App
 from textual.widgets import Button
 
+import nf_core
 from nf_core.pipelines.create import utils
 from nf_core.pipelines.create.basicdetails import BasicDetails
 from nf_core.pipelines.create.custompipeline import CustomPipeline
@@ -66,6 +69,11 @@ class PipelineCreateApp(App[utils.CreateConfig]):
     # Logging state
     LOGGING_STATE = None
 
+    # Template features
+    features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml"
+    with open(features_yml_path) as fh:
+        template_features_yml = yaml.safe_load(fh)
+
     def on_mount(self) -> None:
         self.push_screen("welcome")
 
diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py
index 96b6df5062..fdb7a46d28 100644
--- a/nf_core/pipelines/create/custompipeline.py
+++ b/nf_core/pipelines/create/custompipeline.py
@@ -6,76 +6,7 @@
 from textual.screen import Screen
 from textual.widgets import Button, Footer, Header, Markdown, Switch
 
-from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes, markdown_multiqc
-
-markdown_ci = """
-Nf-core provides a set of Continuous Integration (CI) tests for Github.
-When you open a pull request (PR) on your pipeline repository, these tests will run automatically.
-
-There are different types of tests:
-* Linting tests check that your code is formatted correctly and that it adheres to nf-core standards
-    For code linting they will use [prettier](https://prettier.io/).
-* Pipeline tests run your pipeline on a small dataset to check that it works
-    These tests are run with a small test dataset on GitHub and a larger test dataset on AWS
-* Marking old issues as stale
-"""
-
-markdown_badges = """
-The pipeline `README.md` will include badges for:
-* AWS CI Tests
-* Zenodo DOI
-* Nextflow
-* Conda
-* Docker
-* Singularity
-* Launching on Nextflow Tower
-"""
-
-markdown_configuration = """
-Nf-core has a repository with a collection of configuration profiles.
-
-Those config files define a set of parameters which are specific to compute environments at different Institutions.
-They can be used within all nf-core pipelines.
-If you are likely to be running nf-core pipelines regularly it is a good idea to use or create a custom config file for your organisation.
-
-For more information about nf-core configuration profiles, see the [nf-core/configs repository](https://github.com/nf-core/configs)
-"""
-
-markdown_code_linters = """
-Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers.
-Linters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository.
-The available code linters are:
-
-- pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository.
-- editor-config (https://github.com/editorconfig-checker/editorconfig-checker): checks rules such as indentation or trailing spaces.
-- prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc).
-"""
-
-markdown_citations = """
-If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline.
-
-Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline,
-and the logics to add this section to the output MultiQC report (if the report is generated).
-"""
-
-markdown_gitpod = """
-Gitpod (https://www.gitpod.io/) provides standardized and automated development environments.
-
-Including this to your pipeline will provide an environment with the latest version of nf-core/tools installed and all its requirements.
-This is useful to have all the tools ready for pipeline development.
-"""
-
-markdown_codespaces = """
-The pipeline will include a devcontainer configuration.
-The devcontainer will create a GitHub Codespaces for Nextflow development with nf-core/tools and Nextflow installed.
-
-Github Codespaces (https://github.com/features/codespaces) is an online developer environment that runs in your browser, complete with VSCode and a terminal.
-"""
-
-markdown_changelog = """
-Having a `CHANGELOG.md` file in the pipeline root directory is useful to track the changes added to each version.
-You can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/
-"""
+from nf_core.pipelines.create.utils import PipelineFeature
 
 
 class CustomPipeline(Screen):
@@ -91,75 +22,20 @@ def compose(self) -> ComposeResult:
                 """
             )
         )
-        yield ScrollableContainer(
-            PipelineFeature(
-                markdown_genomes,
-                "Use reference genomes",
-                "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes",
-                "igenomes",
-            ),
-            PipelineFeature(
-                markdown_ci,
-                "Add Github CI tests",
-                "The pipeline will include several GitHub actions for Continuous Integration (CI) testing",
-                "ci",
-            ),
-            PipelineFeature(
-                markdown_badges,
-                "Add Github badges",
-                "The README.md file of the pipeline will include GitHub badges",
-                "github_badges",
-            ),
-            PipelineFeature(
-                markdown_configuration,
-                "Add configuration files",
-                "The pipeline will include configuration profiles containing custom parameters requried to run nf-core pipelines at different institutions",
-                "nf_core_configs",
-            ),
-            PipelineFeature(
-                markdown_code_linters,
-                "Use code linters",
-                "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.",
-                "code_linters",
-            ),
-            PipelineFeature(
-                markdown_citations,
-                "Include citations",
-                "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled).",
-                "citations",
-            ),
-            PipelineFeature(
-                markdown_gitpod,
-                "Include a gitpod environment",
-                "Include the configuration required to use Gitpod.",
-                "gitpod",
-            ),
-            PipelineFeature(
-                markdown_codespaces,
-                "Include GitHub Codespaces",
-                "The pipeline will include a devcontainer configuration for GitHub Codespaces, providing a development environment with nf-core/tools and Nextflow installed.",
-                "codespaces",
-            ),
-            PipelineFeature(
-                markdown_multiqc,
-                "Use multiqc",
-                "The pipeline will include the MultiQC module which generates an HTML report for quality control.",
-                "multiqc",
-            ),
-            PipelineFeature(
-                markdown_changelog,
-                "Add a changelog",
-                "Add a CHANGELOG.md file.",
-                "changelog",
-            ),
-            classes="features-container",
-        )
+        yield ScrollableContainer(id="features")
         yield Center(
             Button("Back", id="back", variant="default"),
             Button("Continue", id="continue", variant="success"),
             classes="cta",
         )
 
+    def on_mount(self) -> None:
+        for name, feature in self.parent.template_features_yml.items():
+            if feature["custom_pipelines"]:
+                self.query_one("#features").mount(
+                    PipelineFeature(feature["help"], feature["short_description"], feature["description"], name)
+                )
+
     @on(Button.Pressed, "#continue")
     def on_button_pressed(self, event: Button.Pressed) -> None:
         """Save fields to the config."""
diff --git a/nf_core/pipelines/create/nfcorepipeline.py b/nf_core/pipelines/create/nfcorepipeline.py
index 8319cb044c..b6a8231694 100644
--- a/nf_core/pipelines/create/nfcorepipeline.py
+++ b/nf_core/pipelines/create/nfcorepipeline.py
@@ -6,7 +6,7 @@
 from textual.screen import Screen
 from textual.widgets import Button, Footer, Header, Markdown, Switch
 
-from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes, markdown_multiqc
+from nf_core.pipelines.create.utils import PipelineFeature
 
 
 class NfcorePipeline(Screen):
@@ -22,27 +22,20 @@ def compose(self) -> ComposeResult:
                 """
             )
         )
-        yield ScrollableContainer(
-            PipelineFeature(
-                markdown_genomes,
-                "Use reference genomes",
-                "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes",
-                "igenomes",
-            ),
-            PipelineFeature(
-                markdown_multiqc,
-                "Use multiqc",
-                "The pipeline will include the MultiQC module which generates an HTML report for quality control.",
-                "multiqc",
-            ),
-            classes="features-container",
-        )
+        yield ScrollableContainer(id="features")
         yield Center(
             Button("Back", id="back", variant="default"),
             Button("Continue", id="continue", variant="success"),
             classes="cta",
         )
 
+    def on_mount(self) -> None:
+        for name, feature in self.parent.template_features_yml.items():
+            if feature["nfcore_pipelines"]:
+                self.query_one("#features").mount(
+                    PipelineFeature(feature["help"], feature["short_description"], feature["description"], name)
+                )
+
     @on(Button.Pressed, "#continue")
     def on_button_pressed(self, event: Button.Pressed) -> None:
         """Save fields to the config."""
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 843203c7f8..a91887a891 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -25,6 +25,8 @@ github:
       - ".github/.dockstore.yml"
     readme:
       - "nextflow_badge"
+  nfcore_pipelines: False
+  custom_pipelines: False
 ci:
   skippable_paths:
     - ".github/workflows/"
@@ -46,6 +48,8 @@ ci:
       - ".github/workflows/ci.yml"
       - ".github/workflows/linting_comment.yml"
       - ".github/workflows/linting.yml"
+  nfcore_pipelines: False
+  custom_pipelines: True
 igenomes:
   skippable_paths:
     - "conf/igenomes.config"
@@ -65,6 +69,8 @@ igenomes:
   linting:
     files_exist:
       - "conf/igenomes.config"
+  nfcore_pipelines: True
+  custom_pipelines: True
 github_badges:
   skippable_paths: False
   short_description: "Add Github badges"
@@ -81,6 +87,8 @@ github_badges:
   linting:
     readme:
       - "nextflow_badge"
+  nfcore_pipelines: False
+  custom_pipelines: True
 nf_core_configs:
   skippable_paths: False
   short_description: "Add configuration files"
@@ -101,6 +109,8 @@ nf_core_configs:
       - "process.memory"
       - "process.time"
       - "custom_config"
+  nfcore_pipelines: False
+  custom_pipelines: True
 is_nfcore:
   skippable_paths:
     - ".github/ISSUE_TEMPLATE/config"
@@ -131,6 +141,8 @@ is_nfcore:
       - "manifest.homePage"
     multiqc_config:
       - "report_comment"
+  nfcore_pipelines: False
+  custom_pipelines: False
 code_linters:
   skippable_paths:
     - ".editorconfig"
@@ -148,6 +160,8 @@ code_linters:
     - pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository.
     - editor-config (https://github.com/editorconfig-checker/editorconfig-checker): checks rules such as indentation or trailing spaces.
     - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc).
+  nfcore_pipelines: False
+  custom_pipelines: True
 citations:
   skippable_paths:
     - "assets/methods_description_template.yml"
@@ -158,6 +172,8 @@ citations:
 
     Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline,
     and the logics to add this section to the output MultiQC report (if the report is generated).
+  nfcore_pipelines: False
+  custom_pipelines: True
 gitpod:
   skippable_paths:
     - ".gitpod.yml"
@@ -168,6 +184,8 @@ gitpod:
 
     Including this to your pipeline will provide an environment with the latest version of nf-core/tools installed and all its requirements.
     This is useful to have all the tools ready for pipeline development.
+  nfcore_pipelines: False
+  custom_pipelines: True
 codespaces:
   skippable_paths:
     - ".devcontainer/devcontainer.json"
@@ -181,6 +199,8 @@ codespaces:
   linting:
     files_unchanged:
       - ".github/CONTRIBUTING.md"
+  nfcore_pipelines: False
+  custom_pipelines: True
 multiqc:
   skippable_paths:
     - "assets/multiqc_config.yml"
@@ -199,6 +219,8 @@ multiqc:
     files_exist:
       - "assets/multiqc_config.yml"
     multiqc_config: False
+  nfcore_pipelines: True
+  custom_pipelines: True
 changelog:
   skippable_paths:
     - "CHANGELOG.md"
@@ -211,3 +233,5 @@ changelog:
   linting:
     files_exist:
       - "CHANGELOG.md"
+  nfcore_pipelines: False
+  custom_pipelines: True
diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
index 43094ab531..dba498d181 100644
--- a/nf_core/pipelines/create/utils.py
+++ b/nf_core/pipelines/create/utils.py
@@ -244,24 +244,3 @@ def add_hide_class(app, widget_id: str) -> None:
 def remove_hide_class(app, widget_id: str) -> None:
     """Remove class 'hide' to a widget. Display widget."""
     app.get_widget_by_id(widget_id).remove_class("hide")
-
-
-## Markdown text to reuse in different screens
-markdown_genomes = """
-Nf-core pipelines are configured to use a copy of the most common reference genome files.
-
-By selecting this option, your pipeline will include a configuration file specifying the paths to these files.
-
-The required code to use these files will also be included in the template.
-When the pipeline user provides an appropriate genome key,
-the pipeline will automatically download the required reference files.
-
-For more information about reference genomes in nf-core pipelines,
-see the [nf-core docs](https://nf-co.re/docs/usage/reference_genomes).
-"""
-
-markdown_multiqc = """
-MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory.
-
-The pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info.
-"""

From 2fa7a033ac1a4d99563e63cdaf76611c223b5da8 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 9 Aug 2024 11:26:29 +0200
Subject: [PATCH 215/414] update textual snapshots

---
 tests/__snapshots__/test_create_app.ambr | 764 +++++++++++------------
 1 file changed, 382 insertions(+), 382 deletions(-)

diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr
index f2c1c45c45..f4eb255087 100644
--- a/tests/__snapshots__/test_create_app.ambr
+++ b/tests/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
           font-weight: 700;
       }
   
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           font-variant-east-asian: full-width;
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From a009e68f594767a90cccd0df0e4fbbbceaf4a3f2 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 9 Aug 2024 11:37:18 +0200
Subject: [PATCH 216/414] try reading yaml keys with a list format

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index d4ff3fc557..15582951de 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -48,7 +48,7 @@ jobs:
         uses: actions/checkout@v3
       - name: Create Matrix
         id: create_matrix
-        run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
+        run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print $2}' | paste -sd "," - | awk '{print "[" $0 "]"}')" >> $GITHUB_OUTPUT
 
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}

From e36bd7fc6411b68c8b22b17aa783ae9680f4fb2c Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 12 Aug 2024 09:37:06 +0200
Subject: [PATCH 217/414] don't read from json on matrix creation

---
 .github/workflows/create-test-lint-wf-template.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 15582951de..fd7a494d0d 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -56,7 +56,7 @@ jobs:
       NXF_ANSI_LOG: false
     strategy:
       matrix:
-        TEMPLATE: ${{ fromJSON(needs.prepare-matrix.outputs.all_features) }}
+        TEMPLATE: ${{ needs.prepare-matrix.outputs.all_features }}
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
@@ -68,6 +68,9 @@ jobs:
           - TEMPLATE: nf_core_configs
             runner: ubuntu-latest
             profile: "docker"
+        exclude:
+          - TEMPLATE: github
+          - TEMPLATE: is_nfcore
       fail-fast: false
 
     steps:

From d4d231444d9a342624b7fb8c2154ba07424bf34d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 12 Aug 2024 10:22:26 +0200
Subject: [PATCH 218/414] reset lintconfigtype

---
 nf_core/utils.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/nf_core/utils.py b/nf_core/utils.py
index 9b3e56da5f..d0546a5c5e 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -19,7 +19,7 @@
 import time
 from contextlib import contextmanager
 from pathlib import Path
-from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, TypedDict, Union
+from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, Union
 
 import git
 import prompt_toolkit.styles
@@ -1077,11 +1077,7 @@ def get(self, item: str, default: Any = None) -> Any:
         return getattr(self, item, default)
 
 
-class LintConfigType(TypedDict):
-    files_exist: Optional[Union[List, List[str], List[Dict[str, List[str]]]]]
-    files_unchanged: Optional[Union[List[str], List[Dict[str, List[str]]]]]
-    nextflow_config: Optional[Union[List[str], List[Dict[str, List[str]]]]]
-    multiqc_config: Optional[Union[List[str], bool]]
+LintConfigType = Optional[Dict[str, Union[List[str], List[Dict[str, List[str]]], bool]]]
 
 
 class NFCoreYamlConfig(BaseModel):

From 78c64c719db446bf84f33137cbce80cd54ee37bc Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Aug 2024 11:07:04 +0200
Subject: [PATCH 219/414] apply suggestions from code review by @mashehu

---
 .../create-test-lint-wf-template.yml          |  9 ++----
 nf_core/pipelines/create/create.py            |  4 ++-
 nf_core/pipelines/create/custompipeline.py    |  2 +-
 nf_core/pipelines/create/nfcorepipeline.py    |  2 +-
 nf_core/pipelines/create/templatefeatures.yml | 28 +++++++++----------
 5 files changed, 21 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index fd7a494d0d..bd661ce07c 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -31,19 +31,14 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
-  install-yq:
-    name: Install yq
-    runs-on: ubuntu-latest
-    steps:
-      - name: 🏗 Set up yq
-        uses: frenck/action-setup-yq@v1
-
   prepare-matrix:
     name: Retrieve all template features
     runs-on: ubuntu-latest
     outputs:
       all_features: ${{ steps.create_matrix.outputs.matrix }}
     steps:
+      - name: 🏗 Set up yq
+        uses: frenck/action-setup-yq@v1
       - name: checkout
         uses: actions/checkout@v3
       - name: Create Matrix
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 584a4673da..1df6cc3f46 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -185,7 +185,9 @@ def update_config(self, organisation, version, force, outdir):
         if self.config.is_nfcore is None:
             self.config.is_nfcore = self.config.org == "nf-core"
 
-    def obtain_jinja_params_dict(self, features_to_skip: List[str], pipeline_dir: Union[str, Path]):
+    def obtain_jinja_params_dict(
+        self, features_to_skip: List[str], pipeline_dir: Union[str, Path]
+    ) -> tuple[dict, list[str]]:
         """Creates a dictionary of parameters for the new pipeline.
 
         Args:
diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py
index fdb7a46d28..5debcfee7f 100644
--- a/nf_core/pipelines/create/custompipeline.py
+++ b/nf_core/pipelines/create/custompipeline.py
@@ -33,7 +33,7 @@ def on_mount(self) -> None:
         for name, feature in self.parent.template_features_yml.items():
             if feature["custom_pipelines"]:
                 self.query_one("#features").mount(
-                    PipelineFeature(feature["help"], feature["short_description"], feature["description"], name)
+                    PipelineFeature(feature["help_text"], feature["short_description"], feature["description"], name)
                 )
 
     @on(Button.Pressed, "#continue")
diff --git a/nf_core/pipelines/create/nfcorepipeline.py b/nf_core/pipelines/create/nfcorepipeline.py
index b6a8231694..ebb9866986 100644
--- a/nf_core/pipelines/create/nfcorepipeline.py
+++ b/nf_core/pipelines/create/nfcorepipeline.py
@@ -33,7 +33,7 @@ def on_mount(self) -> None:
         for name, feature in self.parent.template_features_yml.items():
             if feature["nfcore_pipelines"]:
                 self.query_one("#features").mount(
-                    PipelineFeature(feature["help"], feature["short_description"], feature["description"], name)
+                    PipelineFeature(feature["help_text"], feature["short_description"], feature["description"], name)
                 )
 
     @on(Button.Pressed, "#continue")
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index a91887a891..48ce200551 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -2,9 +2,9 @@ github:
   skippable_paths:
     - ".github/"
     - ".gitignore"
-  short_description: ""
+  short_description: "Skip the creation of a local Git repository."
   description: ""
-  help: ""
+  help_text: ""
   linting:
     files_exist:
       - ".github/ISSUE_TEMPLATE/bug_report.yml"
@@ -32,7 +32,7 @@ ci:
     - ".github/workflows/"
   short_description: "Add Github CI tests"
   description: "The pipeline will include several GitHub actions for Continuous Integration (CI) testing"
-  help: |
+  help_text: |
     Nf-core provides a set of Continuous Integration (CI) tests for Github.
     When you open a pull request (PR) on your pipeline repository, these tests will run automatically.
 
@@ -55,7 +55,7 @@ igenomes:
     - "conf/igenomes.config"
   short_description: "Use reference genomes"
   description: "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes"
-  help: |
+  help_text: |
     Nf-core pipelines are configured to use a copy of the most common reference genome files.
 
     By selecting this option, your pipeline will include a configuration file specifying the paths to these files.
@@ -75,7 +75,7 @@ github_badges:
   skippable_paths: False
   short_description: "Add Github badges"
   description: "The README.md file of the pipeline will include GitHub badges"
-  help: |
+  help_text: |
     The pipeline `README.md` will include badges for:
     * AWS CI Tests
     * Zenodo DOI
@@ -93,7 +93,7 @@ nf_core_configs:
   skippable_paths: False
   short_description: "Add configuration files"
   description: "The pipeline will include configuration profiles containing custom parameters requried to run nf-core pipelines at different institutions"
-  help: |
+  help_text: |
     Nf-core has a repository with a collection of configuration profiles.
 
     Those config files define a set of parameters which are specific to compute environments at different Institutions.
@@ -118,9 +118,9 @@ is_nfcore:
     - ".github/workflows/awsfulltest.yml"
     - ".github/workflows/awstest.yml"
     - ".github/workflows/release-announcements.yml"
-  short_description: ""
+  short_description: "A custom pipeline which won't be part of the nf-core organisation but be compatible with nf-core/tools."
   description: ""
-  help: ""
+  help_text: ""
   linting:
     files_exist:
       - "CODE_OF_CONDUCT.md"
@@ -152,7 +152,7 @@ code_linters:
     - ".github/workflows/fix-linting.yml"
   short_description: "Use code linters"
   description: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier."
-  help: |
+  help_text: |
     Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers.
     Linters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository.
     The available code linters are:
@@ -167,7 +167,7 @@ citations:
     - "assets/methods_description_template.yml"
   short_description: "Include citations"
   description: "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled)."
-  help: |
+  help_text: |
     If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline.
 
     Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline,
@@ -179,7 +179,7 @@ gitpod:
     - ".gitpod.yml"
   short_description: "Include a gitpod environment"
   description: "Include the configuration required to use Gitpod."
-  help: |
+  help_text: |
     Gitpod (https://www.gitpod.io/) provides standardized and automated development environments.
 
     Including this to your pipeline will provide an environment with the latest version of nf-core/tools installed and all its requirements.
@@ -191,7 +191,7 @@ codespaces:
     - ".devcontainer/devcontainer.json"
   short_description: "Include GitHub Codespaces"
   description: "The pipeline will include a devcontainer configuration for GitHub Codespaces, providing a development environment with nf-core/tools and Nextflow installed."
-  help: |
+  help_text: |
     The pipeline will include a devcontainer configuration.
     The devcontainer will create a GitHub Codespaces for Nextflow development with nf-core/tools and Nextflow installed.
 
@@ -208,7 +208,7 @@ multiqc:
     - "modules/nf-core/multiqc/"
   short_description: "Use multiqc"
   description: "The pipeline will include the MultiQC module which generates an HTML report for quality control."
-  help: |
+  help_text: |
     MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory.
 
     The pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info.
@@ -226,7 +226,7 @@ changelog:
     - "CHANGELOG.md"
   short_description: "Add a changelog"
   description: "Add a CHANGELOG.md file."
-  help: |
+  help_text: |
     Having a `CHANGELOG.md` file in the pipeline root directory is useful to track the changes added to each version.
 
     You can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/

From bf07bf24a31850250486000c708c7b6e31b60f01 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Aug 2024 11:32:58 +0200
Subject: [PATCH 220/414] load feature yaml file with a utils function

---
 nf_core/pipelines/create/__init__.py |  4 +---
 nf_core/pipelines/create/create.py   |  6 ++----
 nf_core/pipelines/create/utils.py    | 11 +++++++++++
 tests/pipelines/test_create.py       |  5 ++---
 4 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/nf_core/pipelines/create/__init__.py b/nf_core/pipelines/create/__init__.py
index 1774d0a010..8b0edf34cf 100644
--- a/nf_core/pipelines/create/__init__.py
+++ b/nf_core/pipelines/create/__init__.py
@@ -72,9 +72,7 @@ class PipelineCreateApp(App[utils.CreateConfig]):
     LOGGING_STATE = None
 
     # Template features
-    features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml"
-    with open(features_yml_path) as fh:
-        template_features_yml = yaml.safe_load(fh)
+    template_features_yml = utils.load_features_yaml()
 
     def on_mount(self) -> None:
         self.push_screen("welcome")
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 1df6cc3f46..b3135435ee 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -18,7 +18,7 @@
 import nf_core
 import nf_core.pipelines.schema
 import nf_core.utils
-from nf_core.pipelines.create.utils import CreateConfig
+from nf_core.pipelines.create.utils import CreateConfig, features_yml_path, load_features_yaml
 from nf_core.pipelines.create_logo import create_logo
 from nf_core.pipelines.lint_utils import run_prettier_on_file
 from nf_core.utils import LintConfigType, NFCoreTemplateConfig
@@ -82,9 +82,7 @@ def __init__(
             raise UserWarning("The template configuration was not provided.")
 
         # Read features yaml file
-        features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml"
-        with open(features_yml_path) as fh:
-            self.template_features_yml = yaml.safe_load(fh)
+        self.template_features_yml = load_features_yaml()
 
         if self.config.outdir is None:
             self.config.outdir = str(Path.cwd())
diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
index 89cf0ab65a..2e0015ed90 100644
--- a/nf_core/pipelines/create/utils.py
+++ b/nf_core/pipelines/create/utils.py
@@ -5,6 +5,7 @@
 from pathlib import Path
 from typing import Any, Dict, Iterator, Union
 
+import yaml
 from pydantic import ConfigDict, ValidationError, ValidationInfo, field_validator
 from rich.logging import RichHandler
 from textual import on
@@ -16,6 +17,7 @@
 from textual.widget import Widget
 from textual.widgets import Button, Input, Markdown, RichLog, Static, Switch
 
+import nf_core
 from nf_core.utils import NFCoreTemplateConfig
 
 # Use ContextVar to define a context on the model initialization
@@ -34,6 +36,9 @@ def init_context(value: Dict[str, Any]) -> Iterator[None]:
 # Define a global variable to store the pipeline type
 NFCORE_PIPELINE_GLOBAL: bool = True
 
+# YAML file describing template features
+features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml"
+
 
 class CreateConfig(NFCoreTemplateConfig):
     """Pydantic model for the nf-core create config."""
@@ -242,3 +247,9 @@ def add_hide_class(app, widget_id: str) -> None:
 def remove_hide_class(app, widget_id: str) -> None:
     """Remove class 'hide' to a widget. Display widget."""
     app.get_widget_by_id(widget_id).remove_class("hide")
+
+
+def load_features_yaml() -> dict:
+    """Load the YAML file describing template features."""
+    with open(features_yml_path) as fh:
+        return yaml.safe_load(fh)
diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py
index b684a4669e..13fd3b24cd 100644
--- a/tests/pipelines/test_create.py
+++ b/tests/pipelines/test_create.py
@@ -9,6 +9,7 @@
 import yaml
 
 import nf_core.pipelines.create.create
+from nf_core.pipelines.create.utils import load_features_yaml
 
 from ..utils import TEST_DATA_DIR, with_temporary_folder
 
@@ -101,9 +102,7 @@ def test_pipeline_creation_initiation_customize_template(self, tmp_path):
     @with_temporary_folder
     def test_pipeline_creation_with_yml_skip(self, tmp_path):
         # Update pipeline_create_template_skip.yml file
-        features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml"
-        with open(features_yml_path) as fh:
-            template_features_yml = yaml.safe_load(fh)
+        template_features_yml = load_features_yaml()
         all_features = list(template_features_yml.keys())
         all_features.remove("is_nfcore")
         env = jinja2.Environment(loader=jinja2.PackageLoader("tests", "data"), keep_trailing_newline=True)

From 2c2ec5db394128a947bc874461582e45711648d1 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Aug 2024 11:51:26 +0200
Subject: [PATCH 221/414] set force to true when creating a pipeline from the
 app

---
 nf_core/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/utils.py b/nf_core/utils.py
index d0546a5c5e..96c16130ca 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -1055,7 +1055,7 @@ class NFCoreTemplateConfig(BaseModel):
     description: Optional[str] = None
     author: Optional[str] = None
     version: Optional[str] = None
-    force: Optional[bool] = None
+    force: Optional[bool] = True
     outdir: Optional[Union[str, Path]] = None
     skip_features: Optional[list] = None
     is_nfcore: Optional[bool] = None

From 2535b6fc136fc24bef77249f3fc755b344100b9c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Tue, 13 Aug 2024 12:16:51 +0200
Subject: [PATCH 222/414] Update nf_core/pipelines/create/utils.py
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 nf_core/pipelines/create/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
index 2e0015ed90..0b72c2bcf5 100644
--- a/nf_core/pipelines/create/utils.py
+++ b/nf_core/pipelines/create/utils.py
@@ -249,7 +249,7 @@ def remove_hide_class(app, widget_id: str) -> None:
     app.get_widget_by_id(widget_id).remove_class("hide")
 
 
-def load_features_yaml() -> dict:
+def load_features_yaml() -> Dict:
     """Load the YAML file describing template features."""
     with open(features_yml_path) as fh:
         return yaml.safe_load(fh)

From 6af86cf39306c2bf3c9bd4d0f61057fdea24f590 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Aug 2024 12:29:02 +0200
Subject: [PATCH 223/414] fix typing

---
 nf_core/pipelines/create/create.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index b3135435ee..200507d8a0 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -8,7 +8,7 @@
 import re
 import shutil
 from pathlib import Path
-from typing import Dict, List, Optional, Union, cast
+from typing import Dict, List, Optional, Tuple, Union, cast
 
 import git
 import git.config
@@ -185,7 +185,7 @@ def update_config(self, organisation, version, force, outdir):
 
     def obtain_jinja_params_dict(
         self, features_to_skip: List[str], pipeline_dir: Union[str, Path]
-    ) -> tuple[dict, list[str]]:
+    ) -> Tuple[Dict, List[str]]:
         """Creates a dictionary of parameters for the new pipeline.
 
         Args:

From d6459cba0cf3e96e156350e541850afb61409e57 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Aug 2024 17:39:35 +0200
Subject: [PATCH 224/414] add templatefeatures.yml to python package

---
 MANIFEST.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/MANIFEST.in b/MANIFEST.in
index 68f115d97f..2bec403804 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -10,3 +10,4 @@ include nf_core/assets/logo/nf-core-repo-logo-base-darkbg.png
 include nf_core/assets/logo/placeholder_logo.svg
 include nf_core/assets/logo/MavenPro-Bold.ttf
 include nf_core/pipelines/create/create.tcss
+include nf_core/pipelines/create/templatefeatures.yml

From f6505c2fea94057e66954f45b4c1ad6e37dc8a77 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 13 Aug 2024 15:41:13 +0000
Subject: [PATCH 225/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 398aee5755..c7095e292e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@
 - add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103))
 - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104))
 - handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108))
+- add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112))
 
 ### Linting
 

From afec8773b56cb813c4de59f882f0c056c9b4d114 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Aug 2024 18:11:41 +0200
Subject: [PATCH 226/414] output matrix elements with double quotes

---
 .github/workflows/create-test-lint-wf-template.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index bd661ce07c..0057bdb2d0 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -35,7 +35,7 @@ jobs:
     name: Retrieve all template features
     runs-on: ubuntu-latest
     outputs:
-      all_features: ${{ steps.create_matrix.outputs.matrix }}
+      all_features: ${{ fromJSON(steps.create_matrix.outputs.matrix) }}
     steps:
       - name: 🏗 Set up yq
         uses: frenck/action-setup-yq@v1
@@ -43,7 +43,7 @@ jobs:
         uses: actions/checkout@v3
       - name: Create Matrix
         id: create_matrix
-        run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print $2}' | paste -sd "," - | awk '{print "[" $0 "]"}')" >> $GITHUB_OUTPUT
+        run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print "\""$2"\""}' | paste -sd "," - | awk '{print "[" $0 "]"}')" >> $GITHUB_OUTPUT
 
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}

From c8188130153a4c4192714255b98ecd6fc08155bf Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Aug 2024 18:18:20 +0200
Subject: [PATCH 227/414] don't use fromJSON

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 0057bdb2d0..0c97168f44 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -35,7 +35,7 @@ jobs:
     name: Retrieve all template features
     runs-on: ubuntu-latest
     outputs:
-      all_features: ${{ fromJSON(steps.create_matrix.outputs.matrix) }}
+      all_features: ${{ steps.create_matrix.outputs.matrix }}
     steps:
       - name: 🏗 Set up yq
         uses: frenck/action-setup-yq@v1

From aef4895bf7a1a5b50d855399d37635cc088d7abb Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Aug 2024 18:23:23 +0200
Subject: [PATCH 228/414] try fromJSON when reading the matrix

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 0c97168f44..c2d61c51c8 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -51,7 +51,7 @@ jobs:
       NXF_ANSI_LOG: false
     strategy:
       matrix:
-        TEMPLATE: ${{ needs.prepare-matrix.outputs.all_features }}
+        TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }}
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}

From 3464aa45a689e33a64bbf2ac3390772ae3b4d3d0 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Aug 2024 18:34:47 +0200
Subject: [PATCH 229/414] surround whole matrix by single quotes

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index c2d61c51c8..e097c0c82a 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -43,7 +43,7 @@ jobs:
         uses: actions/checkout@v3
       - name: Create Matrix
         id: create_matrix
-        run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print "\""$2"\""}' | paste -sd "," - | awk '{print "[" $0 "]"}')" >> $GITHUB_OUTPUT
+        run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print "\""$2"\""}' | paste -sd "," - | awk '{print "'\''[" $0 "]'\''"}')" >> $GITHUB_OUTPUT
 
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}

From 5156d0129ae602af54291742cdd7d107bcb2c129 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Aug 2024 18:42:24 +0200
Subject: [PATCH 230/414] escape double quotes to use a json raw string literal

---
 .github/workflows/create-test-lint-wf-template.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index e097c0c82a..3d3726b820 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -43,7 +43,7 @@ jobs:
         uses: actions/checkout@v3
       - name: Create Matrix
         id: create_matrix
-        run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print "\""$2"\""}' | paste -sd "," - | awk '{print "'\''[" $0 "]'\''"}')" >> $GITHUB_OUTPUT
+        run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print "\\""\""$2"\\""\""}' | paste -sd "," - | awk '{print "'\''[" $0 "]'\''"}')" >> $GITHUB_OUTPUT
 
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}
@@ -51,7 +51,7 @@ jobs:
       NXF_ANSI_LOG: false
     strategy:
       matrix:
-        TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }}
+        TEMPLATE: ${{ fromJSON(needs.prepare-matrix.outputs.all_features) }}
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}

From 07858624a4c97c209d5b002a699b1e6d89a6001b Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Aug 2024 08:46:14 +0200
Subject: [PATCH 231/414] allow spaces at the betinning of include statements
 in components

---
 nf_core/components/components_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py
index 01650a643d..dee4fbf6bb 100644
--- a/nf_core/components/components_utils.py
+++ b/nf_core/components/components_utils.py
@@ -143,7 +143,7 @@ def get_components_to_install(subworkflow_dir: str) -> Tuple[List[str], List[str
             regex = re.compile(
                 r"include(?: *{ *)([a-zA-Z\_0-9]*)(?: *as *)?(?:[a-zA-Z\_0-9]*)?(?: *})(?: *from *)(?:'|\")(.*)(?:'|\")"
             )
-            match = regex.match(line)
+            match = regex.search(line)
             if match and len(match.groups()) == 2:
                 name, link = match.groups()
                 if link.startswith("../../../"):

From dea1781dfeb402b99a0c1a209928db7c55ff7c5b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 14 Aug 2024 08:49:56 +0200
Subject: [PATCH 232/414] try simpler yq command

---
 .github/workflows/create-test-lint-wf-template.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 3d3726b820..cc7f272c64 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -43,7 +43,9 @@ jobs:
         uses: actions/checkout@v3
       - name: Create Matrix
         id: create_matrix
-        run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print "\\""\""$2"\\""\""}' | paste -sd "," - | awk '{print "'\''[" $0 "]'\''"}')" >> $GITHUB_OUTPUT
+        run: |
+          echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml >> $GITHUB_OUTPUT
+          echo $GITHUB_OUTPUT
 
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}
@@ -51,7 +53,7 @@ jobs:
       NXF_ANSI_LOG: false
     strategy:
       matrix:
-        TEMPLATE: ${{ fromJSON(needs.prepare-matrix.outputs.all_features) }}
+        TEMPLATE: ${{ needs.prepare-matrix.outputs.all_features }}
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}

From d838c869602c6a08238b7bbc17abdc23046083d6 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 14 Aug 2024 06:51:20 +0000
Subject: [PATCH 233/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 609c3aea06..91e32374d6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -64,6 +64,7 @@
 - Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091))
 - Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094))
 - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102))
+- Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From e19be1d13025b18273f494f86f39d67fc2ba1901 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 14 Aug 2024 08:53:05 +0200
Subject: [PATCH 234/414] add missing parenthesis

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index cc7f272c64..e55f904c7c 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -44,7 +44,7 @@ jobs:
       - name: Create Matrix
         id: create_matrix
         run: |
-          echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml >> $GITHUB_OUTPUT
+          echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml) >> $GITHUB_OUTPUT
           echo $GITHUB_OUTPUT
 
   RunTestWorkflow:

From 7c6281f113cd3cac0a0b570e2c178f3036ae80e2 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 14 Aug 2024 08:54:29 +0200
Subject: [PATCH 235/414] and missing closing quote

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index e55f904c7c..fd20b67937 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -44,7 +44,7 @@ jobs:
       - name: Create Matrix
         id: create_matrix
         run: |
-          echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml) >> $GITHUB_OUTPUT
+          echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
           echo $GITHUB_OUTPUT
 
   RunTestWorkflow:

From 96c2b0a1a8ec5be01cac80c8f418ffacdbd63eda Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 14 Aug 2024 09:01:56 +0200
Subject: [PATCH 236/414] remove debugging

---
 .github/workflows/create-test-lint-wf-template.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index fd20b67937..311c6a0582 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -45,7 +45,6 @@ jobs:
         id: create_matrix
         run: |
           echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
-          echo $GITHUB_OUTPUT
 
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}

From 08888ffeea3ca0a1c1f2a607d4614b14a109887d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 14 Aug 2024 09:06:12 +0200
Subject: [PATCH 237/414] more debugging

---
 .github/workflows/create-test-lint-wf-template.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 311c6a0582..d46d8f7d31 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -44,7 +44,9 @@ jobs:
       - name: Create Matrix
         id: create_matrix
         run: |
-          echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
+          echo "matrix=$(yq 'keys | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)"
+      - name: Setup ssh session
+        uses: Warpbuilds/action-debugger@v1.3
 
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}

From b564d9f451c48888987d6e9ec24ef8cd49fd60b7 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 14 Aug 2024 09:08:18 +0200
Subject: [PATCH 238/414] add output step back

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index d46d8f7d31..e835a2b30c 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -44,7 +44,7 @@ jobs:
       - name: Create Matrix
         id: create_matrix
         run: |
-          echo "matrix=$(yq 'keys | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)"
+          echo "matrix=$(yq 'keys | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
       - name: Setup ssh session
         uses: Warpbuilds/action-debugger@v1.3
 

From 237f888bdb3a3202291a34b03ea0ef2f9981079f Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 14 Aug 2024 09:11:31 +0200
Subject: [PATCH 239/414] add `needs` step

---
 .github/workflows/create-test-lint-wf-template.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index e835a2b30c..4fa41a0d4e 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -45,11 +45,10 @@ jobs:
         id: create_matrix
         run: |
           echo "matrix=$(yq 'keys | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
-      - name: Setup ssh session
-        uses: Warpbuilds/action-debugger@v1.3
 
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}
+    needs: prepare-matrix
     env:
       NXF_ANSI_LOG: false
     strategy:

From d81019f56ba0ebf9ea12c7ed72a80f408e650a51 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 14 Aug 2024 09:16:20 +0200
Subject: [PATCH 240/414] parse output step

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 4fa41a0d4e..71ea02539e 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -53,7 +53,7 @@ jobs:
       NXF_ANSI_LOG: false
     strategy:
       matrix:
-        TEMPLATE: ${{ needs.prepare-matrix.outputs.all_features }}
+        TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }}
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}

From c4a1961e33b23e9eb5f1972b0ab84301770974f7 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 14 Aug 2024 09:18:57 +0200
Subject: [PATCH 241/414] add missing escape character

---
 .github/workflows/create-test-lint-wf-template.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 71ea02539e..29c3933758 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -40,7 +40,7 @@ jobs:
       - name: 🏗 Set up yq
         uses: frenck/action-setup-yq@v1
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
       - name: Create Matrix
         id: create_matrix
         run: |
@@ -102,9 +102,9 @@ jobs:
           export NXF_WORK=$(pwd)
           printf "org: my-prefix\nskip: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml
 
-      - name: Create template skip {{ matrix.TEMPLATE }}
+      - name: Create template skip ${{ matrix.TEMPLATE }}
         run: |
-          printf "org: my-prefix\nskip: {{ matrix.TEMPLATE }}" > create-test-lint-wf/template_skip_{{ matrix.TEMPLATE }}.yml
+          printf "org: my-prefix\nskip: ${{ matrix.TEMPLATE }}" > create-test-lint-wf/template_skip_{{ matrix.TEMPLATE }}.yml
 
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}

From d401a40cc25419e50846d8b01abf0e66d36a5ec5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 14 Aug 2024 09:21:06 +0200
Subject: [PATCH 242/414] more escape characters

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 29c3933758..1c5189f549 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -104,7 +104,7 @@ jobs:
 
       - name: Create template skip ${{ matrix.TEMPLATE }}
         run: |
-          printf "org: my-prefix\nskip: ${{ matrix.TEMPLATE }}" > create-test-lint-wf/template_skip_{{ matrix.TEMPLATE }}.yml
+          printf "org: my-prefix\nskip: ${{ matrix.TEMPLATE }}" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml
 
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}

From 5936e61cf4d44242167550419e5f4f001b4212e0 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Aug 2024 10:08:16 +0200
Subject: [PATCH 243/414] fix creating pipeline from template skip_features

---
 .github/workflows/create-test-lint-wf-template.yml | 4 ++--
 nf_core/pipelines/create/create.py                 | 2 --
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 1c5189f549..c15783e67b 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -100,11 +100,11 @@ jobs:
         run: |
           mkdir create-test-lint-wf
           export NXF_WORK=$(pwd)
-          printf "org: my-prefix\nskip: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml
+          printf "org: my-prefix\nskip_features: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml
 
       - name: Create template skip ${{ matrix.TEMPLATE }}
         run: |
-          printf "org: my-prefix\nskip: ${{ matrix.TEMPLATE }}" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml
+          printf "org: my-prefix\nskip_features: [${{ matrix.TEMPLATE }}]" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml
 
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 200507d8a0..873a2ecb19 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -417,8 +417,6 @@ def fix_linting(self):
         for area in self.skip_areas:
             try:
                 for lint_test in self.template_features_yml[area]["linting"]:
-                    if not lint_config[lint_test]:
-                        pass
                     if self.template_features_yml[area]["linting"][lint_test]:
                         lint_config.setdefault(lint_test, []).extend(
                             self.template_features_yml[area]["linting"][lint_test]

From 4941833dd1fae5720b4b10c3cdf63bb9dbdd3e6f Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Aug 2024 10:23:48 +0200
Subject: [PATCH 244/414] handle linting tests false

---
 nf_core/pipelines/create/create.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 873a2ecb19..c015a43f73 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -417,12 +417,15 @@ def fix_linting(self):
         for area in self.skip_areas:
             try:
                 for lint_test in self.template_features_yml[area]["linting"]:
-                    if self.template_features_yml[area]["linting"][lint_test]:
-                        lint_config.setdefault(lint_test, []).extend(
-                            self.template_features_yml[area]["linting"][lint_test]
-                        )
-                    else:
-                        lint_config[lint_test] = False
+                    try:
+                        if self.template_features_yml[area]["linting"][lint_test]:
+                            lint_config.setdefault(lint_test, []).extend(
+                                self.template_features_yml[area]["linting"][lint_test]
+                            )
+                        else:
+                            lint_config[lint_test] = False
+                    except AttributeError:
+                        pass  # When linting is False
             except KeyError:
                 pass  # Areas without linting
 

From b474a049e7d4cc1cea8d7006e1a2aeb79b810dcc Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Aug 2024 10:33:56 +0200
Subject: [PATCH 245/414] exclude running skip nf_core_configs with
 self_hosted_runner

---
 .github/workflows/create-test-lint-wf-template.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index c15783e67b..6b916fb79c 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -68,6 +68,9 @@ jobs:
         exclude:
           - TEMPLATE: github
           - TEMPLATE: is_nfcore
+          - TEMPLATE: nf_core_configs
+            runner: self-hosted
+            profile: "self_hosted_runner"
       fail-fast: false
 
     steps:

From 442f2f0097226595730dd4e1c9af86696f6c16fb Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Aug 2024 11:56:50 +0200
Subject: [PATCH 246/414] fix pipeline skipping nf_core_configs

---
 .prettierignore                               |  1 +
 .../.github/ISSUE_TEMPLATE/bug_report.yml     |  2 +
 nf_core/pipeline-template/nextflow.config     |  2 +-
 .../pipeline-template/nextflow_schema.json    |  6 ++-
 nf_core/pipelines/create/create.py            | 46 ++-----------------
 nf_core/pipelines/create/templatefeatures.yml |  2 +
 6 files changed, 15 insertions(+), 44 deletions(-)

diff --git a/.prettierignore b/.prettierignore
index 9387ee9509..cbe7274a4a 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -7,6 +7,7 @@ nf_core/module-template/meta.yml
 nf_core/pipeline-template/nextflow_schema.json
 nf_core/pipeline-template/modules.json
 nf_core/pipeline-template/tower.yml
+nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml
 tests/data/pipeline_create_template_skip.yml
 # don't run on things handled by ruff
 *.py
diff --git a/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml b/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml
index 063690f29f..412f5bd3b3 100644
--- a/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -2,6 +2,7 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
+{%- if is_nfcore %}
   - type: markdown
     attributes:
       value: |
@@ -9,6 +10,7 @@ body:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
         - [{{ name }} pipeline documentation](https://nf-co.re/{{ short_name }}/usage)
+{%- endif %}
 
   - type: textarea
     id: description
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 3a7f544805..0469d6cfec 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -41,11 +41,11 @@ params {
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
 
+    {%- if nf_core_configs %}
     // Config options
     config_profile_name        = null
     config_profile_description = null
 
-    {%- if nf_core_configs %}
     custom_config_version      = 'master'
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 1c52e2298d..4a1a22c3ee 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -77,6 +77,7 @@
             }
         },
         {%- endif %}
+        {%- if nf_core_configs %}
         "institutional_config_options": {
             "title": "Institutional config options",
             "type": "object",
@@ -125,6 +126,7 @@
                 }
             }
         },
+        {%- endif %}
         "max_job_request_options": {
             "title": "Max job request options",
             "type": "object",
@@ -289,9 +291,9 @@
         {% if igenomes %}{
             "$ref": "#/definitions/reference_genome_options"
         },{% endif %}
-        {
+        {% if nf_core_configs %}{
             "$ref": "#/definitions/institutional_config_options"
-        },
+        },{% endif %}
         {
             "$ref": "#/definitions/max_job_request_options"
         },
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index c015a43f73..e3f8dc6973 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -349,17 +349,9 @@ def render_template(self) -> None:
                 template_stat = os.stat(template_fn_path)
                 os.chmod(output_path, template_stat.st_mode)
 
-        # Remove all unused parameters in the nextflow schema
-        if not self.jinja_params["igenomes"] or not self.jinja_params["nf_core_configs"]:
-            self.update_nextflow_schema()
         if self.config.is_nfcore:
             # Make a logo and save it, if it is a nf-core pipeline
             self.make_pipeline_logo()
-        else:
-            if self.jinja_params["github"]:
-                # Remove field mentioning nf-core docs
-                # in the github bug report template
-                self.remove_nf_core_in_bug_report_template()
 
         # Update the .nf-core.yml with linting configurations
         self.fix_linting()
@@ -374,38 +366,10 @@ def render_template(self) -> None:
                     log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
                     run_prettier_on_file(self.outdir / config_fn)
 
-    def update_nextflow_schema(self):
-        """
-        Removes unused parameters from the nextflow schema.
-        """
-        schema_path = self.outdir / "nextflow_schema.json"
-
-        schema = nf_core.pipelines.schema.PipelineSchema()
-        schema.schema_filename = schema_path
-        schema.no_prompts = True
-        schema.load_schema()
-        schema.get_wf_params()
-        schema.remove_schema_notfound_configs()
-        schema.save_schema(suppress_logging=True)
-        run_prettier_on_file(schema_path)
-
-    def remove_nf_core_in_bug_report_template(self):
-        """
-        Remove the field mentioning nf-core documentation
-        in the github bug report template
-        """
-        bug_report_path = self.outdir / ".github" / "ISSUE_TEMPLATE" / "bug_report.yml"
-
-        with open(bug_report_path) as fh:
-            contents = yaml.load(fh, Loader=yaml.FullLoader)
-
-        # Remove the first item in the body, which is the information about the docs
-        contents["body"].pop(0)
-
-        with open(bug_report_path, "w") as fh:
-            yaml.dump(contents, fh, default_flow_style=False, sort_keys=False)
-
-        run_prettier_on_file(bug_report_path)
+        # Run prettier on files
+        for file in self.outdir.iterdir():
+            if file.is_file() and file.name.endswith(("yaml", "yml", "json")):
+                run_prettier_on_file(file)
 
     def fix_linting(self):
         """
@@ -414,7 +378,7 @@ def fix_linting(self):
         """
         # Create a lint config
         lint_config = {}
-        for area in self.skip_areas:
+        for area in (self.config.skip_features or []) + self.skip_areas:
             try:
                 for lint_test in self.template_features_yml[area]["linting"]:
                     try:
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 48ce200551..ac026c9e20 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -109,6 +109,8 @@ nf_core_configs:
       - "process.memory"
       - "process.time"
       - "custom_config"
+      - "params.custom_config_version"
+      - "params.custom_config_base"
   nfcore_pipelines: False
   custom_pipelines: True
 is_nfcore:

From c3f669e704de117bff30eb569788669e0f8f26ce Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Aug 2024 12:10:00 +0200
Subject: [PATCH 247/414] fix lint pipeline without code linters

---
 nf_core/pipelines/create/templatefeatures.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index ac026c9e20..b97bf347ab 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -162,6 +162,11 @@ code_linters:
     - pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository.
     - editor-config (https://github.com/editorconfig-checker/editorconfig-checker): checks rules such as indentation or trailing spaces.
     - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc).
+  linting:
+    files_exist:
+      - ".editorconfig"
+      - ".prettierignore"
+      - ".prettierrc.yml"
   nfcore_pipelines: False
   custom_pipelines: True
 citations:

From 6da1adc768e9032887422fd475c524b94e0b3bb2 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Aug 2024 12:12:01 +0200
Subject: [PATCH 248/414] not run skip nf_core_configs with self_hosted_runner

---
 .github/workflows/create-test-lint-wf-template.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 6b916fb79c..fc6338ab40 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -69,7 +69,6 @@ jobs:
           - TEMPLATE: github
           - TEMPLATE: is_nfcore
           - TEMPLATE: nf_core_configs
-            runner: self-hosted
             profile: "self_hosted_runner"
       fail-fast: false
 

From 598bd17acc9ebf949c3e56b057629e899c453e26 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Aug 2024 12:20:20 +0200
Subject: [PATCH 249/414] create template with skip all only once

---
 .github/workflows/create-test-lint-wf-template.yml | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index fc6338ab40..70125a10f3 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -98,15 +98,16 @@ jobs:
           version: latest-everything
 
       # Create template files
-      - name: Create template skip all (except github)
+      - name: Create template skip ${{ matrix.TEMPLATE }}
         run: |
           mkdir create-test-lint-wf
           export NXF_WORK=$(pwd)
-          printf "org: my-prefix\nskip_features: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml
-
-      - name: Create template skip ${{ matrix.TEMPLATE }}
-        run: |
-          printf "org: my-prefix\nskip_features: [${{ matrix.TEMPLATE }}]" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml
+          if [ ${{ matrix.TEMPLATE }} == "all" ]
+          then
+            printf "org: my-prefix\nskip_features: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml
+          else
+            printf "org: my-prefix\nskip_features: [${{ matrix.TEMPLATE }}]" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml
+          fi
 
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}

From c038e81c303926f46cf52daa36ec09a9c95b39e5 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Aug 2024 12:46:58 +0200
Subject: [PATCH 250/414] set is_nfcore false when needed

---
 nf_core/pipelines/create/create.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index e3f8dc6973..dfdcf07a42 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -218,6 +218,7 @@ def obtain_jinja_params_dict(
         # Add is_nfcore as an area to skip for non-nf-core pipelines, to skip all nf-core files
         if not self.config.is_nfcore:
             skip_areas.append("is_nfcore")
+            jinja_params["is_nfcore"] = False
 
         # Set the last parameters based on the ones provided
         jinja_params["short_name"] = (

From 95a57cffa77e6b7a0918454acb04433c94cd5284 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 14 Aug 2024 13:33:09 +0200
Subject: [PATCH 251/414] run prettier on the pipeline output directory

---
 nf_core/pipelines/create/create.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index dfdcf07a42..05b04a5422 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -368,9 +368,7 @@ def render_template(self) -> None:
                     run_prettier_on_file(self.outdir / config_fn)
 
         # Run prettier on files
-        for file in self.outdir.iterdir():
-            if file.is_file() and file.name.endswith(("yaml", "yml", "json")):
-                run_prettier_on_file(file)
+        run_prettier_on_file(self.outdir)
 
     def fix_linting(self):
         """

From a754fe0845f0e28ae0398625d8132a6047aa991e Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 15:07:38 +0200
Subject: [PATCH 252/414] add schema checking for draft 2020-12

---
 nf_core/pipelines/lint/schema_lint.py | 32 ++++++++++++++++++++++-----
 nf_core/pipelines/schema.py           | 21 +++++++++++++-----
 requirements.txt                      |  2 +-
 3 files changed, 44 insertions(+), 11 deletions(-)

diff --git a/nf_core/pipelines/lint/schema_lint.py b/nf_core/pipelines/lint/schema_lint.py
index 6786c5012d..4007bf8fe5 100644
--- a/nf_core/pipelines/lint/schema_lint.py
+++ b/nf_core/pipelines/lint/schema_lint.py
@@ -16,26 +16,26 @@ def schema_lint(self):
     The lint test checks the schema for the following:
 
     * Schema should be a valid JSON file
-    * Schema should adhere to `JSONSchema <https://json-schema.org/>`_, Draft 7.
+    * Schema should adhere to `JSONSchema <https://json-schema.org/>`_, Draft 7 or Draft 2020-12.
     * Parameters can be described in two places:
 
         * As ``properties`` in the top-level schema object
-        * As ``properties`` within subschemas listed in a top-level ``definitions`` objects
+        * As ``properties`` within subschemas listed in a top-level ``definitions``(draft 7) or ``$defs``(draft 2020-12) objects
 
     * The schema must describe at least one parameter
     * There must be no duplicate parameter IDs across the schema and definition subschema
-    * All subschema in ``definitions`` must be referenced in the top-level ``allOf`` key
+    * All subschema in ``definitions`` or ``$defs`` must be referenced in the top-level ``allOf`` key
     * The top-level ``allOf`` key must not describe any non-existent definitions
     * Default parameters in the schema must be valid
     * Core top-level schema attributes should exist and be set as follows:
 
-        * ``$schema``: ``https://json-schema.org/draft-07/schema``
+        * ``$schema``: ``https://json-schema.org/draft-07/schema`` or ``https://json-schema.org/draft/2020-12/schema``
         * ``$id``: URL to the raw schema file, eg. ``https://raw.githubusercontent.com/YOURPIPELINE/master/nextflow_schema.json``
         * ``title``: ``YOURPIPELINE pipeline parameters``
         * ``description``: The pipeline config ``manifest.description``
     * That the ``input`` property is defined and has a mimetype. A list of common mimetypes can be found `here <https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_HTTP/MIME_types/Common_types>`_.
 
-    For example, an *extremely* minimal schema could look like this:
+    For example, an *extremely* minimal schema could look like this (draft 7):
 
     .. code-block:: json
 
@@ -57,6 +57,28 @@ def schema_lint(self):
          "allOf": [{"$ref": "#/definitions/my_first_group"}]
        }
 
+    Or this (draft 2020-12):
+
+    .. code-block:: json
+
+       {
+         "$schema": "https://json-schema.org/draft/2020-12/schema",
+         "$id": "https://raw.githubusercontent.com/YOURPIPELINE/master/nextflow_schema.json",
+         "title": "YOURPIPELINE pipeline parameters",
+         "description": "This pipeline is for testing",
+         "properties": {
+           "first_param": { "type": "string" }
+         },
+         "$defs": {
+           "my_first_group": {
+             "properties": {
+               "second_param": { "type": "string" }
+             }
+           }
+         },
+         "allOf": [{"$ref": "#/$defs/my_first_group"}]
+       }
+
     .. tip:: You can check your pipeline schema without having to run the entire pipeline lint
              by running ``nf-core pipelines schema lint`` instead of ``nf-core pipelines lint``
     """
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 7f562bff38..854bddccc0 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -359,11 +359,22 @@ def validate_schema(self, schema=None):
         """
         if schema is None:
             schema = self.schema
-        try:
-            jsonschema.Draft7Validator.check_schema(schema)
-            log.debug("JSON Schema Draft7 validated")
-        except jsonschema.exceptions.SchemaError as e:
-            raise AssertionError(f"Schema does not validate as Draft 7 JSON Schema:\n {e}")
+
+        schema_draft = schema["$schema"]
+        if schema_draft == "https://json-schema.org/draft-07/schema":
+            try:
+                jsonschema.Draft7Validator.check_schema(schema)
+                log.debug("JSON Schema Draft7 validated")
+            except jsonschema.exceptions.SchemaError as e:
+                raise AssertionError(f"Schema does not validate as Draft 7 JSON Schema:\n {e}")
+        elif schema_draft == "https://json-schema.org/draft/2020-12/schema":
+            try:
+                jsonschema.Draft202012Validator.check_schema(schema)
+                log.debug("JSON Schema Draft2020-12 validated")
+            except jsonschema.exceptions.SchemaError as e:
+                raise AssertionError(f"Schema does not validate as Draft 2020-12 JSON Schema:\n {e}")
+        else:
+            raise AssertionError(f"Unsupported JSON schema draft detected: ${schema_draft}. Use draft 7 or 2020-12 instead.")
 
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
diff --git a/requirements.txt b/requirements.txt
index fb658be2fb..eba6460f03 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,7 +3,7 @@ filetype
 GitPython
 PyGithub
 jinja2
-jsonschema>=3.0
+jsonschema>=4.0
 markdown>=3.3
 packaging
 pillow

From 464f16e982337699382e66e3b1da21af4f01dd7a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 15:26:52 +0200
Subject: [PATCH 253/414] update validate schema

---
 nf_core/pipelines/schema.py | 31 +++++++++++++++++++++++--------
 1 file changed, 23 insertions(+), 8 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 854bddccc0..abdad719f6 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -378,17 +378,32 @@ def validate_schema(self, schema=None):
 
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
-        for d_key, d_schema in schema.get("definitions", {}).items():
+        schema_defs = dict()
+        defs_notation = ""
+        if "$defs" in schema:
+            schema_defs = schema.get("$defs", {}).items()
+            defs_notation = "$defs"
+        elif "definitions" in schema:
+            schema_defs = schema.get("definitions", {}).items()
+            defs_notation = "definitions"
+        elif "defs" in schema:
+            # nf-schema v2.0.0 only supported defs. this has been changed to $defs in nf-schema v2.1.0
+            # this line prevents the breakage of schemas created for v2.0.0
+            schema_defs = schema.get("defs", {}).items()
+            defs_notation = "defs"
+
+        for d_key, d_schema in schema_defs:
             # Check that this definition is mentioned in allOf
             if "allOf" not in schema:
                 raise AssertionError("Schema has definitions, but no allOf key")
             in_allOf = False
             for allOf in schema.get("allOf", []):
-                if allOf["$ref"] == f"#/definitions/{d_key}":
+                if allOf["$ref"] == f"#/{defs_notation}/{d_key}":
                     in_allOf = True
             if not in_allOf:
-                raise AssertionError(f"Definition subschema `{d_key}` not included in schema `allOf`")
+                raise AssertionError(f"Definition subschema `#{defs_notation}/{d_key}` not included in schema `allOf`")
 
+            # TODO add support for nested parameters
             for d_param_id in d_schema.get("properties", {}):
                 # Check that we don't have any duplicate parameter IDs in different definitions
                 if d_param_id in param_keys:
@@ -398,11 +413,11 @@ def validate_schema(self, schema=None):
 
         # Check that everything in allOf exists
         for allOf in schema.get("allOf", []):
-            if "definitions" not in schema:
-                raise AssertionError("Schema has allOf, but no definitions")
-            def_key = allOf["$ref"][14:]
-            if def_key not in schema.get("definitions", {}):
-                raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `definitions`")
+            _, allOf_defs_notation, def_key = allOf["$ref"].split("/") # "#/<defs_notation>/<def_name>"
+            if allOf_defs_notation not in schema:
+                raise AssertionError(f"Schema has allOf, but no {allOf_defs_notation}")
+            if def_key not in schema.get(allOf_defs_notation, {}):
+                raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `{allOf_defs_notation}`")
 
         # Check that the schema describes at least one parameter
         if num_params == 0:

From 6658449cc892021782a22885c3db63c0215254b6 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 15:51:27 +0200
Subject: [PATCH 254/414] update more code to support draft 2020-12

---
 nf_core/pipelines/schema.py | 55 ++++++++++++++++++++-----------------
 1 file changed, 30 insertions(+), 25 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index abdad719f6..398783d5a8 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -116,8 +116,26 @@ def load_schema(self):
             self.schema = json.load(fh)
         self.schema_defaults = {}
         self.schema_params = {}
+        if "$schema" not in self.schema:
+            raise AssertionError("Schema missing top-level `$schema` attribute")        
+        self.schema_draft = self.schema["$schema"]
+        self.defs_notation = self.get_defs_notation()
         log.debug(f"JSON file loaded: {self.schema_filename}")
 
+    def get_defs_notation(self, schema=None):
+        if schema is None:
+            schema = self.schema
+
+        if "$defs" in schema:
+            defs_notation = "$defs"
+        elif "definitions" in schema:
+            defs_notation = "definitions"
+        elif "defs" in schema:
+            # nf-schema v2.0.0 only supported defs. this has been changed to $defs in nf-schema v2.1.0
+            # this line prevents the breakage of schemas created for v2.0.0
+            defs_notation = "defs"
+        return defs_notation
+
     def sanitise_param_default(self, param):
         """
         Given a param, ensure that the default value is the correct variable type
@@ -168,10 +186,11 @@ def get_schema_defaults(self) -> None:
                 if param["default"] is not None:
                     self.schema_defaults[p_key] = param["default"]
 
+        # TODO add support for nested parameters
         # Grouped schema properties in subschema definitions
-        for defn_name, definition in self.schema.get("definitions", {}).items():
+        for defn_name, definition in self.schema.get(self.defs_notation, {}).items():
             for p_key, param in definition.get("properties", {}).items():
-                self.schema_params[p_key] = ("definitions", defn_name, "properties", p_key)
+                self.schema_params[p_key] = (self.defs_notation, defn_name, "properties", p_key)
                 if "default" in param:
                     param = self.sanitise_param_default(param)
                     if param["default"] is not None:
@@ -248,13 +267,14 @@ def validate_default_params(self):
         if self.schema is None:
             log.error("[red][✗] Pipeline schema not found")
         try:
+            # TODO add support for nested parameters
             # Make copy of schema and remove required flags
             schema_no_required = copy.deepcopy(self.schema)
             if "required" in schema_no_required:
                 schema_no_required.pop("required")
-            for group_key, group in schema_no_required.get("definitions", {}).items():
+            for group_key, group in schema_no_required.get(self.defs_notation, {}).items():
                 if "required" in group:
-                    schema_no_required["definitions"][group_key].pop("required")
+                    schema_no_required[self.defs_notation][group_key].pop("required")
             jsonschema.validate(self.schema_defaults, schema_no_required)
         except jsonschema.exceptions.ValidationError as e:
             raise AssertionError(f"Default parameters are invalid: {e.message}")
@@ -360,6 +380,8 @@ def validate_schema(self, schema=None):
         if schema is None:
             schema = self.schema
 
+        if "$schema" not in schema:
+            raise AssertionError("Schema missing top-level `$schema` attribute")
         schema_draft = schema["$schema"]
         if schema_draft == "https://json-schema.org/draft-07/schema":
             try:
@@ -374,25 +396,14 @@ def validate_schema(self, schema=None):
             except jsonschema.exceptions.SchemaError as e:
                 raise AssertionError(f"Schema does not validate as Draft 2020-12 JSON Schema:\n {e}")
         else:
-            raise AssertionError(f"Unsupported JSON schema draft detected: ${schema_draft}. Use draft 7 or 2020-12 instead.")
+            raise AssertionError(f"Schema `$schema` should be `https://json-schema.org/draft/2020-12/schema` or `https://json-schema.org/draft-07/schema` \n Found `{schema_draft}`")
 
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
         schema_defs = dict()
-        defs_notation = ""
-        if "$defs" in schema:
-            schema_defs = schema.get("$defs", {}).items()
-            defs_notation = "$defs"
-        elif "definitions" in schema:
-            schema_defs = schema.get("definitions", {}).items()
-            defs_notation = "definitions"
-        elif "defs" in schema:
-            # nf-schema v2.0.0 only supported defs. this has been changed to $defs in nf-schema v2.1.0
-            # this line prevents the breakage of schemas created for v2.0.0
-            schema_defs = schema.get("defs", {}).items()
-            defs_notation = "defs"
+        defs_notation = self.get_defs_notation(schema)
 
-        for d_key, d_schema in schema_defs:
+        for d_key, d_schema in schema.get(defs_notation, {}).items():
             # Check that this definition is mentioned in allOf
             if "allOf" not in schema:
                 raise AssertionError("Schema has definitions, but no allOf key")
@@ -428,7 +439,7 @@ def validate_schema(self, schema=None):
     def validate_schema_title_description(self, schema=None):
         """
         Extra validation command for linting.
-        Checks that the schema "$id", "title" and "description" attributes match the piipeline config.
+        Checks that the schema "$id", "title" and "description" attributes match the pipeline config.
         """
         if schema is None:
             schema = self.schema
@@ -436,12 +447,6 @@ def validate_schema_title_description(self, schema=None):
             log.debug("Pipeline schema not set - skipping validation of top-level attributes")
             return None
 
-        if "$schema" not in self.schema:
-            raise AssertionError("Schema missing top-level `$schema` attribute")
-        schema_attr = "http://json-schema.org/draft-07/schema"
-        if self.schema["$schema"] != schema_attr:
-            raise AssertionError(f"Schema `$schema` should be `{schema_attr}`\n Found `{self.schema['$schema']}`")
-
         if self.pipeline_manifest == {}:
             self.get_wf_params()
 

From 6ecde202d05baa2944f582f0b0835ea73765006b Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 16:11:47 +0200
Subject: [PATCH 255/414] fix draft 7 schema using http

---
 nf_core/pipelines/schema.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 398783d5a8..e1931b9007 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -383,7 +383,7 @@ def validate_schema(self, schema=None):
         if "$schema" not in schema:
             raise AssertionError("Schema missing top-level `$schema` attribute")
         schema_draft = schema["$schema"]
-        if schema_draft == "https://json-schema.org/draft-07/schema":
+        if schema_draft == "https://json-schema.org/draft-07/schema" or schema_draft == "http://json-schema.org/draft-07/schema":
             try:
                 jsonschema.Draft7Validator.check_schema(schema)
                 log.debug("JSON Schema Draft7 validated")

From 36fad24c7eda672fce4a885fe2e7d5610b022a9c Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 16:18:08 +0200
Subject: [PATCH 256/414] ruff

---
 nf_core/pipelines/schema.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index e1931b9007..188861fff1 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -400,7 +400,6 @@ def validate_schema(self, schema=None):
 
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
-        schema_defs = dict()
         defs_notation = self.get_defs_notation(schema)
 
         for d_key, d_schema in schema.get(defs_notation, {}).items():
@@ -424,11 +423,11 @@ def validate_schema(self, schema=None):
 
         # Check that everything in allOf exists
         for allOf in schema.get("allOf", []):
-            _, allOf_defs_notation, def_key = allOf["$ref"].split("/") # "#/<defs_notation>/<def_name>"
-            if allOf_defs_notation not in schema:
-                raise AssertionError(f"Schema has allOf, but no {allOf_defs_notation}")
-            if def_key not in schema.get(allOf_defs_notation, {}):
-                raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `{allOf_defs_notation}`")
+            _, allof_defs_notation, def_key = allOf["$ref"].split("/") # "#/<defs_notation>/<def_name>"
+            if allof_defs_notation not in schema:
+                raise AssertionError(f"Schema has allOf, but no {allof_defs_notation}")
+            if def_key not in schema.get(allof_defs_notation, {}):
+                raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `{allof_defs_notation}`")
 
         # Check that the schema describes at least one parameter
         if num_params == 0:

From 6777694b20726f333dd8eae416917c3324c3e158 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 16:33:00 +0200
Subject: [PATCH 257/414] fix tests + add draft 2020-12 as default draft

---
 nf_core/pipelines/schema.py    | 2 ++
 tests/pipelines/test_schema.py | 5 ++++-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 188861fff1..1555a4198d 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -46,6 +46,8 @@ def __init__(self):
         self.web_schema_build_url = "https://nf-co.re/pipeline_schema_builder"
         self.web_schema_build_web_url = None
         self.web_schema_build_api_url = None
+        self.schema_draft = "https://json-schema.org/draft/2020-12/schema"
+        self.defs_notation = "$defs"
 
     def get_schema_path(
         self, path: Union[str, Path], local_only: bool = False, revision: Union[str, None] = None
diff --git a/tests/pipelines/test_schema.py b/tests/pipelines/test_schema.py
index 633de3db69..777d959e66 100644
--- a/tests/pipelines/test_schema.py
+++ b/tests/pipelines/test_schema.py
@@ -175,6 +175,7 @@ def test_validate_schema_fail_duplicate_ids(self):
         Check that the schema validation fails when we have duplicate IDs in definition subschema
         """
         self.schema_obj.schema = {
+            "$schema": "http://json-schema.org/draft-07/schema",
             "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"foo": {}}}},
             "allOf": [{"$ref": "#/definitions/groupOne"}, {"$ref": "#/definitions/groupTwo"}],
         }
@@ -187,18 +188,20 @@ def test_validate_schema_fail_missing_def(self):
         Check that the schema validation fails when we a definition in allOf is not in definitions
         """
         self.schema_obj.schema = {
+            "$schema": "http://json-schema.org/draft-07/schema",
             "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
             "allOf": [{"$ref": "#/definitions/groupOne"}],
         }
         with pytest.raises(AssertionError) as exc_info:
             self.schema_obj.validate_schema(self.schema_obj.schema)
-        assert exc_info.value.args[0] == "Definition subschema `groupTwo` not included in schema `allOf`"
+        assert exc_info.value.args[0] == "Definition subschema `#/definitions/groupTwo` not included in schema `allOf`"
 
     def test_validate_schema_fail_unexpected_allof(self):
         """
         Check that the schema validation fails when we an unrecognised definition is in allOf
         """
         self.schema_obj.schema = {
+            "$schema": "http://json-schema.org/draft-07/schema",
             "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
             "allOf": [
                 {"$ref": "#/definitions/groupOne"},

From 0dfd15ded935054fc8d185b5fd36223505441ff7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 16:34:01 +0200
Subject: [PATCH 258/414] fix typo

---
 nf_core/pipelines/schema.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 1555a4198d..ba5af51f96 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -413,7 +413,7 @@ def validate_schema(self, schema=None):
                 if allOf["$ref"] == f"#/{defs_notation}/{d_key}":
                     in_allOf = True
             if not in_allOf:
-                raise AssertionError(f"Definition subschema `#{defs_notation}/{d_key}` not included in schema `allOf`")
+                raise AssertionError(f"Definition subschema `#/{defs_notation}/{d_key}` not included in schema `allOf`")
 
             # TODO add support for nested parameters
             for d_param_id in d_schema.get("properties", {}):

From 7f29f373a82ed1ada16b6b493f10d724a4b879cc Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 16:37:06 +0200
Subject: [PATCH 259/414] ruff

---
 nf_core/pipelines/schema.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index ba5af51f96..43058d4e6f 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -119,7 +119,7 @@ def load_schema(self):
         self.schema_defaults = {}
         self.schema_params = {}
         if "$schema" not in self.schema:
-            raise AssertionError("Schema missing top-level `$schema` attribute")        
+            raise AssertionError("Schema missing top-level `$schema` attribute")
         self.schema_draft = self.schema["$schema"]
         self.defs_notation = self.get_defs_notation()
         log.debug(f"JSON file loaded: {self.schema_filename}")
@@ -385,7 +385,10 @@ def validate_schema(self, schema=None):
         if "$schema" not in schema:
             raise AssertionError("Schema missing top-level `$schema` attribute")
         schema_draft = schema["$schema"]
-        if schema_draft == "https://json-schema.org/draft-07/schema" or schema_draft == "http://json-schema.org/draft-07/schema":
+        if (
+            schema_draft == "https://json-schema.org/draft-07/schema"
+            or schema_draft == "http://json-schema.org/draft-07/schema"
+        ):
             try:
                 jsonschema.Draft7Validator.check_schema(schema)
                 log.debug("JSON Schema Draft7 validated")
@@ -398,7 +401,9 @@ def validate_schema(self, schema=None):
             except jsonschema.exceptions.SchemaError as e:
                 raise AssertionError(f"Schema does not validate as Draft 2020-12 JSON Schema:\n {e}")
         else:
-            raise AssertionError(f"Schema `$schema` should be `https://json-schema.org/draft/2020-12/schema` or `https://json-schema.org/draft-07/schema` \n Found `{schema_draft}`")
+            raise AssertionError(
+                f"Schema `$schema` should be `https://json-schema.org/draft/2020-12/schema` or `https://json-schema.org/draft-07/schema` \n Found `{schema_draft}`"
+            )
 
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
@@ -425,7 +430,7 @@ def validate_schema(self, schema=None):
 
         # Check that everything in allOf exists
         for allOf in schema.get("allOf", []):
-            _, allof_defs_notation, def_key = allOf["$ref"].split("/") # "#/<defs_notation>/<def_name>"
+            _, allof_defs_notation, def_key = allOf["$ref"].split("/")  # "#/<defs_notation>/<def_name>"
             if allof_defs_notation not in schema:
                 raise AssertionError(f"Schema has allOf, but no {allof_defs_notation}")
             if def_key not in schema.get(allof_defs_notation, {}):

From 730c6779779d4e14512df25c043eb02efe6d1659 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 17:34:53 +0200
Subject: [PATCH 260/414] add checks for nf-validation and nf-schema plugin
 config

---
 nf_core/pipelines/lint/nextflow_config.py | 33 +++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 96323af94d..8fe933d102 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -336,6 +336,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             )
 
     # Check for the availability of the "test" configuration profile by parsing nextflow.config
+    # Also check for the presence of nf-validation/nf-schema and check if they have pinned versions
     with open(Path(self.wf_path, "nextflow.config")) as f:
         content = f.read()
 
@@ -363,6 +364,38 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             else:
                 failed.append("nextflow.config does not contain configuration profile `test`")
 
+        match_plugins = re.search(r"\bplugins\s*\{([^}]+)}", cleaned_content, re.MULTILINE)
+        if not match_plugins:
+            failed.append(
+                "nextflow.config does not contain `plugins` scope, but `nf-validation` or `nf-schema` plugins are required"
+            )
+        else:
+            found_plugins = {}
+            for line in match_plugins.group(1).split("\n"):
+                cleaned_line = line.split("//")[0].strip().replace("\"", "'")
+                if "id" not in line: continue
+                match_line = re.search(r"\bid\s'([^']+)'", cleaned_line)
+                if not match_line:
+                    failed.append(f"nextflow.config contains an invalid plugins identifier: {cleaned_line}")
+                    continue
+                plugin = match_line.group(1)
+                name = plugin.split("@")[0]
+                version = ""
+                if "@" in plugin:
+                    version = plugin.split("@")[1]
+                found_plugins[name] = version
+
+            if len(found_plugins) == 0:
+                failed.append("nextflow.config contains an empty plugins scope")
+            elif "nf-validation" in found_plugins and "nf-schema" in found_plugins:
+                failed.append("nextflow.config contains both nf-validation and nf-schema")
+            elif "nf-validation" in found_plugins and found_plugins["nf-validation"] == "":
+                failed.append("nextflow.config contains an unpinned version of nf-validation")
+            elif "nf-schema" in found_plugins and found_plugins["nf-schema"] == "":
+                failed.append("nextflow.config contains an unpinned version of nf-schema")
+            elif "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
+                failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
+
     # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json
     ignore_defaults = []
     for item in ignore_configs:

From 7fbbff7a412c64ef67417dd60a722d67f6d37647 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 17:39:10 +0200
Subject: [PATCH 261/414] linting fully works now!

---
 nf_core/pipelines/lint/schema_description.py | 5 +++--
 nf_core/pipelines/schema.py                  | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipelines/lint/schema_description.py b/nf_core/pipelines/lint/schema_description.py
index d617e40949..b586cc5242 100644
--- a/nf_core/pipelines/lint/schema_description.py
+++ b/nf_core/pipelines/lint/schema_description.py
@@ -36,8 +36,9 @@ def schema_description(self):
                 warned.append(f"Ungrouped param in schema: `{up}`")
 
     # Iterate over groups and add warning for parameters without a description
-    for group_key in self.schema_obj.schema["definitions"].keys():
-        group = self.schema_obj.schema["definitions"][group_key]
+    defs_notation = self.schema_obj.defs_notation
+    for group_key in self.schema_obj.schema[defs_notation].keys():
+        group = self.schema_obj.schema[defs_notation][group_key]
         for param_key, param in group["properties"].items():
             if param_key in ignore_params:
                 ignored.append(f"Ignoring description check for param in schema: `{param_key}`")
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 43058d4e6f..c70332beb2 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -203,7 +203,7 @@ def get_schema_types(self) -> None:
         for name, param in self.schema.get("properties", {}).items():
             if "type" in param:
                 self.schema_types[name] = param["type"]
-        for _, definition in self.schema.get("definitions", {}).items():
+        for _, definition in self.schema.get(self.defs_notation, {}).items():
             for name, param in definition.get("properties", {}).items():
                 if "type" in param:
                     self.schema_types[name] = param["type"]

From 1c69f9d84e5c342a54ed733c4497de53ee8c1cea Mon Sep 17 00:00:00 2001
From: laurencekuhl <laurence.kuhlburger@gmail.com>
Date: Thu, 15 Aug 2024 15:37:21 +0200
Subject: [PATCH 262/414] Add a verbose click option

---
 nf_core/__main__.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 153b8b7e75..7da60180cd 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1136,6 +1136,13 @@ def command_modules_create(
 @modules.command("test")
 @click.pass_context
 @click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.option(
+    "-v",
+    "--verbose",
+    is_flag=True,
+    default=False,
+    help="Print verbose output to the console.",
+)
 @click.option(
     "-d",
     "--dir",
@@ -1171,11 +1178,11 @@ def command_modules_create(
     default=False,
     help="Migrate a module with pytest tests to nf-test",
 )
-def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest):
+def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest, verbose):
     """
     Run nf-test for a module.
     """
-    modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest)
+    modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest, verbose)
 
 
 # nf-core modules lint

From 9f6c1f4710ee10d094b0b9b1e011c891d62e5b8c Mon Sep 17 00:00:00 2001
From: laurencekuhl <laurence.kuhlburger@gmail.com>
Date: Thu, 15 Aug 2024 16:44:24 +0200
Subject: [PATCH 263/414] Overwrite the verbose in ctx in case the user uses it

---
 nf_core/__main__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 7da60180cd..64956e5f3f 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1182,7 +1182,8 @@ def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile
     """
     Run nf-test for a module.
     """
-    modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest, verbose)
+    ctx.obj['verbose'] = verbose
+    modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest)
 
 
 # nf-core modules lint

From 7d873b5a456e6a13f77c4a8a6ff8f947b5eafc04 Mon Sep 17 00:00:00 2001
From: laurencekuhl <laurence.kuhlburger@gmail.com>
Date: Thu, 15 Aug 2024 16:44:46 +0200
Subject: [PATCH 264/414] Overwrite the verbose in ctx in case the user uses it

---
 nf_core/__main__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 64956e5f3f..3b56bda66c 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1182,7 +1182,8 @@ def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile
     """
     Run nf-test for a module.
     """
-    ctx.obj['verbose'] = verbose
+    if verbose:
+        ctx.obj['verbose'] = verbose
     modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest)
 
 

From 22a18a4273bd4db1c2343a90742c1b5b9a3b62eb Mon Sep 17 00:00:00 2001
From: laurencekuhl <laurence.kuhlburger@gmail.com>
Date: Thu, 15 Aug 2024 16:48:05 +0200
Subject: [PATCH 265/414] add matthias' suggestion woops

---
 nf_core/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 3b56bda66c..23930ccd3c 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1141,7 +1141,7 @@ def command_modules_create(
     "--verbose",
     is_flag=True,
     default=False,
-    help="Print verbose output to the console.",
+    help="Print verbose output to the console. Sets `--debug` inside the nf-test command.",
 )
 @click.option(
     "-d",

From 7aead16a057bc0e30344aec26d4e12d9512bfa11 Mon Sep 17 00:00:00 2001
From: laurencekuhl <laurence.kuhlburger@gmail.com>
Date: Thu, 15 Aug 2024 17:26:25 +0200
Subject: [PATCH 266/414] Ran pre commit

---
 nf_core/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 23930ccd3c..0efea13ec9 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1183,7 +1183,7 @@ def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile
     Run nf-test for a module.
     """
     if verbose:
-        ctx.obj['verbose'] = verbose
+        ctx.obj["verbose"] = verbose
     modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest)
 
 

From e5714d3cccdfce236c6c3ee3878282761d598be2 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 16 Aug 2024 04:56:51 +0000
Subject: [PATCH 267/414] Update pre-commit hook astral-sh/ruff-pre-commit to
 v0.6.0

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 815e980270..4f08d8419d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.6
+    rev: v0.6.0
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

From 5da0e06d4f7b55e1ec8851c85380b36dbad7919e Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Fri, 16 Aug 2024 04:57:40 +0000
Subject: [PATCH 268/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bc78a1628a..ddc346b9dc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -69,6 +69,7 @@
 - Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094))
 - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102))
 - Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 ([#3122](https://github.com/nf-core/tools/pull/3122))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From 85461c5e47c7527e4879513e90c7150b19bb9013 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 16 Aug 2024 15:34:04 +0000
Subject: [PATCH 269/414] Update python:3.12-slim Docker digest to 59c7332

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index c88abcb1ce..fb1a867937 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:740d94a19218c8dd584b92f804b1158f85b0d241e5215ea26ed2dcade2b9d138
+FROM python:3.12-slim@sha256:59c7332a4a24373861c4a5f0eec2c92b87e3efeb8ddef011744ef9a751b1d11c
 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for nf-core/tools"
 

From 129858342d0529ef59f1f04f7da0332fec038a1a Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Sat, 17 Aug 2024 16:36:57 +0000
Subject: [PATCH 270/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ddc346b9dc..0a450a6728 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -70,6 +70,7 @@
 - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102))
 - Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 ([#3122](https://github.com/nf-core/tools/pull/3122))
+- Update python:3.12-slim Docker digest to 59c7332 ([#3124](https://github.com/nf-core/tools/pull/3124))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From 0838d6bb040b8218493fad13c5fc33fa355b84af Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 19 Aug 2024 14:58:27 +0200
Subject: [PATCH 271/414] warning for nf-validation

---
 nf_core/pipelines/lint/nextflow_config.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 8fe933d102..84bb492cb0 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -396,6 +396,9 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             elif "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
                 failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
 
+            if "nf-validation" in found_plugins:
+                warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
+
     # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json
     ignore_defaults = []
     for item in ignore_configs:

From 8559c2d6a18624c5096957e6a941011c8725e580 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 19 Aug 2024 16:54:38 +0200
Subject: [PATCH 272/414] fetch plugin on schema filename setting

---
 nf_core/pipelines/lint/nextflow_config.py |  1 +
 nf_core/pipelines/schema.py               | 81 +++++++++++++++--------
 2 files changed, 54 insertions(+), 28 deletions(-)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 84bb492cb0..a5b7cf325f 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -364,6 +364,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             else:
                 failed.append("nextflow.config does not contain configuration profile `test`")
 
+        # Lint for nf-validation and nf-schema
         match_plugins = re.search(r"\bplugins\s*\{([^}]+)}", cleaned_content, re.MULTILINE)
         if not match_plugins:
             failed.append(
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index c70332beb2..77f421724e 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -5,6 +5,7 @@
 import logging
 import tempfile
 import webbrowser
+import re
 from pathlib import Path
 from typing import Union
 
@@ -32,7 +33,7 @@ def __init__(self):
 
         self.schema = {}
         self.pipeline_dir = ""
-        self.schema_filename = ""
+        self._schema_filename = ""
         self.schema_defaults = {}
         self.schema_types = {}
         self.schema_params = {}
@@ -46,8 +47,46 @@ def __init__(self):
         self.web_schema_build_url = "https://nf-co.re/pipeline_schema_builder"
         self.web_schema_build_web_url = None
         self.web_schema_build_api_url = None
-        self.schema_draft = "https://json-schema.org/draft/2020-12/schema"
-        self.defs_notation = "$defs"
+        self.validation_plugin = None
+        self.schema_draft = None
+        self.defs_notation = None
+
+    # Update the validation plugin code everytime the schema gets changed
+    def set_schema_filename(self, schema: str) -> None:
+        self._schema_filename = schema
+        basepath = "/".join(str(schema).split("/")[:-1])
+        config = f"{basepath}/nextflow.config" if basepath != "" else "nextflow.config"
+        self._update_validation_plugin_from_config(config)
+    
+    def get_schema_filename(self) -> str:
+        return self._schema_filename
+    
+    def del_schema_filename(self) -> None:
+        del self._schema_filename
+
+    schema_filename = property(get_schema_filename, set_schema_filename, del_schema_filename)
+
+    def _update_validation_plugin_from_config(self, config: str) -> None:
+        plugin = "nf-schema"
+        with open(Path(config)) as conf:
+            nf_schema_pattern = re.compile("id\s*[\"']nf-schema", re.MULTILINE)
+            nf_validation_pattern = re.compile("id\s*[\"']nf-validation", re.MULTILINE)
+            config_content = conf.read()
+            if re.search(nf_validation_pattern, config_content):
+                plugin = "nf-validation"
+            elif re.search(nf_schema_pattern, config_content):
+                plugin = "nf-schema"
+            else:
+                log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema")
+            
+        self.validation_plugin = plugin
+        # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
+        if plugin == "nf-schema":
+            self.defs_notation = "$defs"
+            self.schema_draft = "https://json-schema.org/draft/2020-12/schema"
+        else:
+            self.defs_notation = "definitions"
+            self.schema_draft = "https://json-schema.org/draft-07/schema"
 
     def get_schema_path(
         self, path: Union[str, Path], local_only: bool = False, revision: Union[str, None] = None
@@ -120,24 +159,8 @@ def load_schema(self):
         self.schema_params = {}
         if "$schema" not in self.schema:
             raise AssertionError("Schema missing top-level `$schema` attribute")
-        self.schema_draft = self.schema["$schema"]
-        self.defs_notation = self.get_defs_notation()
         log.debug(f"JSON file loaded: {self.schema_filename}")
 
-    def get_defs_notation(self, schema=None):
-        if schema is None:
-            schema = self.schema
-
-        if "$defs" in schema:
-            defs_notation = "$defs"
-        elif "definitions" in schema:
-            defs_notation = "definitions"
-        elif "defs" in schema:
-            # nf-schema v2.0.0 only supported defs. this has been changed to $defs in nf-schema v2.1.0
-            # this line prevents the breakage of schemas created for v2.0.0
-            defs_notation = "defs"
-        return defs_notation
-
     def sanitise_param_default(self, param):
         """
         Given a param, ensure that the default value is the correct variable type
@@ -385,16 +408,15 @@ def validate_schema(self, schema=None):
         if "$schema" not in schema:
             raise AssertionError("Schema missing top-level `$schema` attribute")
         schema_draft = schema["$schema"]
-        if (
-            schema_draft == "https://json-schema.org/draft-07/schema"
-            or schema_draft == "http://json-schema.org/draft-07/schema"
-        ):
+        if self.schema_draft != schema_draft:
+            raise AssertionError(f"Schema is using the wrong draft: {schema_draft}, should be {self.schema_draft}")
+        if self.schema_draft == "https://json-schema.org/draft-07/schema":
             try:
                 jsonschema.Draft7Validator.check_schema(schema)
                 log.debug("JSON Schema Draft7 validated")
             except jsonschema.exceptions.SchemaError as e:
                 raise AssertionError(f"Schema does not validate as Draft 7 JSON Schema:\n {e}")
-        elif schema_draft == "https://json-schema.org/draft/2020-12/schema":
+        elif self.schema_draft == "https://json-schema.org/draft/2020-12/schema":
             try:
                 jsonschema.Draft202012Validator.check_schema(schema)
                 log.debug("JSON Schema Draft2020-12 validated")
@@ -407,18 +429,21 @@ def validate_schema(self, schema=None):
 
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
-        defs_notation = self.get_defs_notation(schema)
 
-        for d_key, d_schema in schema.get(defs_notation, {}).items():
+        print(self.defs_notation)
+
+        for d_key, d_schema in schema.get(self.defs_notation, {}).items():
+            print(d_key)
+            print(d_schema)
             # Check that this definition is mentioned in allOf
             if "allOf" not in schema:
                 raise AssertionError("Schema has definitions, but no allOf key")
             in_allOf = False
             for allOf in schema.get("allOf", []):
-                if allOf["$ref"] == f"#/{defs_notation}/{d_key}":
+                if allOf["$ref"] == f"#/{self.defs_notation}/{d_key}":
                     in_allOf = True
             if not in_allOf:
-                raise AssertionError(f"Definition subschema `#/{defs_notation}/{d_key}` not included in schema `allOf`")
+                raise AssertionError(f"Definition subschema `#/{self.defs_notation}/{d_key}` not included in schema `allOf`")
 
             # TODO add support for nested parameters
             for d_param_id in d_schema.get("properties", {}):

From 0296f7d8fa6c5cc7a8dac62b450a8babcd77bab7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 19 Aug 2024 17:00:33 +0200
Subject: [PATCH 273/414] add a check for defs usage instead of $defs

---
 nf_core/pipelines/schema.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 77f421724e..9c65f34fde 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -430,11 +430,11 @@ def validate_schema(self, schema=None):
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
 
-        print(self.defs_notation)
+        # Add a small check for older nf-schema JSON schemas
+        if "defs" in schema:
+            raise AssertionError(f'Using "defs" for schema definitions is not supported. Please use {self.defs_notation} instead')
 
         for d_key, d_schema in schema.get(self.defs_notation, {}).items():
-            print(d_key)
-            print(d_schema)
             # Check that this definition is mentioned in allOf
             if "allOf" not in schema:
                 raise AssertionError("Schema has definitions, but no allOf key")

From 0b8d04f89eb7f348bce87cc93f04d983e48e218f Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 19 Aug 2024 17:16:31 +0200
Subject: [PATCH 274/414] change all definitions to self.defs_notation

---
 nf_core/pipelines/schema.py | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 9c65f34fde..9db9457516 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -235,7 +235,7 @@ def save_schema(self, suppress_logging=False):
         """Save a pipeline schema to a file"""
         # Write results to a JSON file
         num_params = len(self.schema.get("properties", {}))
-        num_params += sum(len(d.get("properties", {})) for d in self.schema.get("definitions", {}).values())
+        num_params += sum(len(d.get("properties", {})) for d in self.schema.get(self.defs_notation, {}).values())
         if not suppress_logging:
             log.info(f"Writing schema with {num_params} params: '{self.schema_filename}'")
         dump_json_with_prettier(self.schema_filename, self.schema)
@@ -321,7 +321,7 @@ def validate_default_params(self):
             params_ignore = []
 
         # Go over group keys
-        for group_key, group in schema_no_required.get("definitions", {}).items():
+        for group_key, group in schema_no_required.get(self.defs_notation, {}).items():
             group_properties = group.get("properties")
             for param in group_properties:
                 if param in params_ignore:
@@ -527,9 +527,9 @@ def check_for_input_mimetype(self):
         if "input" not in self.schema_params:
             raise LookupError("Parameter `input` not found in schema")
         # Check that the input parameter is defined in the right place
-        if "input" not in self.schema.get("definitions", {}).get("input_output_options", {}).get("properties", {}):
+        if "input" not in self.schema.get(self.defs_notation, {}).get("input_output_options", {}).get("properties", {}):
             raise LookupError("Parameter `input` is not defined in the correct subschema (input_output_options)")
-        input_entry = self.schema["definitions"]["input_output_options"]["properties"]["input"]
+        input_entry = self.schema[self.defs_notation]["input_output_options"]["properties"]["input"]
         if "mimetype" not in input_entry:
             return None
         mimetype = input_entry["mimetype"]
@@ -581,7 +581,7 @@ def schema_to_markdown(self, columns):
         out = f"# {self.schema['title']}\n\n"
         out += f"{self.schema['description']}\n"
         # Grouped parameters
-        for definition in self.schema.get("definitions", {}).values():
+        for definition in self.schema.get(self.defs_notation, {}).values():
             out += f"\n## {definition.get('title', {})}\n\n"
             out += f"{definition.get('description', '')}\n\n"
             required = definition.get("required", [])
@@ -763,15 +763,15 @@ def remove_schema_empty_definitions(self):
         """
         # Identify and remove empty definitions from the schema
         empty_definitions = []
-        for d_key, d_schema in list(self.schema.get("definitions", {}).items()):
+        for d_key, d_schema in list(self.schema.get(self.defs_notation, {}).items()):
             if not d_schema.get("properties"):
-                del self.schema["definitions"][d_key]
+                del self.schema[self.defs_notation][d_key]
                 empty_definitions.append(d_key)
                 log.warning(f"Removing empty group: '{d_key}'")
 
         # Remove "allOf" group with empty definitions from the schema
         for d_key in empty_definitions:
-            allOf = {"$ref": f"#/definitions/{d_key}"}
+            allOf = {"$ref": f"#/{self.defs_notation}/{d_key}"}
             if allOf in self.schema.get("allOf", []):
                 self.schema["allOf"].remove(allOf)
 
@@ -780,8 +780,8 @@ def remove_schema_empty_definitions(self):
             del self.schema["allOf"]
 
         # If we don't have anything left in "definitions", remove it
-        if self.schema.get("definitions") == {}:
-            del self.schema["definitions"]
+        if self.schema.get(self.defs_notation) == {}:
+            del self.schema[self.defs_notation]
 
     def remove_schema_notfound_configs(self):
         """
@@ -791,9 +791,9 @@ def remove_schema_notfound_configs(self):
         # Top-level properties
         self.schema, params_removed = self.remove_schema_notfound_configs_single_schema(self.schema)
         # Sub-schemas in definitions
-        for d_key, definition in self.schema.get("definitions", {}).items():
+        for d_key, definition in self.schema.get(self.defs_notation, {}).items():
             cleaned_schema, p_removed = self.remove_schema_notfound_configs_single_schema(definition)
-            self.schema["definitions"][d_key] = cleaned_schema
+            self.schema[self.defs_notation][d_key] = cleaned_schema
             params_removed.extend(p_removed)
 
         return params_removed

From 544381310c6e5ac57664524f63105441246c34fd Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 19 Aug 2024 18:33:52 +0200
Subject: [PATCH 275/414] migrate template part 1

---
 nf_core/pipeline-template/conf/colors.config  |  61 ++++++++
 nf_core/pipeline-template/nextflow.config     |  44 ++++--
 .../pipeline-template/nextflow_schema.json    |  55 +++----
 .../utils_nfcore_pipeline_pipeline/main.nf    |  17 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     |  46 ------
 .../nf-core/utils_nfvalidation_plugin/main.nf |  25 +--
 .../tests/main.nf.test                        | 145 +-----------------
 .../tests/nextflow.config                     |   1 +
 .../pipeline-template/workflows/pipeline.nf   |   2 +-
 9 files changed, 130 insertions(+), 266 deletions(-)
 create mode 100644 nf_core/pipeline-template/conf/colors.config
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config

diff --git a/nf_core/pipeline-template/conf/colors.config b/nf_core/pipeline-template/conf/colors.config
new file mode 100644
index 0000000000..00f2963267
--- /dev/null
+++ b/nf_core/pipeline-template/conf/colors.config
@@ -0,0 +1,61 @@
+// For now, there is no easy way to set monochromeLogs
+colors {
+    // Reset / Meta
+    reset      = "\033[0m"
+    bold       = "\033[1m"
+    dim        = "\033[2m"
+    underlined = "\033[4m"
+    blink      = "\033[5m"
+    reverse    = "\033[7m"
+    hidden     = "\033[8m"
+
+    // Regular Colors
+    black      = "\033[0;30m"
+    red        = "\033[0;31m"
+    green      = "\033[0;32m"
+    yellow     = "\033[0;33m"
+    blue       = "\033[0;34m"
+    purple     = "\033[0;35m"
+    cyan       = "\033[0;36m"
+    white      = "\033[0;37m"
+
+    // Bold
+    bblack     = "\033[1;30m"
+    bred       = "\033[1;31m"
+    bgreen     = "\033[1;32m"
+    byellow    = "\033[1;33m"
+    bblue      = "\033[1;34m"
+    bpurple    = "\033[1;35m"
+    bcyan      = "\033[1;36m"
+    bwhite     = "\033[1;37m"
+
+    // Underline
+    ublack     = "\033[4;30m"
+    ured       = "\033[4;31m"
+    ugreen     = "\033[4;32m"
+    uyellow    = "\033[4;33m"
+    ublue      = "\033[4;34m"
+    upurple    = "\033[4;35m"
+    ucyan      = "\033[4;36m"
+    uwhite     = "\033[4;37m"
+
+    // High Intensity
+    iblack     = "\033[0;90m"
+    ired       = "\033[0;91m"
+    igreen     = "\033[0;92m"
+    iyellow    = "\033[0;93m"
+    iblue      = "\033[0;94m"
+    ipurple    = "\033[0;95m"
+    icyan      = "\033[0;96m"
+    iwhite     = "\033[0;97m"
+
+    // Bold High Intensity
+    biblack    = "\033[1;90m"
+    bired      = "\033[1;91m"
+    bigreen    = "\033[1;92m"
+    biyellow   = "\033[1;93m"
+    biblue     = "\033[1;94m"
+    bipurple   = "\033[1;95m"
+    bicyan     = "\033[1;96m"
+    biwhite    = "\033[1;97m"
+}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 0469d6cfec..3d3841ba49 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -38,6 +38,8 @@ params {
     monochrome_logs              = false
     hook_url                     = null
     help                         = false
+    helpFull                     = false
+    showHidden                   = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
 
@@ -59,10 +61,6 @@ params {
     max_time                   = '240.h'
 
     // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    validationShowHiddenParams       = false
     validate_params                  = true
 
 }
@@ -200,11 +198,6 @@ podman.registry       = 'quay.io'
 singularity.registry  = 'quay.io'
 charliecloud.registry = 'quay.io'
 
-// Nextflow plugins
-plugins {
-    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
-}
-
 {% if igenomes -%}
 // Load igenomes.config if required
 if (!params.igenomes_ignore) {
@@ -267,6 +260,39 @@ manifest {
     doi             = ''
 }
 
+// Nextflow plugins
+plugins {
+    id 'nf-schema@2.1.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+}
+
+includeConfig "conf/colors.config"
+
+validation {
+    parametersSchema = "${projectDir}/nextflow_schema.json"
+    help {
+        enabled = true
+        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        beforeText = """
+-${colors.dim}----------------------------------------------------${colors.reset}-
+                                        ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                        ${colors.green}`._,._,\'${colors.reset}
+${colors.purple}  ${manifest.name} ${manifest.version}${colors.reset}
+-${colors.dim}----------------------------------------------------${colors.reset}-
+"""
+        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+* The nf-core framework 
+  https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies
+  https://github.com/${manifest.name}/blob/master/CITATIONS.md
+"""
+    }
+}
+
+
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
 
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 4a1a22c3ee..14120bbabc 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/{{ name }}/master/nextflow_schema.json",
     "title": "{{ name }} pipeline parameters",
     "description": "{{ description }}",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -73,6 +73,20 @@
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
                     "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
+                },
+                "igenomes_base": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The base path to the igenomes reference files",
+                    "fa_icon": "fas fa-ban",
+                    "hidden": true,
+                    "default": "s3://ngi-igenomes/igenomes/"
+                },
+                "genomes": {
+                    "type": "object",
+                    "description": "An object containing all reference data availabe in igenomes",
+                    "fa_icon": "fas fa-ban",
+                    "hidden": true
                 }
             }
         },
@@ -169,12 +183,6 @@
             "description": "Less common options for the pipeline, typically set in a config file.",
             "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
             "properties": {
-                "help": {
-                    "type": "boolean",
-                    "description": "Display help text.",
-                    "fa_icon": "fas fa-question-circle",
-                    "hidden": true
-                },
                 "version": {
                     "type": "boolean",
                     "description": "Display version and exit.",
@@ -253,27 +261,6 @@
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
                 },
-                "validationShowHiddenParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-eye-slash",
-                    "description": "Show all params when using `--help`",
-                    "hidden": true,
-                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "validationFailUnrecognisedParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
-                    "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
-                },
-                "validationLenientMode": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters in lenient more.",
-                    "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
-                },
                 "pipelines_testdata_base_path": {
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
@@ -286,19 +273,19 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {% if igenomes %}{
-            "$ref": "#/definitions/reference_genome_options"
+            "$ref": "#/$defs/reference_genome_options"
         },{% endif %}
         {% if nf_core_configs %}{
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/$defs/institutional_config_options"
         },{% endif %}
         {
-            "$ref": "#/definitions/max_job_request_options"
+            "$ref": "#/$defs/max_job_request_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 72c9be85eb..c83d2ae0cb 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -9,8 +9,8 @@
 */
 
 include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-validation'
-include { fromSamplesheet           } from 'plugin/nf-validation'
+include { paramsSummaryMap          } from 'plugin/nf-schema'
+include { samplesheetToList         } from 'plugin/nf-schema'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
@@ -30,7 +30,6 @@ workflow PIPELINE_INITIALISATION {
 
     take:
     version           // boolean: Display version and exit
-    help              // boolean: Display help text
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
     monochrome_logs   // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
@@ -54,16 +53,8 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    pre_help_text = nfCoreLogo(monochrome_logs)
-    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
-    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
     UTILS_NFVALIDATION_PLUGIN (
-        help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
-        validate_params,
-        "nextflow_schema.json"
+        validate_params
     )
 
     //
@@ -84,7 +75,7 @@ workflow PIPELINE_INITIALISATION {
     // Create channel from input file provided through params.input
     //
     Channel
-        .fromSamplesheet("input")
+        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map {
             meta, fastq_1, fastq_2 ->
                 if (!fastq_2) {
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 14558c3927..a5dcd5f83d 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -61,25 +61,6 @@ def checkProfileProvided(nextflow_cli_args) {
     }
 }
 
-//
-// Citation string for pipeline
-//
-def workflowCitation() {
-    def temp_doi_ref = ""
-    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
-    // Using a loop to handle multiple DOIs
-    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
-    // Removing ` ` since the manifest.doi is a string and not a proper list
-    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-        "* The pipeline\n" +
-        temp_doi_ref + "\n" +
-        "* The nf-core framework\n" +
-        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-        "* Software dependencies\n" +
-        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-}
-
 //
 // Generate workflow version string
 //
@@ -157,33 +138,6 @@ def paramsSummaryMultiqc(summary_params) {
     return yaml_file_text
 }
 
-//
-// nf-core logo
-//
-def nfCoreLogo(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
-    String.format(
-        """\n
-        ${dashedLine(monochrome_logs)}
-                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                ${colors.green}`._,._,\'${colors.reset}
-        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
-        ${dashedLine(monochrome_logs)}
-        """.stripIndent()
-    )
-}
-
-//
-// Return dashed line
-//
-def dashedLine(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
-    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-}
-
 //
 // ANSII colours used for terminal logging
 //
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
index 2585b65d1b..453894a64a 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
@@ -8,9 +8,8 @@
 ========================================================================================
 */
 
-include { paramsHelp         } from 'plugin/nf-validation'
-include { paramsSummaryLog   } from 'plugin/nf-validation'
-include { validateParameters } from 'plugin/nf-validation'
+include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
 
 /*
 ========================================================================================
@@ -21,12 +20,7 @@ include { validateParameters } from 'plugin/nf-validation'
 workflow UTILS_NFVALIDATION_PLUGIN {
 
     take:
-    print_help       // boolean: print help
-    workflow_command //  string: default commmand used to run pipeline
-    pre_help_text    //  string: string to be printed before help text and summary log
-    post_help_text   //  string: string to be printed after help text and summary log
     validate_params  // boolean: validate parameters
-    schema_filename  //    path: JSON schema file, null to use default value
 
     main:
 
@@ -37,24 +31,11 @@ workflow UTILS_NFVALIDATION_PLUGIN {
     post_help_text   = post_help_text   ?: ''
     workflow_command = workflow_command ?: ''
 
-    //
-    // Print help message if needed
-    //
-    if (print_help) {
-        log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
-        System.exit(0)
-    }
-
-    //
-    // Print parameter summary to stdout
-    //
-    log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
-
     //
     // Validate parameters relative to the parameter JSON schema
     //
     if (validate_params){
-        validateParameters(parameters_schema: schema_filename)
+        validateParameters()
     }
 
     emit:
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
index 5784a33f2f..354b817545 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -10,30 +10,21 @@ nextflow_workflow {
     tag "utils_nfvalidation_plugin"
     tag "subworkflows/utils_nfvalidation_plugin"
 
+    config "./nextflow.config"
+
     test("Should run nothing") {
 
         when {
 
             params {
-                monochrome_logs = true
                 test_data       = ''
             }
 
             workflow {
                 """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
                 validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
 
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
+                input[0] = validate_params
                 """
             }
         }
@@ -45,147 +36,19 @@ nextflow_workflow {
         }
     }
 
-    test("Should run help") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with command") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with extra text") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = "pre-help-text"
-                post_help_text   = "post-help-text"
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('pre-help-text') } },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } },
-                { assert workflow.stdout.any { it.contains('post-help-text') } }
-            )
-        }
-    }
-
     test("Should validate params") {
 
         when {
 
             params {
-                monochrome_logs = true
                 test_data       = ''
                 outdir          = 1
             }
             workflow {
                 """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
                 validate_params  = true
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
 
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
+                input[0] = validate_params
                 """
             }
         }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config
new file mode 100644
index 0000000000..8d047ed59e
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config
@@ -0,0 +1 @@
+validation.monochromeLogs = true
\ No newline at end of file
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index d98c392f0c..4bb0913211 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -6,7 +6,7 @@
 
 include { FASTQC                 } from '../modules/nf-core/fastqc/main'
 {% if multiqc %}include { MULTIQC                } from '../modules/nf-core/multiqc/main'{% endif %}
-include { paramsSummaryMap       } from 'plugin/nf-validation'
+include { paramsSummaryMap       } from 'plugin/nf-schema'
 {% if multiqc %}include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 {% if citations or multiqc %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}

From 7931c7f658712e15d522531616c3e001849e338b Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 20 Aug 2024 12:43:06 +0200
Subject: [PATCH 276/414] add option to exclude license from pipeline template

---
 nf_core/pipelines/create/templatefeatures.yml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index b97bf347ab..dc3f072710 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -242,3 +242,18 @@ changelog:
       - "CHANGELOG.md"
   nfcore_pipelines: False
   custom_pipelines: True
+license:
+  skippable_paths:
+    - "LICENSE"
+  short_description: "Add a license"
+  description: "Add the MIT license file."
+  help_text: |
+    To protect the copyright of the pipeline, you can add a LICENSE file.
+    This option ads the MIT License. You can read the conditions here: https://opensource.org/license/MIT
+  linting:
+    files_exist:
+      - "LICENSE"
+    files_unchanged:
+      - "LICENSE"
+  nfcore_pipelines: False
+  custom_pipelines: True

From 6ff0929c0956b148839c231133b440f5f0cd876a Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 20 Aug 2024 10:46:47 +0000
Subject: [PATCH 277/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0a450a6728..b530f597bc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@
 - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104))
 - handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108))
 - add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112))
+- add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125))
 
 ### Linting
 

From 78d469fd893a6e1c45aa59330378f213a994fdbf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Tue, 20 Aug 2024 12:56:04 +0200
Subject: [PATCH 278/414] Update nf_core/pipelines/create/templatefeatures.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 nf_core/pipelines/create/templatefeatures.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index dc3f072710..a8a6ce5656 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -245,7 +245,7 @@ changelog:
 license:
   skippable_paths:
     - "LICENSE"
-  short_description: "Add a license"
+  short_description: "Add a license File"
   description: "Add the MIT license file."
   help_text: |
     To protect the copyright of the pipeline, you can add a LICENSE file.

From 34565c1e12ce20cda823e4e92eed6c084501821f Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 20 Aug 2024 13:00:04 +0200
Subject: [PATCH 279/414] update textual snapshots

---
 .../__snapshots__/test_create_app.ambr        | 512 +++++++++---------
 1 file changed, 256 insertions(+), 256 deletions(-)

diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index f4eb255087..66c08faba0 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
           font-weight: 700;
       }
   
-      .terminal-3220763577-matrix {
+      .terminal-2278814444-matrix {
           font-family: Fira Code, monospace;
           font-size: 20px;
           line-height: 24.4px;
           font-variant-east-asian: full-width;
       }
   
-      .terminal-3220763577-title {
+      .terminal-2278814444-title {
           font-size: 18px;
           font-weight: bold;
           font-family: arial;
       }
   
-      .terminal-3220763577-r1 { fill: #c5c8c6 }
-  .terminal-3220763577-r2 { fill: #e3e3e3 }
-  .terminal-3220763577-r3 { fill: #989898 }
-  .terminal-3220763577-r4 { fill: #e1e1e1 }
-  .terminal-3220763577-r5 { fill: #4ebf71;font-weight: bold }
-  .terminal-3220763577-r6 { fill: #1e1e1e }
-  .terminal-3220763577-r7 { fill: #507bb3 }
-  .terminal-3220763577-r8 { fill: #e2e2e2 }
-  .terminal-3220763577-r9 { fill: #808080 }
-  .terminal-3220763577-r10 { fill: #dde6ed;font-weight: bold }
-  .terminal-3220763577-r11 { fill: #001541 }
-  .terminal-3220763577-r12 { fill: #0178d4 }
-  .terminal-3220763577-r13 { fill: #454a50 }
-  .terminal-3220763577-r14 { fill: #e2e3e3;font-weight: bold }
-  .terminal-3220763577-r15 { fill: #000000 }
-  .terminal-3220763577-r16 { fill: #e4e4e4 }
-  .terminal-3220763577-r17 { fill: #14191f }
-  .terminal-3220763577-r18 { fill: #7ae998 }
-  .terminal-3220763577-r19 { fill: #0a180e;font-weight: bold }
-  .terminal-3220763577-r20 { fill: #008139 }
-  .terminal-3220763577-r21 { fill: #fea62b;font-weight: bold }
-  .terminal-3220763577-r22 { fill: #a7a9ab }
-  .terminal-3220763577-r23 { fill: #e2e3e3 }
+      .terminal-2278814444-r1 { fill: #c5c8c6 }
+  .terminal-2278814444-r2 { fill: #e3e3e3 }
+  .terminal-2278814444-r3 { fill: #989898 }
+  .terminal-2278814444-r4 { fill: #e1e1e1 }
+  .terminal-2278814444-r5 { fill: #4ebf71;font-weight: bold }
+  .terminal-2278814444-r6 { fill: #1e1e1e }
+  .terminal-2278814444-r7 { fill: #507bb3 }
+  .terminal-2278814444-r8 { fill: #e2e2e2 }
+  .terminal-2278814444-r9 { fill: #808080 }
+  .terminal-2278814444-r10 { fill: #dde6ed;font-weight: bold }
+  .terminal-2278814444-r11 { fill: #001541 }
+  .terminal-2278814444-r12 { fill: #0178d4 }
+  .terminal-2278814444-r13 { fill: #454a50 }
+  .terminal-2278814444-r14 { fill: #e2e3e3;font-weight: bold }
+  .terminal-2278814444-r15 { fill: #000000 }
+  .terminal-2278814444-r16 { fill: #e4e4e4 }
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From ceb78a84c90d7955e903f3ffbfa26000d62557fb Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 20 Aug 2024 15:11:26 +0200
Subject: [PATCH 280/414] add option to exclude email from pipeline template

---
 nf_core/pipeline-template/.editorconfig       |   2 +
 nf_core/pipeline-template/.prettierignore     |   2 +
 nf_core/pipeline-template/docs/output.md      |   2 +-
 nf_core/pipeline-template/main.nf             |   4 +-
 nf_core/pipeline-template/nextflow.config     |   2 +
 .../pipeline-template/nextflow_schema.json    |   8 +-
 .../utils_nfcore_pipeline_pipeline/main.nf    |   6 +
 nf_core/pipelines/create/templatefeatures.yml |  18 +
 .../__snapshots__/test_create_app.ambr        | 510 +++++++++---------
 9 files changed, 293 insertions(+), 261 deletions(-)

diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig
index 72dda289a0..5efa586109 100644
--- a/nf_core/pipeline-template/.editorconfig
+++ b/nf_core/pipeline-template/.editorconfig
@@ -25,8 +25,10 @@ insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
 
+{%- if email %}
 [/assets/email*]
 indent_size = unset
+{%- endif %}
 
 # ignore python and markdown
 [*.{py,md}]
diff --git a/nf_core/pipeline-template/.prettierignore b/nf_core/pipeline-template/.prettierignore
index 437d763d0c..3b3d5ff08e 100644
--- a/nf_core/pipeline-template/.prettierignore
+++ b/nf_core/pipeline-template/.prettierignore
@@ -1,4 +1,6 @@
+{%- if email %}
 email_template.html
+{%- endif %}
 adaptivecard.json
 slackreport.json
 .nextflow*
diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md
index edd48b83f4..76195a6825 100644
--- a/nf_core/pipeline-template/docs/output.md
+++ b/nf_core/pipeline-template/docs/output.md
@@ -55,7 +55,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 
 - `pipeline_info/`
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
-  - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
+    {% if email %}- Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. {% endif %}
   - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
   - Parameters used by the pipeline run: `params.json`.
 
diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index fddfc5489e..0cf688a7e9 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -20,7 +20,7 @@
 include { {{ short_name|upper }}  } from './workflows/{{ short_name }}'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
-{% if igenomes %}
+{%- if igenomes %}
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 
 /*
@@ -95,9 +95,11 @@ workflow {
     // SUBWORKFLOW: Run completion tasks
     //
     PIPELINE_COMPLETION (
+        {%- if email %}
         params.email,
         params.email_on_fail,
         params.plaintext_email,
+        {%- endif %}
         params.outdir,
         params.monochrome_logs,
         params.hook_url,
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 0469d6cfec..daa1c5e369 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -32,9 +32,11 @@ params {
     // Boilerplate options
     outdir                       = null
     publish_dir_mode             = 'copy'
+    {%- if email %}
     email                        = null
     email_on_fail                = null
     plaintext_email              = false
+    {%- endif %}
     monochrome_logs              = false
     hook_url                     = null
     help                         = false
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 4a1a22c3ee..4a376330bd 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -28,14 +28,14 @@
                     "format": "directory-path",
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
-                },
+                }{% if email %},
                 "email": {
                     "type": "string",
                     "description": "Email address for completion summary.",
                     "fa_icon": "fas fa-envelope",
                     "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                     "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
-                }{% if multiqc %},
+                }{% endif %}{% if multiqc %},
                 "multiqc_title": {
                     "type": "string",
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
@@ -189,7 +189,7 @@
                     "fa_icon": "fas fa-copy",
                     "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
-                },
+                },{% if email %}
                 "email_on_fail": {
                     "type": "string",
                     "description": "Email address for completion summary, only when pipeline fails.",
@@ -203,7 +203,7 @@
                     "description": "Send plain-text email instead of HTML.",
                     "fa_icon": "fas fa-remove-format",
                     "hidden": true
-                },
+                },{% endif %}
                 {%- if multiqc %}
                 "max_multiqc_email_size": {
                     "type": "string",
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 72c9be85eb..62ef73d65d 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -12,7 +12,9 @@ include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plu
 include { paramsSummaryMap          } from 'plugin/nf-validation'
 include { fromSamplesheet           } from 'plugin/nf-validation'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+{%- if email %}
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
+{%- endif %}
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
 include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
 include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
@@ -117,9 +119,11 @@ workflow PIPELINE_INITIALISATION {
 workflow PIPELINE_COMPLETION {
 
     take:
+    {%- if email %}
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
+    {% endif %}
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
@@ -133,6 +137,7 @@ workflow PIPELINE_COMPLETION {
     // Completion email and summary
     //
     workflow.onComplete {
+        {%- if email %}
         if (email || email_on_fail) {
             {%- if multiqc %}
             completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
@@ -140,6 +145,7 @@ workflow PIPELINE_COMPLETION {
             completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, [])
             {%- endif %}
         }
+        {%- endif %}
 
         completionSummary(monochrome_logs)
 
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index a8a6ce5656..5dafd7e312 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -257,3 +257,21 @@ license:
       - "LICENSE"
   nfcore_pipelines: False
   custom_pipelines: True
+email:
+  skippable_paths:
+    - "assets/email_template.html"
+    - "assets/sendmail_template.txt"
+    - "assets/email_template.txt"
+  short_description: "Enable email updates"
+  description: "Enable sending emails on pipeline completion."
+  help_text: |
+    Enable the option of sending an email which will include pipeline execution reports on pipeline completion.
+  linting:
+    files_exist:
+      - "assets/email_template.html"
+      - "assets/sendmail_template.txt"
+      - "assets/email_template.txt"
+    files_unchanged:
+      - ".prettierignore"
+  nfcore_pipelines: False
+  custom_pipelines: True
diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index 66c08faba0..f2a0578474 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
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+  </text><text class="terminal-1370375189-r6" x="0" y="1093.6" textLength="12.2" clip-path="url(#terminal-1370375189-line-44)">▊</text><text class="terminal-1370375189-r6" x="109.8" y="1093.6" textLength="12.2" clip-path="url(#terminal-1370375189-line-44)">▎</text><text class="terminal-1370375189-r4" x="122" y="1093.6" textLength="305" clip-path="url(#terminal-1370375189-line-44)">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;Include&#160;citations</text><text class="terminal-1370375189-r9" x="585.6" y="1093.6" textLength="268.4" clip-path="url(#terminal-1370375189-line-44)">Include&#160;pipeline&#160;tools</text><text class="terminal-1370375189-r10" x="976" y="1093.6" textLength="134.2" clip-path="url(#terminal-1370375189-line-44)">&#160;Show&#160;help&#160;</text><text class="terminal-1370375189-r1" x="1220" y="1093.6" textLength="12.2" clip-path="url(#terminal-1370375189-line-44)">
+  </text><text class="terminal-1370375189-r13" x="366" y="1118" textLength="195.2" clip-path="url(#terminal-1370375189-line-45)">▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔</text><text class="terminal-1370375189-r14" x="597.8" y="1118" textLength="195.2" clip-path="url(#terminal-1370375189-line-45)">▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔</text><text class="terminal-1370375189-r1" x="1220" y="1118" textLength="12.2" clip-path="url(#terminal-1370375189-line-45)">
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+  </text><text class="terminal-1370375189-r17" x="366" y="1166.8" textLength="195.2" clip-path="url(#terminal-1370375189-line-47)">▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁</text><text class="terminal-1370375189-r18" x="597.8" y="1166.8" textLength="195.2" clip-path="url(#terminal-1370375189-line-47)">▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁</text><text class="terminal-1370375189-r1" x="1220" y="1166.8" textLength="12.2" clip-path="url(#terminal-1370375189-line-47)">
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From 1390a6d5e2bb259c6004a845e212abe2b80ff167 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 20 Aug 2024 13:19:14 +0000
Subject: [PATCH 281/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b530f597bc..98fb925338 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,7 @@
 - handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108))
 - add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112))
 - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125))
+- add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126))
 
 ### Linting
 

From 5519c83d5b582af797ff4ae242fa98113bbe847a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 20 Aug 2024 15:24:51 +0200
Subject: [PATCH 282/414] some small updates for the new release

---
 nf_core/pipeline-template/conf/colors.config  | 61 -------------------
 nf_core/pipeline-template/modules.json        |  4 +-
 nf_core/pipeline-template/nextflow.config     | 22 ++++---
 .../nf-core/utils_nfschema_plugin/main.nf     | 32 ++++++++++
 .../nf-core/utils_nfschema_plugin/meta.yml    | 22 +++++++
 .../tests/main.nf.test                        | 27 ++++----
 .../tests/nextflow.config                     |  8 +++
 .../tests/nextflow_schema.json                |  8 +--
 .../nf-core/utils_nfvalidation_plugin/main.nf | 43 -------------
 .../utils_nfvalidation_plugin/meta.yml        | 44 -------------
 .../tests/nextflow.config                     |  1 -
 .../utils_nfvalidation_plugin/tests/tags.yml  |  2 -
 12 files changed, 93 insertions(+), 181 deletions(-)
 delete mode 100644 nf_core/pipeline-template/conf/colors.config
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
 rename nf_core/pipeline-template/subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/main.nf.test (62%)
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
 rename nf_core/pipeline-template/subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%)
 delete mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
 delete mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
 delete mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config
 delete mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml

diff --git a/nf_core/pipeline-template/conf/colors.config b/nf_core/pipeline-template/conf/colors.config
deleted file mode 100644
index 00f2963267..0000000000
--- a/nf_core/pipeline-template/conf/colors.config
+++ /dev/null
@@ -1,61 +0,0 @@
-// For now, there is no easy way to set monochromeLogs
-colors {
-    // Reset / Meta
-    reset      = "\033[0m"
-    bold       = "\033[1m"
-    dim        = "\033[2m"
-    underlined = "\033[4m"
-    blink      = "\033[5m"
-    reverse    = "\033[7m"
-    hidden     = "\033[8m"
-
-    // Regular Colors
-    black      = "\033[0;30m"
-    red        = "\033[0;31m"
-    green      = "\033[0;32m"
-    yellow     = "\033[0;33m"
-    blue       = "\033[0;34m"
-    purple     = "\033[0;35m"
-    cyan       = "\033[0;36m"
-    white      = "\033[0;37m"
-
-    // Bold
-    bblack     = "\033[1;30m"
-    bred       = "\033[1;31m"
-    bgreen     = "\033[1;32m"
-    byellow    = "\033[1;33m"
-    bblue      = "\033[1;34m"
-    bpurple    = "\033[1;35m"
-    bcyan      = "\033[1;36m"
-    bwhite     = "\033[1;37m"
-
-    // Underline
-    ublack     = "\033[4;30m"
-    ured       = "\033[4;31m"
-    ugreen     = "\033[4;32m"
-    uyellow    = "\033[4;33m"
-    ublue      = "\033[4;34m"
-    upurple    = "\033[4;35m"
-    ucyan      = "\033[4;36m"
-    uwhite     = "\033[4;37m"
-
-    // High Intensity
-    iblack     = "\033[0;90m"
-    ired       = "\033[0;91m"
-    igreen     = "\033[0;92m"
-    iyellow    = "\033[0;93m"
-    iblue      = "\033[0;94m"
-    ipurple    = "\033[0;95m"
-    icyan      = "\033[0;96m"
-    iwhite     = "\033[0;97m"
-
-    // Bold High Intensity
-    biblack    = "\033[1;90m"
-    bired      = "\033[1;91m"
-    bigreen    = "\033[1;92m"
-    biyellow   = "\033[1;93m"
-    biblue     = "\033[1;94m"
-    bipurple   = "\033[1;95m"
-    bicyan     = "\033[1;96m"
-    biwhite    = "\033[1;97m"
-}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index eb9391b29a..1a3b96490d 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -30,9 +30,9 @@
                         "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
-                    "utils_nfvalidation_plugin": {
+                    "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "a3e87febb28bd0461c22a917c5b2c1492053ef85",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 3d3841ba49..346292c980 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -265,22 +265,20 @@ plugins {
     id 'nf-schema@2.1.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
-includeConfig "conf/colors.config"
-
 validation {
     parametersSchema = "${projectDir}/nextflow_schema.json"
     help {
         enabled = true
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         beforeText = """
--${colors.dim}----------------------------------------------------${colors.reset}-
-                                        ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                        ${colors.green}`._,._,\'${colors.reset}
-${colors.purple}  ${manifest.name} ${manifest.version}${colors.reset}
--${colors.dim}----------------------------------------------------${colors.reset}-
+-\033[2m----------------------------------------------------\033[0m-
+                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
+\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
+\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
+\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
+                                        \033[0;32m`._,._,\'\033[0m
+\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
+-\033[2m----------------------------------------------------\033[0m-
 """
         afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
 * The nf-core framework 
@@ -290,6 +288,10 @@ ${colors.purple}  ${manifest.name} ${manifest.version}${colors.reset}
   https://github.com/${manifest.name}/blob/master/CITATIONS.md
 """
     }
+    summary {
+        beforeText = validation.help.beforeText
+        afterText = validation.help.afterText
+    }
 }
 
 
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
new file mode 100644
index 0000000000..5d1dc7c928
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -0,0 +1,32 @@
+//
+// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
+//
+
+include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
+
+workflow UTILS_NFSCHEMA_PLUGIN {
+
+    take:
+    validate_params // boolean: validate the parameters
+
+    main:
+
+    //
+    // Print parameter summary to stdout. This will display the parameters
+    // that differ from the default given in the JSON schema
+    //
+    log.info paramsSummaryLog(workflow)
+
+    //
+    // Validate the parameters using nextflow_schema.json or the schema
+    // given via the validation.parametersSchema configuration option
+    //
+    if(validate_params) {
+        validateParameters()
+    }
+
+    emit:
+    dummy_emit = true
+}
+
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
new file mode 100644
index 0000000000..90b8cb1898
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -0,0 +1,22 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "utils_nfschema_plugin"
+description: Run nf-schema to validate parameters and create a summary of changed parameters
+keywords:
+  - validation
+  - JSON schema
+  - plugin
+  - parameters
+  - summary
+components: []
+input:
+  - validate_params:
+      type: boolean
+      description: Validate the parameters and error if invalid.
+output:
+  - dummy_emit:
+      type: boolean
+      description: Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
similarity index 62%
rename from nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
rename to nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 354b817545..703d3a9b86 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -1,14 +1,14 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core subworkflows test utils_nfschema_plugin
 nextflow_workflow {
 
-    name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
+    name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
     script "../main.nf"
-    workflow "UTILS_NFVALIDATION_PLUGIN"
+    workflow "UTILS_NFSCHEMA_PLUGIN"
+
     tag "subworkflows"
     tag "subworkflows_nfcore"
-    tag "plugin/nf-validation"
-    tag "'plugin/nf-validation'"
-    tag "utils_nfvalidation_plugin"
-    tag "subworkflows/utils_nfvalidation_plugin"
+    tag "subworkflows/utils_nfschema_plugin"
 
     config "./nextflow.config"
 
@@ -17,13 +17,12 @@ nextflow_workflow {
         when {
 
             params {
-                test_data       = ''
+                test_data   = ''
             }
 
             workflow {
                 """
-                validate_params  = false
-
+                validate_params = false
                 input[0] = validate_params
                 """
             }
@@ -41,13 +40,13 @@ nextflow_workflow {
         when {
 
             params {
-                test_data       = ''
-                outdir          = 1
+                test_data   = ''
+                outdir      = 1
             }
+
             workflow {
                 """
-                validate_params  = true
-
+                validate_params = true
                 input[0] = validate_params
                 """
             }
@@ -56,7 +55,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.failed },
-                { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } }
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
             )
         }
     }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
new file mode 100644
index 0000000000..0907ac58f0
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -0,0 +1,8 @@
+plugins {
+    id "nf-schema@2.1.0"
+}
+
+validation {
+    parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+    monochromeLogs = true
+}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
similarity index 95%
rename from nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
rename to nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
index 7626c1c93e..331e0d2f44 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
     "title": ". pipeline parameters",
     "description": "",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -87,10 +87,10 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
deleted file mode 100644
index 453894a64a..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
+++ /dev/null
@@ -1,43 +0,0 @@
-//
-// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
-//
-
-/*
-========================================================================================
-    IMPORT NF-VALIDATION PLUGIN
-========================================================================================
-*/
-
-include { paramsSummaryLog   } from 'plugin/nf-schema'
-include { validateParameters } from 'plugin/nf-schema'
-
-/*
-========================================================================================
-    SUBWORKFLOW DEFINITION
-========================================================================================
-*/
-
-workflow UTILS_NFVALIDATION_PLUGIN {
-
-    take:
-    validate_params  // boolean: validate parameters
-
-    main:
-
-    log.debug "Using schema file: ${schema_filename}"
-
-    // Default values for strings
-    pre_help_text    = pre_help_text    ?: ''
-    post_help_text   = post_help_text   ?: ''
-    workflow_command = workflow_command ?: ''
-
-    //
-    // Validate parameters relative to the parameter JSON schema
-    //
-    if (validate_params){
-        validateParameters()
-    }
-
-    emit:
-    dummy_emit = true
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
deleted file mode 100644
index 3d4a6b04f5..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "UTILS_NFVALIDATION_PLUGIN"
-description: Use nf-validation to initiate and validate a pipeline
-keywords:
-  - utility
-  - pipeline
-  - initialise
-  - validation
-components: []
-input:
-  - print_help:
-      type: boolean
-      description: |
-        Print help message and exit
-  - workflow_command:
-      type: string
-      description: |
-        The command to run the workflow e.g. "nextflow run main.nf"
-  - pre_help_text:
-      type: string
-      description: |
-        Text to print before the help message
-  - post_help_text:
-      type: string
-      description: |
-        Text to print after the help message
-  - validate_params:
-      type: boolean
-      description: |
-        Validate the parameters and error if invalid.
-  - schema_filename:
-      type: string
-      description: |
-        The filename of the schema to validate against.
-output:
-  - dummy_emit:
-      type: boolean
-      description: |
-        Dummy emit to make nf-core subworkflows lint happy
-authors:
-  - "@adamrtalbot"
-maintainers:
-  - "@adamrtalbot"
-  - "@maxulysse"
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config
deleted file mode 100644
index 8d047ed59e..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config
+++ /dev/null
@@ -1 +0,0 @@
-validation.monochromeLogs = true
\ No newline at end of file
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
deleted file mode 100644
index 60b1cfff49..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfvalidation_plugin:
-  - subworkflows/nf-core/utils_nfvalidation_plugin/**

From 171640b62dddcb81feddced4f674df88c47654ab Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 20 Aug 2024 16:13:59 +0200
Subject: [PATCH 283/414] some more small updates to the template

---
 nf_core/pipeline-template/nextflow.config                     | 2 +-
 .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 346292c980..ef067dcfab 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -255,7 +255,7 @@ manifest {
     homePage        = 'https://github.com/{{ name }}'
     description     = """{{ description }}"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=23.10.0'
     version         = '{{ version }}'
     doi             = ''
 }
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index c83d2ae0cb..a994cfd584 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -8,7 +8,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
+include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
 include { paramsSummaryMap          } from 'plugin/nf-schema'
 include { samplesheetToList         } from 'plugin/nf-schema'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
@@ -53,7 +53,7 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    UTILS_NFVALIDATION_PLUGIN (
+    UTILS_NFSCHEMA_PLUGIN (
         validate_params
     )
 

From f72a2c325324dfc21d494d4135ae03da416ee709 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 20 Aug 2024 16:19:19 +0200
Subject: [PATCH 284/414] update pytest test_make_pipeline_schema

---
 tests/pipelines/test_launch.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py
index da7618d486..7c6e3d6196 100644
--- a/tests/pipelines/test_launch.py
+++ b/tests/pipelines/test_launch.py
@@ -60,7 +60,7 @@ def test_make_pipeline_schema(self, tmp_path):
         Path(test_pipeline_dir, "nextflow_schema.json").unlink()
         self.launcher = nf_core.pipelines.launch.Launch(test_pipeline_dir, params_out=self.nf_params_fn)
         self.launcher.get_pipeline_schema()
-        assert len(self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]) > 2
+        assert len(self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]) >= 2
         assert self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]["outdir"] == {
             "type": "string",
             "format": "directory-path",

From 249b3da383f17ab0beecfeb9e8346619edaf6776 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 20 Aug 2024 16:59:22 +0200
Subject: [PATCH 285/414] update handling of ignored parameters

---
 .../.github/workflows/ci.yml                  |  2 +-
 nf_core/pipeline-template/README.md           |  2 +-
 nf_core/pipelines/lint/nextflow_config.py     | 15 +++++--------
 nf_core/pipelines/schema.py                   | 22 ++++++++++++++-----
 4 files changed, 23 insertions(+), 18 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index 6b2547765d..63fa99cec8 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "23.10.0"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index 7718d2e5f8..d31dee93f4 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -16,7 +16,7 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.10.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index a5b7cf325f..150a89e102 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -65,14 +65,6 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         * Should always be set to default value:
         ``https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}``
 
-    * ``params.validationShowHiddenParams``
-
-        * Determines whether boilerplate params are showed by schema. Set to ``false`` by default
-
-    * ``params.validationSchemaIgnoreParams``
-
-        * A comma separated string of inputs the schema validation should ignore.
-
     **The following variables throw warnings if missing:**
 
     * ``manifest.mainScript``: The filename of the main pipeline script (should be ``main.nf``)
@@ -151,8 +143,11 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["process.time"],
         ["params.outdir"],
         ["params.input"],
-        ["params.validationShowHiddenParams"],
-        ["params.validationSchemaIgnoreParams"],
+        ["validation.help.enabled"],
+        ["validation.help.beforeText"],
+        ["validation.help.afterText"],
+        ["validation.summary.beforeText"],
+        ["validation.summary.afterText"]
     ]
     # Throw a warning if these are missing
     config_warn = [
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 9db9457516..78f4317094 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -50,6 +50,7 @@ def __init__(self):
         self.validation_plugin = None
         self.schema_draft = None
         self.defs_notation = None
+        self.ignored_params = []
 
     # Update the validation plugin code everytime the schema gets changed
     def set_schema_filename(self, schema: str) -> None:
@@ -69,16 +70,26 @@ def del_schema_filename(self) -> None:
     def _update_validation_plugin_from_config(self, config: str) -> None:
         plugin = "nf-schema"
         with open(Path(config)) as conf:
-            nf_schema_pattern = re.compile("id\s*[\"']nf-schema", re.MULTILINE)
-            nf_validation_pattern = re.compile("id\s*[\"']nf-validation", re.MULTILINE)
+            nf_schema_pattern = re.compile(r"id\s*[\"']nf-schema", re.MULTILINE)
+            nf_validation_pattern = re.compile(r"id\s*[\"']nf-validation", re.MULTILINE)
             config_content = conf.read()
             if re.search(nf_validation_pattern, config_content):
                 plugin = "nf-validation"
+                self.ignored_params = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
+                self.ignored_params.append("validationSchemaIgnoreParams")
             elif re.search(nf_schema_pattern, config_content):
                 plugin = "nf-schema"
+                ignored_params_pattern = re.compile(r"defaultIgnoreParams\s*=\s*\[([^\]]*)\]", re.MULTILINE)
+                ignored_params_match = re.search(ignored_params_pattern, config_content)
+                ignored_params = ["help", "helpFull", "showHidden"] # Help parameter should be ignored by default
+                if ignored_params_match and len(ignored_params_match.groups()) == 1:
+                    ignored_params.extend(ignored_params_match.group(1).replace("\"", "").replace("'", '').replace(" ", "").split(","))
+                self.ignored_params = ignored_params
             else:
                 log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema")
             
+
+            
         self.validation_plugin = plugin
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
         if plugin == "nf-schema":
@@ -845,13 +856,12 @@ def add_schema_found_configs(self):
         Update defaults if they have changed
         """
         params_added = []
-        params_ignore = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
-        params_ignore.append("validationSchemaIgnoreParams")
+
         for p_key, p_val in self.pipeline_params.items():
             s_key = self.schema_params.get(p_key)
             # Check if key is in schema parameters
             # Key is in pipeline but not in schema or ignored from schema
-            if p_key not in self.schema_params and p_key not in params_ignore:
+            if p_key not in self.schema_params and p_key not in self.ignored_params:
                 if (
                     self.no_prompts
                     or self.schema_from_scratch
@@ -884,7 +894,7 @@ def add_schema_found_configs(self):
             elif (
                 s_key
                 and (p_key not in self.schema_defaults)
-                and (p_key not in params_ignore)
+                and (p_key not in self.ignored_params)
                 and (p_def := self.build_schema_param(p_val).get("default"))
             ):
                 if self.no_prompts or Confirm.ask(

From af34d0718db98544a8da402952aea87ca778a60e Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 20 Aug 2024 17:50:32 +0200
Subject: [PATCH 286/414] update validation plugin fetching

---
 nf_core/pipeline-template/nextflow.config |  2 +-
 nf_core/pipelines/schema.py               | 58 ++++++++++++-----------
 2 files changed, 32 insertions(+), 28 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index ef067dcfab..3a98c40f0a 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -61,7 +61,7 @@ params {
     max_time                   = '240.h'
 
     // Schema validation default options
-    validate_params                  = true
+    validate_params            = true
 
 }
 
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 78f4317094..e9c5556dbb 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -69,35 +69,45 @@ def del_schema_filename(self) -> None:
 
     def _update_validation_plugin_from_config(self, config: str) -> None:
         plugin = "nf-schema"
-        with open(Path(config)) as conf:
-            nf_schema_pattern = re.compile(r"id\s*[\"']nf-schema", re.MULTILINE)
-            nf_validation_pattern = re.compile(r"id\s*[\"']nf-validation", re.MULTILINE)
-            config_content = conf.read()
-            if re.search(nf_validation_pattern, config_content):
-                plugin = "nf-validation"
-                self.ignored_params = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
-                self.ignored_params.append("validationSchemaIgnoreParams")
-            elif re.search(nf_schema_pattern, config_content):
+        conf = nf_core.utils.fetch_wf_config(Path(self.schema_filename).parent)
+
+        plugins = str(conf.get("plugins", "")).strip("\"").strip("'").strip(" ").split(",")
+        plugin_found = False
+        for plugin_instance in plugins:
+            if "nf-schema" in plugin_instance:
                 plugin = "nf-schema"
-                ignored_params_pattern = re.compile(r"defaultIgnoreParams\s*=\s*\[([^\]]*)\]", re.MULTILINE)
-                ignored_params_match = re.search(ignored_params_pattern, config_content)
-                ignored_params = ["help", "helpFull", "showHidden"] # Help parameter should be ignored by default
-                if ignored_params_match and len(ignored_params_match.groups()) == 1:
-                    ignored_params.extend(ignored_params_match.group(1).replace("\"", "").replace("'", '').replace(" ", "").split(","))
-                self.ignored_params = ignored_params
-            else:
-                log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema")
-            
+                plugin_found = True
+                break
+            elif "nf-validation" in plugin_instance:
+                plugin = "nf-validation"
+                plugin_found = True
+                break
+
+        if not plugin_found:
+            log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema")
+
+        if "nf-validation" in plugins:
+            plugin = "nf-validation"
+        elif "nf-schema" in plugins:
+            plugin = "nf-schema"
 
-            
         self.validation_plugin = plugin
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
         if plugin == "nf-schema":
             self.defs_notation = "$defs"
+            ignored_params = ["help", "helpFull", "showHidden"] # Help parameter should be ignored by default
+            ignored_params_config = conf.get("validation", {}).get("defaultIgnoreParams", [])
+            if len(ignored_params_config) > 0:
+                ignored_params.extend(ignored_params_config)
+            self.ignored_params = ignored_params
             self.schema_draft = "https://json-schema.org/draft/2020-12/schema"
+
         else:
             self.defs_notation = "definitions"
             self.schema_draft = "https://json-schema.org/draft-07/schema"
+            self.get_wf_params()
+            self.ignored_params = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
+            self.ignored_params.append("validationSchemaIgnoreParams")
 
     def get_schema_path(
         self, path: Union[str, Path], local_only: bool = False, revision: Union[str, None] = None
@@ -325,17 +335,11 @@ def validate_default_params(self):
         if self.pipeline_params == {}:
             self.get_wf_params()
 
-        # Collect parameters to ignore
-        if "validationSchemaIgnoreParams" in self.pipeline_params:
-            params_ignore = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
-        else:
-            params_ignore = []
-
         # Go over group keys
         for group_key, group in schema_no_required.get(self.defs_notation, {}).items():
             group_properties = group.get("properties")
             for param in group_properties:
-                if param in params_ignore:
+                if param in self.ignored_params:
                     continue
                 if param in self.pipeline_params:
                     self.validate_config_default_parameter(param, group_properties[param], self.pipeline_params[param])
@@ -348,7 +352,7 @@ def validate_default_params(self):
         ungrouped_properties = self.schema.get("properties")
         if ungrouped_properties:
             for param in ungrouped_properties:
-                if param in params_ignore:
+                if param in self.ignored_params:
                     continue
                 if param in self.pipeline_params:
                     self.validate_config_default_parameter(

From e6381b71c67fcc1ecb18c8b3c6e796dd6df0dec7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 21 Aug 2024 10:59:31 +0200
Subject: [PATCH 287/414] update plugin linting

---
 nf_core/pipelines/lint/nextflow_config.py | 56 ++++++++---------------
 1 file changed, 20 insertions(+), 36 deletions(-)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 150a89e102..bd2f4f768b 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -1,3 +1,4 @@
+import ast
 import logging
 import re
 from pathlib import Path
@@ -330,6 +331,25 @@ def nextflow_config(self) -> Dict[str, List[str]]:
                 )
             )
 
+    # Lint for plugins
+    config_plugins = ast.literal_eval(self.nf_config.get("plugins", "").strip("\""))
+    found_plugins = []
+    if len(config_plugins) == 0:
+        failed.append("nextflow.config contains an empty plugins scope")
+    for plugin in config_plugins:
+        if "@" not in plugin:
+            failed.append(f"Plugin '{plugin}' does not have a pinned version")
+        found_plugins.append(plugin.split("@")[0])
+
+    if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
+        failed.append("nextflow.config contains both nf-validation and nf-schema")
+    if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
+        failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
+
+    if "nf-validation" in found_plugins:
+        warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
+
+
     # Check for the availability of the "test" configuration profile by parsing nextflow.config
     # Also check for the presence of nf-validation/nf-schema and check if they have pinned versions
     with open(Path(self.wf_path, "nextflow.config")) as f:
@@ -359,42 +379,6 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             else:
                 failed.append("nextflow.config does not contain configuration profile `test`")
 
-        # Lint for nf-validation and nf-schema
-        match_plugins = re.search(r"\bplugins\s*\{([^}]+)}", cleaned_content, re.MULTILINE)
-        if not match_plugins:
-            failed.append(
-                "nextflow.config does not contain `plugins` scope, but `nf-validation` or `nf-schema` plugins are required"
-            )
-        else:
-            found_plugins = {}
-            for line in match_plugins.group(1).split("\n"):
-                cleaned_line = line.split("//")[0].strip().replace("\"", "'")
-                if "id" not in line: continue
-                match_line = re.search(r"\bid\s'([^']+)'", cleaned_line)
-                if not match_line:
-                    failed.append(f"nextflow.config contains an invalid plugins identifier: {cleaned_line}")
-                    continue
-                plugin = match_line.group(1)
-                name = plugin.split("@")[0]
-                version = ""
-                if "@" in plugin:
-                    version = plugin.split("@")[1]
-                found_plugins[name] = version
-
-            if len(found_plugins) == 0:
-                failed.append("nextflow.config contains an empty plugins scope")
-            elif "nf-validation" in found_plugins and "nf-schema" in found_plugins:
-                failed.append("nextflow.config contains both nf-validation and nf-schema")
-            elif "nf-validation" in found_plugins and found_plugins["nf-validation"] == "":
-                failed.append("nextflow.config contains an unpinned version of nf-validation")
-            elif "nf-schema" in found_plugins and found_plugins["nf-schema"] == "":
-                failed.append("nextflow.config contains an unpinned version of nf-schema")
-            elif "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
-                failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
-
-            if "nf-validation" in found_plugins:
-                warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
-
     # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json
     ignore_defaults = []
     for item in ignore_configs:

From e66a732e7db6452fb12b0f311762b19bbe7f3418 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 21 Aug 2024 11:01:16 +0200
Subject: [PATCH 288/414] ignore genomes for now

---
 nf_core/pipeline-template/nextflow.config      | 2 +-
 nf_core/pipeline-template/nextflow_schema.json | 6 ------
 2 files changed, 1 insertion(+), 7 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 3a98c40f0a..bb55678001 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -266,7 +266,7 @@ plugins {
 }
 
 validation {
-    parametersSchema = "${projectDir}/nextflow_schema.json"
+    defaultIgnoreParams = ["genomes"]
     help {
         enabled = true
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 14120bbabc..908d310171 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -81,12 +81,6 @@
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
                     "default": "s3://ngi-igenomes/igenomes/"
-                },
-                "genomes": {
-                    "type": "object",
-                    "description": "An object containing all reference data availabe in igenomes",
-                    "fa_icon": "fas fa-ban",
-                    "hidden": true
                 }
             }
         },

From b6ae8d01dd440558cb3a2af821a04ea8fc89591a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 21 Aug 2024 12:23:52 +0200
Subject: [PATCH 289/414] improve config linting for validation even more

---
 nf_core/pipelines/lint/nextflow_config.py | 59 ++++++++++++++---------
 1 file changed, 35 insertions(+), 24 deletions(-)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index bd2f4f768b..6e292deb09 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -144,11 +144,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["process.time"],
         ["params.outdir"],
         ["params.input"],
-        ["validation.help.enabled"],
-        ["validation.help.beforeText"],
-        ["validation.help.afterText"],
-        ["validation.summary.beforeText"],
-        ["validation.summary.afterText"]
+        ["validation.help.enabled"]
     ]
     # Throw a warning if these are missing
     config_warn = [
@@ -157,6 +153,11 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["trace.file"],
         ["report.file"],
         ["dag.file"],
+        ["validation.help.beforeText"],
+        ["validation.help.afterText"],
+        ["validation.help.command"],
+        ["validation.summary.beforeText"],
+        ["validation.summary.afterText"]
     ]
     # Old depreciated vars - fail if present
     config_fail_ifdefined = [
@@ -168,6 +169,35 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         "params.enable_conda",
     ]
 
+    # Lint for plugins
+    config_plugins = ast.literal_eval(self.nf_config.get("plugins", "").strip("\""))
+    found_plugins = []
+    if len(config_plugins) == 0:
+        failed.append("nextflow.config contains an empty plugins scope")
+    for plugin in config_plugins:
+        if "@" not in plugin:
+            failed.append(f"Plugin '{plugin}' does not have a pinned version")
+        found_plugins.append(plugin.split("@")[0])
+
+    if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
+        failed.append("nextflow.config contains both nf-validation and nf-schema")
+    if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
+        failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
+
+    if "nf-schema" in found_plugins:
+        if self.nf_config.get("validation.help.enabled", "false") == "false":
+            failed.append("The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages")
+        config_fail_ifdefined.extend([
+            "params.validationFailUnrecognisedParams",
+            "params.validationLenientMode",
+            "params.validationSchemaIgnoreParams",
+            "params.validationShowHiddenParams"
+        ])
+
+    if "nf-validation" in found_plugins:
+        warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
+
+
     # Remove field that should be ignored according to the linting config
     ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else []
 
@@ -331,25 +361,6 @@ def nextflow_config(self) -> Dict[str, List[str]]:
                 )
             )
 
-    # Lint for plugins
-    config_plugins = ast.literal_eval(self.nf_config.get("plugins", "").strip("\""))
-    found_plugins = []
-    if len(config_plugins) == 0:
-        failed.append("nextflow.config contains an empty plugins scope")
-    for plugin in config_plugins:
-        if "@" not in plugin:
-            failed.append(f"Plugin '{plugin}' does not have a pinned version")
-        found_plugins.append(plugin.split("@")[0])
-
-    if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
-        failed.append("nextflow.config contains both nf-validation and nf-schema")
-    if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
-        failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
-
-    if "nf-validation" in found_plugins:
-        warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
-
-
     # Check for the availability of the "test" configuration profile by parsing nextflow.config
     # Also check for the presence of nf-validation/nf-schema and check if they have pinned versions
     with open(Path(self.wf_path, "nextflow.config")) as f:

From 1ede989be403e25f8b7485503d6a07bb6f20301d Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 21 Aug 2024 11:27:40 +0200
Subject: [PATCH 290/414] add option to exclude adaptivecard and slackreport
 from pipeline template

---
 nf_core/pipeline-template/.prettierignore     |  4 +++
 nf_core/pipeline-template/main.nf             |  4 +--
 .../utils_nfcore_pipeline_pipeline/main.nf    |  6 ++++-
 nf_core/pipelines/create/templatefeatures.yml | 25 +++++++++++++++++++
 4 files changed, 36 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/.prettierignore b/nf_core/pipeline-template/.prettierignore
index 3b3d5ff08e..c8e8ad9e11 100644
--- a/nf_core/pipeline-template/.prettierignore
+++ b/nf_core/pipeline-template/.prettierignore
@@ -1,8 +1,12 @@
 {%- if email %}
 email_template.html
 {%- endif %}
+{%- if adaptivecard %}
 adaptivecard.json
+{%- endif %}
+{%- if slackreport %}
 slackreport.json
+{%- endif %}
 .nextflow*
 work/
 data/
diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index 0cf688a7e9..7002a9c2d5 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -102,8 +102,8 @@ workflow {
         {%- endif %}
         params.outdir,
         params.monochrome_logs,
-        params.hook_url,
-        {%- if multiqc %}{{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %}
+        {% if adaptivecard or slackreport %}params.hook_url,{% endif %}
+        {% if multiqc %}{{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %}
     )
 }
 
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 62ef73d65d..3db8f66cb6 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -18,7 +18,9 @@ include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
 include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
 include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
+{%- if adaptivecard or slackreport %}
 include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
+{%- endif %}
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
 include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
 
@@ -126,7 +128,7 @@ workflow PIPELINE_COMPLETION {
     {% endif %}
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
-    hook_url        //  string: hook URL for notifications
+    {% if adaptivecard or slackreport %}hook_url        //  string: hook URL for notifications{% endif %}
     {% if multiqc %}multiqc_report  //  string: Path to MultiQC report{% endif %}
 
     main:
@@ -149,9 +151,11 @@ workflow PIPELINE_COMPLETION {
 
         completionSummary(monochrome_logs)
 
+        {%- if adaptivecard or slackreport %}
         if (hook_url) {
             imNotification(summary_params, hook_url)
         }
+        {%- endif %}
     }
 
     workflow.onError {
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 5dafd7e312..ff56ee190e 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -275,3 +275,28 @@ email:
       - ".prettierignore"
   nfcore_pipelines: False
   custom_pipelines: True
+adaptivecard:
+  skippable_paths:
+    - "assets/adaptivecard.json"
+  short_description: "Add template for status messages"
+  description: "Enable pipeline status update messages through Microsoft Teams"
+  help_text: |
+    This adds an Adaptive Card. A snippets of user interface.
+    This Adaptive Card is used as a template for pipeline update messages and it is compatible with Microsoft Teams.
+  linting:
+    files_unchanged:
+      - ".prettierignore"
+  nfcore_pipelines: False
+  custom_pipelines: True
+slackreport:
+  skippable_paths:
+    - "assets/slackreport.json"
+  short_description: "Add template for slack status messages"
+  description: "Enable pipeline status update messages through Slack"
+  help_text: |
+    This adds an JSON template used as a template for pipeline update messages in Slack.
+  linting:
+    files_unchanged:
+      - ".prettierignore"
+  nfcore_pipelines: False
+  custom_pipelines: True

From c9adbd5bff432f4370a6901e00a576a687cdc416 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 21 Aug 2024 13:58:07 +0200
Subject: [PATCH 291/414] update textual snapshot

---
 .../__snapshots__/test_create_app.ambr        | 512 +++++++++---------
 1 file changed, 256 insertions(+), 256 deletions(-)

diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index f2a0578474..ee470c915c 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
           font-weight: 700;
       }
   
-      .terminal-2220422576-matrix {
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           font-family: Fira Code, monospace;
           font-size: 20px;
           line-height: 24.4px;
           font-variant-east-asian: full-width;
       }
   
-      .terminal-2220422576-title {
+      .terminal-3293903238-title {
           font-size: 18px;
           font-weight: bold;
           font-family: arial;
       }
   
-      .terminal-2220422576-r1 { fill: #c5c8c6 }
-  .terminal-2220422576-r2 { fill: #e3e3e3 }
-  .terminal-2220422576-r3 { fill: #989898 }
-  .terminal-2220422576-r4 { fill: #e1e1e1 }
-  .terminal-2220422576-r5 { fill: #4ebf71;font-weight: bold }
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-  .terminal-2220422576-r15 { fill: #000000 }
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-  .terminal-2220422576-r22 { fill: #a7a9ab }
-  .terminal-2220422576-r23 { fill: #e2e3e3 }
+      .terminal-3293903238-r1 { fill: #c5c8c6 }
+  .terminal-3293903238-r2 { fill: #e3e3e3 }
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+  .terminal-3293903238-r16 { fill: #14191f }
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+  .terminal-3293903238-r19 { fill: #0a180e;font-weight: bold }
+  .terminal-3293903238-r20 { fill: #008139 }
+  .terminal-3293903238-r21 { fill: #fea62b;font-weight: bold }
+  .terminal-3293903238-r22 { fill: #a7a9ab }
+  .terminal-3293903238-r23 { fill: #e2e3e3 }
       </style>
   
       <defs>
-      <clipPath id="terminal-2220422576-clip-terminal">
+      <clipPath id="terminal-3293903238-clip-terminal">
         <rect x="0" y="0" width="1219.0" height="1219.0" />
       </clipPath>
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+  </text><text class="terminal-2443134963-r17" x="366" y="1166.8" textLength="195.2" clip-path="url(#terminal-2443134963-line-47)">▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁</text><text class="terminal-2443134963-r18" x="597.8" y="1166.8" textLength="195.2" clip-path="url(#terminal-2443134963-line-47)">▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁</text><text class="terminal-2443134963-r1" x="1220" y="1166.8" textLength="12.2" clip-path="url(#terminal-2443134963-line-47)">
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From 1be17370b30fe34adccb5b698d26145e05522e99 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 21 Aug 2024 14:56:37 +0200
Subject: [PATCH 292/414] check plugin includes in pipeline

---
 nf_core/pipelines/lint/__init__.py        |  3 ++
 nf_core/pipelines/lint/nextflow_config.py |  4 ++-
 nf_core/pipelines/lint/plugin_includes.py | 38 +++++++++++++++++++++++
 3 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 nf_core/pipelines/lint/plugin_includes.py

diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
index ed833d3219..219cdd8f5c 100644
--- a/nf_core/pipelines/lint/__init__.py
+++ b/nf_core/pipelines/lint/__init__.py
@@ -45,6 +45,7 @@
 from .nfcore_yml import nfcore_yml
 from .pipeline_name_conventions import pipeline_name_conventions
 from .pipeline_todos import pipeline_todos
+from .plugin_includes import plugin_includes
 from .readme import readme
 from .schema_description import schema_description
 from .schema_lint import schema_lint
@@ -92,6 +93,7 @@ class PipelineLint(nf_core.utils.Pipeline):
     nfcore_yml = nfcore_yml
     pipeline_name_conventions = pipeline_name_conventions
     pipeline_todos = pipeline_todos
+    plugin_includes = plugin_includes
     readme = readme
     schema_description = schema_description
     schema_lint = schema_lint
@@ -135,6 +137,7 @@ def _get_all_lint_tests(release_mode):
             "actions_awsfulltest",
             "readme",
             "pipeline_todos",
+            "plugin_includes",
             "pipeline_name_conventions",
             "template_strings",
             "schema_lint",
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 6e292deb09..a735c5042b 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -170,7 +170,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     ]
 
     # Lint for plugins
-    config_plugins = ast.literal_eval(self.nf_config.get("plugins", "").strip("\""))
+    config_plugins = ast.literal_eval(self.nf_config.get("plugins", ""))
     found_plugins = []
     if len(config_plugins) == 0:
         failed.append("nextflow.config contains an empty plugins scope")
@@ -185,6 +185,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
 
     if "nf-schema" in found_plugins:
+        passed.append("Found nf-schema plugin")
         if self.nf_config.get("validation.help.enabled", "false") == "false":
             failed.append("The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages")
         config_fail_ifdefined.extend([
@@ -195,6 +196,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ])
 
     if "nf-validation" in found_plugins:
+        passed.append("Found nf-validation plugin")
         warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
 
 
diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py
new file mode 100644
index 0000000000..247c4e493b
--- /dev/null
+++ b/nf_core/pipelines/lint/plugin_includes.py
@@ -0,0 +1,38 @@
+import ast
+import glob
+import logging
+import re
+from typing import Dict, List
+
+log = logging.getLogger(__name__)
+
+
+def plugin_includes(self) -> Dict[str, List[str]]:
+    """Checks the include statements in the all *.nf files for plugin includes
+
+    When nf-schema is used in an nf-core pipeline, the include statements of the plugin
+    functions have to use nf-schema instead of nf-validation and vice versa
+    """
+    config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", ""))]
+    validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema"
+
+    passed = []
+    warned = []
+    failed = []
+    ignored = []
+
+    plugin_include_pattern = re.compile(r"^include\s*{[^}]+}\s*from\s*[\"']plugin/([^\"']+)[\"']\s*$", re.MULTILINE)
+    workflow_files = [file for file in glob.glob(f"{self.wf_path}/**/*.nf", recursive=True) if not file.startswith("./modules/")]
+    test_passed = True
+    for file in workflow_files:
+        with open(file, "r") as of:
+            plugin_includes = re.findall(plugin_include_pattern, of.read())
+            for include in plugin_includes:
+                if include not in ["nf-validation", "nf-schema"]: continue
+                if include != validation_plugin:
+                    test_passed = False
+                    failed.append(f"Found a `{include}` plugin import in `{file[2:]}`, but `{validation_plugin}` was used in `nextflow.config`")
+
+    if test_passed: passed.append("No wrong validation plugin imports have been found")
+
+    return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored}

From f7137ca3c6e0240033cb56e690125cfbed54301b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Wed, 21 Aug 2024 16:44:58 +0200
Subject: [PATCH 293/414] Apply suggestions from code review

---
 nf_core/pipelines/create/templatefeatures.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index ff56ee190e..6a5fac358d 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -278,7 +278,7 @@ email:
 adaptivecard:
   skippable_paths:
     - "assets/adaptivecard.json"
-  short_description: "Add template for status messages"
+  short_description: "Support Microsoft Teams notifications"
   description: "Enable pipeline status update messages through Microsoft Teams"
   help_text: |
     This adds an Adaptive Card. A snippets of user interface.
@@ -291,7 +291,7 @@ adaptivecard:
 slackreport:
   skippable_paths:
     - "assets/slackreport.json"
-  short_description: "Add template for slack status messages"
+  short_description: "Support Slack notifications"
   description: "Enable pipeline status update messages through Slack"
   help_text: |
     This adds an JSON template used as a template for pipeline update messages in Slack.

From 2f1a4428dc73e15aea2fc001bec4df323700035e Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 22 Aug 2024 14:51:07 +0200
Subject: [PATCH 294/414] make nf-schema optional in the template

---
 .../assets/schema_input.json                  |  2 +-
 nf_core/pipeline-template/main.nf             |  1 -
 nf_core/pipeline-template/modules.json        |  4 +-
 nf_core/pipeline-template/nextflow.config     |  9 ++--
 .../pipeline-template/nextflow_schema.json    |  3 +-
 .../utils_nfcore_pipeline_pipeline/main.nf    | 18 +++++---
 .../nf-core/utils_nfcore_pipeline/main.nf     | 46 +++++++++++++++++++
 .../pipeline-template/workflows/pipeline.nf   |  2 +-
 nf_core/pipelines/create/templatefeatures.yml | 10 ++++
 nf_core/pipelines/lint/nextflow_config.py     | 20 ++++----
 10 files changed, 90 insertions(+), 25 deletions(-)

diff --git a/nf_core/pipeline-template/assets/schema_input.json b/nf_core/pipeline-template/assets/schema_input.json
index e76b95fa99..28a468adaf 100644
--- a/nf_core/pipeline-template/assets/schema_input.json
+++ b/nf_core/pipeline-template/assets/schema_input.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/{{ name }}/master/assets/schema_input.json",
     "title": "{{ name }} pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index fddfc5489e..f644f52afc 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -76,7 +76,6 @@ workflow {
     //
     PIPELINE_INITIALISATION (
         params.version,
-        params.help,
         params.validate_params,
         params.monochrome_logs,
         args,
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 1a3b96490d..0a883b60b7 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -29,12 +29,12 @@
                         "branch": "master",
                         "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
-                    },
+                    }{% if nf_schema %},
                     "utils_nfschema_plugin": {
                         "branch": "master",
                         "git_sha": "a3e87febb28bd0461c22a917c5b2c1492053ef85",
                         "installed_by": ["subworkflows"]
-                    }
+                    }{% endif %}
                 }
             }
         }
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index bb55678001..4acc34e409 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -37,9 +37,9 @@ params {
     plaintext_email              = false
     monochrome_logs              = false
     hook_url                     = null
-    help                         = false
+    {% if nf_schema %}help                         = false
     helpFull                     = false
-    showHidden                   = false
+    showHidden                   = false{% endif %}
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
 
@@ -260,13 +260,14 @@ manifest {
     doi             = ''
 }
 
+{% if nf_schema -%}
 // Nextflow plugins
 plugins {
     id 'nf-schema@2.1.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
-    defaultIgnoreParams = ["genomes"]
+    defaultIgnoreParams = ["genomes", "helpFull", "showHidden", "help-full", "show-hidden"] // The last 4 parameters are here because of a bug in nf-schema. This will be fixed in a later version
     help {
         enabled = true
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
@@ -293,7 +294,7 @@ validation {
         afterText = validation.help.afterText
     }
 }
-
+{% endif -%}
 
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 908d310171..c729c370bf 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -40,8 +40,7 @@
                     "type": "string",
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                     "fa_icon": "fas fa-file-signature"
-                }
-                {% endif %}
+                }{% endif %}
             }
         },
         {%- if igenomes %}
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index a994cfd584..1fef6912b3 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -8,17 +8,14 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
+{% if nf_schema %}include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
 include { paramsSummaryMap          } from 'plugin/nf-schema'
-include { samplesheetToList         } from 'plugin/nf-schema'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { samplesheetToList         } from 'plugin/nf-schema'{% endif %}
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
-include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
 include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
 ========================================================================================
@@ -50,12 +47,14 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
+    {% if nf_schema %}
     //
     // Validate parameters and generate parameter summary to stdout
     //
     UTILS_NFSCHEMA_PLUGIN (
         validate_params
     )
+    {% endif %}
 
     //
     // Check config provided to the pipeline
@@ -74,6 +73,7 @@ workflow PIPELINE_INITIALISATION {
     //
     // Create channel from input file provided through params.input
     //
+    {% if nf_schema %}
     Channel
         .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map {
@@ -93,6 +93,12 @@ workflow PIPELINE_INITIALISATION {
                 return [ meta, fastqs.flatten() ]
         }
         .set { ch_samplesheet }
+    {% else %}
+    Channel
+        .fromPath(params.input)
+        .splitCsv(header: true, strip: true)
+        .set { ch_samplesheet }
+    {% endif %}
 
     emit:
     samplesheet = ch_samplesheet
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a5dcd5f83d..14558c3927 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -61,6 +61,25 @@ def checkProfileProvided(nextflow_cli_args) {
     }
 }
 
+//
+// Citation string for pipeline
+//
+def workflowCitation() {
+    def temp_doi_ref = ""
+    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Using a loop to handle multiple DOIs
+    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+    // Removing ` ` since the manifest.doi is a string and not a proper list
+    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+        "* The pipeline\n" +
+        temp_doi_ref + "\n" +
+        "* The nf-core framework\n" +
+        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+        "* Software dependencies\n" +
+        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+}
+
 //
 // Generate workflow version string
 //
@@ -138,6 +157,33 @@ def paramsSummaryMultiqc(summary_params) {
     return yaml_file_text
 }
 
+//
+// nf-core logo
+//
+def nfCoreLogo(monochrome_logs=true) {
+    Map colors = logColours(monochrome_logs)
+    String.format(
+        """\n
+        ${dashedLine(monochrome_logs)}
+                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                                ${colors.green}`._,._,\'${colors.reset}
+        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
+        ${dashedLine(monochrome_logs)}
+        """.stripIndent()
+    )
+}
+
+//
+// Return dashed line
+//
+def dashedLine(monochrome_logs=true) {
+    Map colors = logColours(monochrome_logs)
+    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+}
+
 //
 // ANSII colours used for terminal logging
 //
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 4bb0913211..8d2773820d 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -6,7 +6,7 @@
 
 include { FASTQC                 } from '../modules/nf-core/fastqc/main'
 {% if multiqc %}include { MULTIQC                } from '../modules/nf-core/multiqc/main'{% endif %}
-include { paramsSummaryMap       } from 'plugin/nf-schema'
+{% if nf_schema %}include { paramsSummaryMap       } from 'plugin/nf-schema'{% endif %}
 {% if multiqc %}include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 {% if citations or multiqc %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index b97bf347ab..7a24b3d91a 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -242,3 +242,13 @@ changelog:
       - "CHANGELOG.md"
   nfcore_pipelines: False
   custom_pipelines: True
+nf_schema:
+  skippable_paths:
+    - "subworkflows/nf-core/utils_nfschema_plugin"
+  short_description: "Use nf-schema for this pipeline."
+  help_text: |
+    nf-schema is used to validate input parameters based on a JSON schema.
+    It also provides helper functionality to create help messages, get a summary
+    of changed parameters and validate and convert a samplesheet to a channel.
+  nfcore_pipelines: False
+  custom_pipelines: False
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index a735c5042b..1dfdabaf10 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -143,8 +143,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["process.memory"],
         ["process.time"],
         ["params.outdir"],
-        ["params.input"],
-        ["validation.help.enabled"]
+        ["params.input"]
     ]
     # Throw a warning if these are missing
     config_warn = [
@@ -152,12 +151,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["timeline.file"],
         ["trace.file"],
         ["report.file"],
-        ["dag.file"],
-        ["validation.help.beforeText"],
-        ["validation.help.afterText"],
-        ["validation.help.command"],
-        ["validation.summary.beforeText"],
-        ["validation.summary.afterText"]
+        ["dag.file"]
     ]
     # Old depreciated vars - fail if present
     config_fail_ifdefined = [
@@ -188,6 +182,16 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         passed.append("Found nf-schema plugin")
         if self.nf_config.get("validation.help.enabled", "false") == "false":
             failed.append("The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages")
+        config_fail.extend([
+            ["validation.help.enabled"]
+        ])
+        config_warn.extend([
+            ["validation.help.beforeText"],
+            ["validation.help.afterText"],
+            ["validation.help.command"],
+            ["validation.summary.beforeText"],
+            ["validation.summary.afterText"]
+        ])
         config_fail_ifdefined.extend([
             "params.validationFailUnrecognisedParams",
             "params.validationLenientMode",

From 364b54bde2994927d3124bfdf53d97bd1ecc6350 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 22 Aug 2024 15:57:29 +0200
Subject: [PATCH 295/414] small fixes for template without nf-schema

---
 .../utils_nfcore_pipeline_pipeline/main.nf    | 33 ++++++++++---------
 .../pipeline-template/workflows/pipeline.nf   |  6 ++--
 nf_core/pipelines/lint/nextflow_config.py     |  6 ++--
 nf_core/pipelines/lint/plugin_includes.py     |  2 +-
 4 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index d96f203544..0867a0a4c9 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -77,9 +77,14 @@ workflow PIPELINE_INITIALISATION {
     //
     // Create channel from input file provided through params.input
     //
-    {% if nf_schema %}
-    Channel
-        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
+
+    Channel{% if nf_schema %}
+        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")){% else %}
+        .fromPath(params.input)
+        .splitCsv(header: true, strip: true)
+        .map { row ->
+            [[id:row.sample], row.fastq_1, row.fastq_2]
+        }{% endif %}
         .map {
             meta, fastq_1, fastq_2 ->
                 if (!fastq_2) {
@@ -97,12 +102,6 @@ workflow PIPELINE_INITIALISATION {
                 return [ meta, fastqs.flatten() ]
         }
         .set { ch_samplesheet }
-    {% else %}
-    Channel
-        .fromPath(params.input)
-        .splitCsv(header: true, strip: true)
-        .set { ch_samplesheet }
-    {% endif %}
 
     emit:
     samplesheet = ch_samplesheet
@@ -130,19 +129,21 @@ workflow PIPELINE_COMPLETION {
 
     main:
 
-    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-
     //
     // Completion email and summary
     //
     workflow.onComplete {
         {%- if email %}
         if (email || email_on_fail) {
-            {%- if multiqc %}
-            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
-            {%- else %}
-            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, [])
-            {%- endif %}
+            completionEmail(
+                {% if nf_schema %}paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json"){% else %}{}{% endif %},
+                email,
+                email_on_fail,
+                plaintext_email,
+                outdir,
+                monochrome_logs,
+                {% if multiqc %}multiqc_report.toList(){% else %}[]{% endif %}
+            )
         }
         {%- endif %}
 
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 8d2773820d..ca5de36a61 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -60,9 +60,13 @@ workflow {{ short_name|upper }} {
         Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
         Channel.empty()
 
+    {% if nf_schema %}
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    {% endif %}
 
     {%- if citations %}
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
@@ -72,8 +76,6 @@ workflow {{ short_name|upper }} {
         methodsDescriptionText(ch_multiqc_custom_methods_description))
     {%- endif %}
 
-    ch_multiqc_files = ch_multiqc_files.mix(
-        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
     {%- if citations %}
     ch_multiqc_files = ch_multiqc_files.mix(
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 1dfdabaf10..f5689813a4 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -164,10 +164,10 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     ]
 
     # Lint for plugins
-    config_plugins = ast.literal_eval(self.nf_config.get("plugins", ""))
+    config_plugins = ast.literal_eval(self.nf_config.get("plugins", "[]"))
     found_plugins = []
     if len(config_plugins) == 0:
-        failed.append("nextflow.config contains an empty plugins scope")
+        warned.append("nextflow.config contains an empty plugins scope")
     for plugin in config_plugins:
         if "@" not in plugin:
             failed.append(f"Plugin '{plugin}' does not have a pinned version")
@@ -176,7 +176,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
         failed.append("nextflow.config contains both nf-validation and nf-schema")
     if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
-        failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
+        warned.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
 
     if "nf-schema" in found_plugins:
         passed.append("Found nf-schema plugin")
diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py
index 247c4e493b..740c001a11 100644
--- a/nf_core/pipelines/lint/plugin_includes.py
+++ b/nf_core/pipelines/lint/plugin_includes.py
@@ -13,7 +13,7 @@ def plugin_includes(self) -> Dict[str, List[str]]:
     When nf-schema is used in an nf-core pipeline, the include statements of the plugin
     functions have to use nf-schema instead of nf-validation and vice versa
     """
-    config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", ""))]
+    config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", "[]"))]
     validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema"
 
     passed = []

From 4e631384906d2c02ab537276f22ea47c3ceb438d Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 22 Aug 2024 16:02:58 +0200
Subject: [PATCH 296/414] bump nextflow version

---
 .github/workflows/create-lint-wf.yml                            | 2 +-
 .github/workflows/create-test-wf.yml                            | 2 +-
 .../nf-core/utils_nextflow_pipeline/tests/nextflow.config       | 2 +-
 .../nf-core/utils_nfcore_pipeline/tests/nextflow.config         | 2 +-
 nf_core/pipelines/lint/readme.py                                | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 7e90febb74..f07b31e9de 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -38,7 +38,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "23.10.0"
           - "latest-everything"
     steps:
       - name: go to subdirectory and change nextflow workdir
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index a95a477459..56c6c822a9 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -39,7 +39,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "23.10.0"
           - "latest-everything"
     steps:
       - name: go to working directory
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index d0a926bf6d..0fa4abaf43 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
+    nextflowVersion  = '!>=23.10.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
index d0a926bf6d..0fa4abaf43 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
+    nextflowVersion  = '!>=23.10.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
diff --git a/nf_core/pipelines/lint/readme.py b/nf_core/pipelines/lint/readme.py
index 4c16243690..1c09104258 100644
--- a/nf_core/pipelines/lint/readme.py
+++ b/nf_core/pipelines/lint/readme.py
@@ -36,7 +36,7 @@ def readme(self):
 
     if "nextflow_badge" not in ignore_configs:
         # Check that there is a readme badge showing the minimum required version of Nextflow
-        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.10.0-23aa62.svg)](https://www.nextflow.io/)
         # and that it has the correct version
         nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-23aa62\.svg\)\]\(https://www\.nextflow\.io/\)"
         match = re.search(nf_badge_re, content)

From 11efc5547be76f1a6412d049dbfcd10cd337c660 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 22 Aug 2024 16:08:41 +0200
Subject: [PATCH 297/414] update changelog

---
 CHANGELOG.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 98fb925338..b4fcfe8646 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,8 @@
 - add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112))
 - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125))
 - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126))
+- Use nf-schema instead of nf-validation ([#3116](https://github.com/nf-core/tools/pull/3116))
+- add option to exclude nf-schema from the template ([#3116](https://github.com/nf-core/tools/pull/3116))
 
 ### Linting
 
@@ -26,6 +28,10 @@
 - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014))
 - Restructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070))
 - Fix module linting warning for process_high_memory ([#3086](https://github.com/nf-core/tools/issues/3086))
+- Linting will now fail when an unpinned plugin is used ([#3116](https://github.com/nf-core/tools/pull/3116))
+- Linting will now check if the schema is correct for the used validation plugin ([#3116])(https://github.com/nf-core/tools/pull/3116)
+- Linting will now check the use of the right validation plugin include statements in the workflow scripts ([#3116])(https://github.com/nf-core/tools/pull/3116)
+- Full linting for correct use of nf-schema and nf-validation ([#3116](https://github.com/nf-core/tools/pull/3116))
 
 ### Download
 

From 47c3fe324280a54d4cae4227ab7679ac488b1edb Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 22 Aug 2024 16:13:04 +0200
Subject: [PATCH 298/414] fix ruff linting

---
 nf_core/pipelines/lint/nextflow_config.py | 53 +++++++++++------------
 nf_core/pipelines/lint/plugin_includes.py | 24 ++++++----
 nf_core/pipelines/schema.py               | 17 +++++---
 3 files changed, 51 insertions(+), 43 deletions(-)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index f5689813a4..255042ce5a 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -143,16 +143,10 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["process.memory"],
         ["process.time"],
         ["params.outdir"],
-        ["params.input"]
+        ["params.input"],
     ]
     # Throw a warning if these are missing
-    config_warn = [
-        ["manifest.mainScript"],
-        ["timeline.file"],
-        ["trace.file"],
-        ["report.file"],
-        ["dag.file"]
-    ]
+    config_warn = [["manifest.mainScript"], ["timeline.file"], ["trace.file"], ["report.file"], ["dag.file"]]
     # Old depreciated vars - fail if present
     config_fail_ifdefined = [
         "params.nf_required_version",
@@ -181,28 +175,33 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     if "nf-schema" in found_plugins:
         passed.append("Found nf-schema plugin")
         if self.nf_config.get("validation.help.enabled", "false") == "false":
-            failed.append("The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages")
-        config_fail.extend([
-            ["validation.help.enabled"]
-        ])
-        config_warn.extend([
-            ["validation.help.beforeText"],
-            ["validation.help.afterText"],
-            ["validation.help.command"],
-            ["validation.summary.beforeText"],
-            ["validation.summary.afterText"]
-        ])
-        config_fail_ifdefined.extend([
-            "params.validationFailUnrecognisedParams",
-            "params.validationLenientMode",
-            "params.validationSchemaIgnoreParams",
-            "params.validationShowHiddenParams"
-        ])
+            failed.append(
+                "The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages"
+            )
+        config_fail.extend([["validation.help.enabled"]])
+        config_warn.extend(
+            [
+                ["validation.help.beforeText"],
+                ["validation.help.afterText"],
+                ["validation.help.command"],
+                ["validation.summary.beforeText"],
+                ["validation.summary.afterText"],
+            ]
+        )
+        config_fail_ifdefined.extend(
+            [
+                "params.validationFailUnrecognisedParams",
+                "params.validationLenientMode",
+                "params.validationSchemaIgnoreParams",
+                "params.validationShowHiddenParams",
+            ]
+        )
 
     if "nf-validation" in found_plugins:
         passed.append("Found nf-validation plugin")
-        warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
-
+        warned.append(
+            "nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/"
+        )
 
     # Remove field that should be ignored according to the linting config
     ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else []
diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py
index 740c001a11..6a57b1d280 100644
--- a/nf_core/pipelines/lint/plugin_includes.py
+++ b/nf_core/pipelines/lint/plugin_includes.py
@@ -16,23 +16,29 @@ def plugin_includes(self) -> Dict[str, List[str]]:
     config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", "[]"))]
     validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema"
 
-    passed = []
-    warned = []
-    failed = []
-    ignored = []
+    passed: list[str] = []
+    warned: list[str] = []
+    failed: list[str] = []
+    ignored: list[str] = []
 
     plugin_include_pattern = re.compile(r"^include\s*{[^}]+}\s*from\s*[\"']plugin/([^\"']+)[\"']\s*$", re.MULTILINE)
-    workflow_files = [file for file in glob.glob(f"{self.wf_path}/**/*.nf", recursive=True) if not file.startswith("./modules/")]
+    workflow_files = [
+        file for file in glob.glob(f"{self.wf_path}/**/*.nf", recursive=True) if not file.startswith("./modules/")
+    ]
     test_passed = True
     for file in workflow_files:
-        with open(file, "r") as of:
+        with open(file) as of:
             plugin_includes = re.findall(plugin_include_pattern, of.read())
             for include in plugin_includes:
-                if include not in ["nf-validation", "nf-schema"]: continue
+                if include not in ["nf-validation", "nf-schema"]:
+                    continue
                 if include != validation_plugin:
                     test_passed = False
-                    failed.append(f"Found a `{include}` plugin import in `{file[2:]}`, but `{validation_plugin}` was used in `nextflow.config`")
+                    failed.append(
+                        f"Found a `{include}` plugin import in `{file[2:]}`, but `{validation_plugin}` was used in `nextflow.config`"
+                    )
 
-    if test_passed: passed.append("No wrong validation plugin imports have been found")
+    if test_passed:
+        passed.append("No wrong validation plugin imports have been found")
 
     return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored}
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index e9c5556dbb..ccbc86645e 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -5,7 +5,6 @@
 import logging
 import tempfile
 import webbrowser
-import re
 from pathlib import Path
 from typing import Union
 
@@ -58,10 +57,10 @@ def set_schema_filename(self, schema: str) -> None:
         basepath = "/".join(str(schema).split("/")[:-1])
         config = f"{basepath}/nextflow.config" if basepath != "" else "nextflow.config"
         self._update_validation_plugin_from_config(config)
-    
+
     def get_schema_filename(self) -> str:
         return self._schema_filename
-    
+
     def del_schema_filename(self) -> None:
         del self._schema_filename
 
@@ -71,7 +70,7 @@ def _update_validation_plugin_from_config(self, config: str) -> None:
         plugin = "nf-schema"
         conf = nf_core.utils.fetch_wf_config(Path(self.schema_filename).parent)
 
-        plugins = str(conf.get("plugins", "")).strip("\"").strip("'").strip(" ").split(",")
+        plugins = str(conf.get("plugins", "")).strip('"').strip("'").strip(" ").split(",")
         plugin_found = False
         for plugin_instance in plugins:
             if "nf-schema" in plugin_instance:
@@ -95,7 +94,7 @@ def _update_validation_plugin_from_config(self, config: str) -> None:
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
         if plugin == "nf-schema":
             self.defs_notation = "$defs"
-            ignored_params = ["help", "helpFull", "showHidden"] # Help parameter should be ignored by default
+            ignored_params = ["help", "helpFull", "showHidden"]  # Help parameter should be ignored by default
             ignored_params_config = conf.get("validation", {}).get("defaultIgnoreParams", [])
             if len(ignored_params_config) > 0:
                 ignored_params.extend(ignored_params_config)
@@ -447,7 +446,9 @@ def validate_schema(self, schema=None):
 
         # Add a small check for older nf-schema JSON schemas
         if "defs" in schema:
-            raise AssertionError(f'Using "defs" for schema definitions is not supported. Please use {self.defs_notation} instead')
+            raise AssertionError(
+                f'Using "defs" for schema definitions is not supported. Please use {self.defs_notation} instead'
+            )
 
         for d_key, d_schema in schema.get(self.defs_notation, {}).items():
             # Check that this definition is mentioned in allOf
@@ -458,7 +459,9 @@ def validate_schema(self, schema=None):
                 if allOf["$ref"] == f"#/{self.defs_notation}/{d_key}":
                     in_allOf = True
             if not in_allOf:
-                raise AssertionError(f"Definition subschema `#/{self.defs_notation}/{d_key}` not included in schema `allOf`")
+                raise AssertionError(
+                    f"Definition subschema `#/{self.defs_notation}/{d_key}` not included in schema `allOf`"
+                )
 
             # TODO add support for nested parameters
             for d_param_id in d_schema.get("properties", {}):

From 09bfca2663275c37173ce8018c858164974479f8 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 22 Aug 2024 16:29:39 +0200
Subject: [PATCH 299/414] add a plugin includes test

---
 tests/pipelines/lint/test_plugin_includes.py | 23 ++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 tests/pipelines/lint/test_plugin_includes.py

diff --git a/tests/pipelines/lint/test_plugin_includes.py b/tests/pipelines/lint/test_plugin_includes.py
new file mode 100644
index 0000000000..21e6107c14
--- /dev/null
+++ b/tests/pipelines/lint/test_plugin_includes.py
@@ -0,0 +1,23 @@
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+class TestLintNextflowConfig(TestLint):
+    def setUp(self) -> None:
+        super().setUp()
+        self.new_pipeline = self._make_pipeline_copy()
+    
+    def test_default_values_match(self):
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        result = lint_obj.plugin_includes()
+        assert len(result["failed"]) == 0
+        assert len(result["warned"]) == 0
+
+    def test_wrong_include(self):
+        test_path = self.new_pipeline / "test.nf"
+        with open(test_path, "w") as of:
+            of.write("include { paramsSummary } from 'plugin/nf-validation'\n")
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        result = lint_obj.plugin_includes()
+        assert len(result["failed"]) == 1
+        assert len(result["warned"]) == 0
\ No newline at end of file

From 44dbbf7a2b095144cb954bb1ed09578776979c92 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 23 Aug 2024 09:50:51 +0200
Subject: [PATCH 300/414] update review comments

---
 nf_core/pipeline-template/nextflow.config     | 7 ++++---
 nf_core/pipelines/create/templatefeatures.yml | 7 ++++---
 nf_core/pipelines/lint/nextflow_config.py     | 1 -
 nf_core/pipelines/schema.py                   | 2 +-
 4 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index ad800cc55b..3b3183ece1 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -273,6 +273,7 @@ validation {
     help {
         enabled = true
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        {% if is_nfcore %}
         beforeText = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
@@ -289,12 +290,12 @@ validation {
 
 * Software dependencies
   https://github.com/${manifest.name}/blob/master/CITATIONS.md
-"""
-    }
+"""{% endif %}
+    }{% if is_nfcore %}
     summary {
         beforeText = validation.help.beforeText
         afterText = validation.help.afterText
-    }
+    }[% endif %]
 }
 {% endif -%}
 
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 29b53eb0a7..224bc38266 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -245,13 +245,14 @@ changelog:
 nf_schema:
   skippable_paths:
     - "subworkflows/nf-core/utils_nfschema_plugin"
-  short_description: "Use nf-schema for this pipeline."
+  short_description: "Use nf-schema"
+  description: "Use nf-schema for this pipeline."
   help_text: |
     nf-schema is used to validate input parameters based on a JSON schema.
     It also provides helper functionality to create help messages, get a summary
     of changed parameters and validate and convert a samplesheet to a channel.
-  nfcore_pipelines: False
-  custom_pipelines: False
+  nfcore_pipelines: True
+  custom_pipelines: True
 license:
   skippable_paths:
     - "LICENSE"
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 255042ce5a..71eb6f118f 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -367,7 +367,6 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             )
 
     # Check for the availability of the "test" configuration profile by parsing nextflow.config
-    # Also check for the presence of nf-validation/nf-schema and check if they have pinned versions
     with open(Path(self.wf_path, "nextflow.config")) as f:
         content = f.read()
 
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index ccbc86645e..04f5ca2ace 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -447,7 +447,7 @@ def validate_schema(self, schema=None):
         # Add a small check for older nf-schema JSON schemas
         if "defs" in schema:
             raise AssertionError(
-                f'Using "defs" for schema definitions is not supported. Please use {self.defs_notation} instead'
+                f'Using "defs" for schema definitions is not supported. Please use "{self.defs_notation}" instead'
             )
 
         for d_key, d_schema in schema.get(self.defs_notation, {}).items():

From ea51814bc2b1549c14605ba66591e7043bb5e4b3 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 23 Aug 2024 10:17:15 +0200
Subject: [PATCH 301/414] remove duplicate code

---
 nf_core/pipelines/schema.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 04f5ca2ace..dbe851415f 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -85,11 +85,6 @@ def _update_validation_plugin_from_config(self, config: str) -> None:
         if not plugin_found:
             log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema")
 
-        if "nf-validation" in plugins:
-            plugin = "nf-validation"
-        elif "nf-schema" in plugins:
-            plugin = "nf-schema"
-
         self.validation_plugin = plugin
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
         if plugin == "nf-schema":

From 113fa4226cbdb471607615cf9c45b61bcfbc55c5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Fri, 23 Aug 2024 10:06:12 +0000
Subject: [PATCH 302/414] update utils_nextflow_pipeline

---
 nf_core/pipeline-template/modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index eb9391b29a..8b156083f3 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -22,7 +22,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "20c03aede5a80ff520a905cea1f8ca121b5bb661",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {

From 195fc5168c9810d36f994996d588c219b72b9eef Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 23 Aug 2024 11:35:43 +0000
Subject: [PATCH 303/414] Uncomment nextflow extension and align comments

---
 .gitpod.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitpod.yml b/.gitpod.yml
index b2fbb73133..b93095c780 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -11,12 +11,12 @@ tasks:
       unset JAVA_TOOL_OPTIONS
 
 vscode:
-  extensions: # based on nf-core.nf-core-extensionpack
+  extensions:
     - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                    # Nextflow syntax highlighting
+    - nextflow.nextflow # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
     - charliermarsh.ruff # Code linter Ruff

From 65f26b1455b5592ec301fb618464372b3a8280da Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 23 Aug 2024 11:44:48 +0000
Subject: [PATCH 304/414] Add Digest comment and remove conda defaults channel

---
 nf_core/gitpod/gitpod.Dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
index fd0e8bb799..944222668b 100644
--- a/nf_core/gitpod/gitpod.Dockerfile
+++ b/nf_core/gitpod/gitpod.Dockerfile
@@ -1,6 +1,7 @@
 # Test build locally before making a PR
 #   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
 
+# See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
 FROM gitpod/workspace-base@sha256:f189a4195c3861365356f9c1b438ab26fd88e1ff46ce2843afc62861fc982e0c
 
 USER root
@@ -40,9 +41,8 @@ RUN chown -R gitpod:gitpod /opt/conda /usr/src/nf_core
 
 # Change user to gitpod
 USER gitpod
-# Install nextflow, nf-core, Mamba, and pytest-workflow
-RUN conda config --add channels defaults && \
-    conda config --add channels bioconda && \
+# Install nextflow, nf-core, nf-test, and other useful tools
+RUN conda config --add channels bioconda && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
     conda install --quiet --yes --name base \

From 506491f66e3dd612e726b508ab72e125fd8e31b8 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 23 Aug 2024 12:04:32 +0000
Subject: [PATCH 305/414] Blank JAVA_TOOL_OPTIONS

---
 nf_core/gitpod/gitpod.Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
index 944222668b..849729966b 100644
--- a/nf_core/gitpod/gitpod.Dockerfile
+++ b/nf_core/gitpod/gitpod.Dockerfile
@@ -63,3 +63,4 @@ RUN nextflow self-update && \
 # Setup pdiff for nf-test diffs
 ENV NFT_DIFF="pdiff"
 ENV NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
+ENV JAVA_TOOL_OPTIONS=

From 411cd22da23380799e7535b7340a5a0e16510bd7 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 23 Aug 2024 12:07:25 +0000
Subject: [PATCH 306/414] Remove unset JAVA_TOOL_OPTIONS

---
 .gitpod.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.gitpod.yml b/.gitpod.yml
index b93095c780..efe193f35f 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -6,9 +6,6 @@ tasks:
       python -m pip install -r requirements-dev.txt
       pre-commit install --install-hooks
       nextflow self-update
-  - name: unset JAVA_TOOL_OPTIONS
-    command: |
-      unset JAVA_TOOL_OPTIONS
 
 vscode:
   extensions:

From bc6ecda3aec81e24b858b6e98e62eb30ad13dd0a Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 23 Aug 2024 12:11:13 +0000
Subject: [PATCH 307/414] Remove unset JAVA_TOOL_OPTIONS from pipeline template

---
 nf_core/pipeline-template/.gitpod.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml
index 30e85ed977..5907fb59c9 100644
--- a/nf_core/pipeline-template/.gitpod.yml
+++ b/nf_core/pipeline-template/.gitpod.yml
@@ -4,9 +4,6 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-  - name: unset JAVA_TOOL_OPTIONS
-    command: |
-      unset JAVA_TOOL_OPTIONS
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
@@ -15,7 +12,7 @@ vscode:
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files{% endif %}
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                    # Nextflow syntax highlighting
+    - nextflow.nextflow # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
     - charliermarsh.ruff # Code linter Ruff

From d324760487b25de1f12027699099bc5d649eaf60 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Fri, 23 Aug 2024 12:14:18 +0000
Subject: [PATCH 308/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 98fb925338..2e13e82f5e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -73,6 +73,7 @@
 - Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 ([#3122](https://github.com/nf-core/tools/pull/3122))
 - Update python:3.12-slim Docker digest to 59c7332 ([#3124](https://github.com/nf-core/tools/pull/3124))
+- Update gitpod ([#3136](https://github.com/nf-core/tools/pull/3136))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From 1bcb70fbfc3b17b3a73dec382a96a20d02108617 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 23 Aug 2024 14:26:26 +0200
Subject: [PATCH 309/414] Update CHANGELOG.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2e13e82f5e..aca2e6f200 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -73,7 +73,7 @@
 - Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 ([#3122](https://github.com/nf-core/tools/pull/3122))
 - Update python:3.12-slim Docker digest to 59c7332 ([#3124](https://github.com/nf-core/tools/pull/3124))
-- Update gitpod ([#3136](https://github.com/nf-core/tools/pull/3136))
+- Update gitpod setup ([#3136](https://github.com/nf-core/tools/pull/3136))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

From 6e018ce6981548fb11ae5f34e3c476305695ad8f Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 23 Aug 2024 15:41:07 +0200
Subject: [PATCH 310/414] organise changelog and bump version to 3.0.0dev

---
 CHANGELOG.md | 55 +++++++++++++++++++++++++++-------------------------
 setup.py     |  2 +-
 2 files changed, 30 insertions(+), 27 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index aca2e6f200..42cb2a62aa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,18 @@
 # nf-core/tools: Changelog
 
-## v2.14.2dev
+## v3.0.0dev
+
+**Highlights**
+
+- Pipeline commands are renamed from nf-core <comand> to nf-core pipelines <command>
+- More customisation for pipeline templates
+- A Text User Interface app when running nf-core pipelines create
+- The pipeline template will come with the nf-schema plugin
+- New command nf-core pipelines rocrate to create a Research Object (RO) crate for a pipeline
+- `nf-core licences` command is deprecated.
+- Pipeline linting will run with the used version of the template
+- The structure of nf-core/tools pytests has been updated
+- The structure of the API docs has been updated
 
 ### Template
 
@@ -9,14 +21,13 @@
 - Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046))
 - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055))
 - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072))
+- handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108), [#3112](https://github.com/nf-core/tools/pull/3112))
 - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084))
 - add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101))
 - add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100))
 - add option to exclude codespaces from pipeline template ([#3105](https://github.com/nf-core/tools/pull/3105))
 - add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103))
 - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104))
-- handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108))
-- add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112))
 - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125))
 - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126))
 
@@ -27,53 +38,45 @@
 - Restructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070))
 - Fix module linting warning for process_high_memory ([#3086](https://github.com/nf-core/tools/issues/3086))
 
-### Download
+### Pipeline create command
+
+- Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008))
+- Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007))
+- Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038))
+- Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094))
 
 ### Components
 
 - The `modules_nfcore` tag in the `main.nf.test` file of modules/subworkflows now displays the organization name in custom modules repositories ([#3005](https://github.com/nf-core/tools/pull/3005))
+- Add `--migrate_pytest` option to `nf-core <modules|subworkflows> test` command ([#3085](https://github.com/nf-core/tools/pull/3085))
+- Components: allow spaces at the beginning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115))
 
 ### General
 
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.4 ([#2974](https://github.com/nf-core/tools/pull/2974))
-- Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982))
 - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988))
 - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991))
 - update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998))
 - move pipeline subcommands for v3.0 ([#2983](https://github.com/nf-core/tools/pull/2983))
 - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006))
-- Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008))
 - Remove nf-core licences command ([#3012](https://github.com/nf-core/tools/pull/3012))
 - README - absolute image paths ([#3013](https://github.com/nf-core/tools/pull/3013))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.7 ([#3015](https://github.com/nf-core/tools/pull/3015))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.8 ([#3017](https://github.com/nf-core/tools/pull/3017))
-- Update python:3.12-slim Docker digest to e3ae8cf ([#3020](https://github.com/nf-core/tools/pull/3020))
-- Update python:3.12-slim Docker digest to 2fba8e7 ([#3023](https://github.com/nf-core/tools/pull/3023))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 ([#3031](https://github.com/nf-core/tools/pull/3031))
 - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036))
-- Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007))
 - move pipeline commands to functions to avoid duplication ([#3039](https://github.com/nf-core/tools/pull/3039))
-- Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038))
-- Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041))
-- Update gitpod/workspace-base Docker digest to 0f38224 ([#3048](https://github.com/nf-core/tools/pull/3048))
 - update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052))
 - Add `--limit-output` argument for modules/subworkflow update ([#3047](https://github.com/nf-core/tools/pull/3047))
 - update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054))
-- Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058))
 - handle new jsonschema error type ([#3061](https://github.com/nf-core/tools/pull/3061))
-- Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071))
 - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074))
-- Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079))
-- Add `--migrate_pytest` option to `nf-core <modules|subworkflows> test` command ([#3085](https://github.com/nf-core/tools/pull/3085))
-- Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091))
-- Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094))
 - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102))
-- Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115))
+- Update gitpod setup ([#3136](https://github.com/nf-core/tools/pull/3136))
+
+## Version updates
+
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 ([#3122](https://github.com/nf-core/tools/pull/3122))
+- Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982))
 - Update python:3.12-slim Docker digest to 59c7332 ([#3124](https://github.com/nf-core/tools/pull/3124))
-- Update gitpod setup ([#3136](https://github.com/nf-core/tools/pull/3136))
+- Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091))
+- Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 
diff --git a/setup.py b/setup.py
index 8f32daa904..45df29b8bc 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "2.14.2dev"
+version = "3.0.0dev"
 
 with open("README.md") as f:
     readme = f.read()

From 41b2676c8746e92960907c3263f296ea7f606d96 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 23 Aug 2024 15:52:40 +0200
Subject: [PATCH 311/414] more details! :D

---
 CHANGELOG.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 42cb2a62aa..2a3e98f63b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,13 +4,13 @@
 
 **Highlights**
 
-- Pipeline commands are renamed from nf-core <comand> to nf-core pipelines <command>
-- More customisation for pipeline templates
-- A Text User Interface app when running nf-core pipelines create
-- The pipeline template will come with the nf-schema plugin
-- New command nf-core pipelines rocrate to create a Research Object (RO) crate for a pipeline
+- Pipeline commands are renamed from `nf-core <comand>` to `nf-core pipelines <command>` to match the structure of modules and subworkflows commands.
+- More customisation for pipeline templates. The template has been divided into features which can be skipped, making it easier to avoid annoying merge conflicts, for example, for pipeline which don't have a FastQC module.
+- A new Text User Interface app when running nf-core pipelines create
+- The pipeline template will come with the `nf-schema` plugin
+- Pipeline linting will run with the used version of the template to minimise errors in opened PRs with every new tools release.
+- New command `nf-core pipelines rocrate` to create a [Research Object (RO) crate](https://www.researchobject.org/ro-crate/about_ro_crate) for a pipeline
 - `nf-core licences` command is deprecated.
-- Pipeline linting will run with the used version of the template
 - The structure of nf-core/tools pytests has been updated
 - The structure of the API docs has been updated
 

From 8000e1f5c31e7903ff72bb2453b67ca8db262f67 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 23 Aug 2024 16:04:19 +0200
Subject: [PATCH 312/414] add suggestions from @mashehu

---
 CHANGELOG.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2a3e98f63b..5590abc04a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,12 +4,12 @@
 
 **Highlights**
 
-- Pipeline commands are renamed from `nf-core <comand>` to `nf-core pipelines <command>` to match the structure of modules and subworkflows commands.
-- More customisation for pipeline templates. The template has been divided into features which can be skipped, making it easier to avoid annoying merge conflicts, for example, for pipeline which don't have a FastQC module.
-- A new Text User Interface app when running nf-core pipelines create
-- The pipeline template will come with the `nf-schema` plugin
-- Pipeline linting will run with the used version of the template to minimise errors in opened PRs with every new tools release.
-- New command `nf-core pipelines rocrate` to create a [Research Object (RO) crate](https://www.researchobject.org/ro-crate/about_ro_crate) for a pipeline
+- Pipeline commands are renamed from `nf-core <comand>` to `nf-core pipelines <command>` to follow the same command structure as modules and subworkflows commands.
+- More customisation for pipeline templates. The template has been divided into features which can be skipped, e.g. you can create a new pipeline without any traces of FastQC in it.
+- A new Text User Interface app when running `nf-core pipelines create` to help us guide you through the process better (no worries, you can still use the cli if you give all values as parameters)
+- We replaced nf-validation with nf-schema in the pipeline template
+- CI tests now lint with the nf-core tools version matching the template version of the pipeline, to minimise errors in opened PRs with every new tools release.
+- New command `nf-core pipelines ro-crate` to create a [Research Object (RO) crate](https://www.researchobject.org/ro-crate/) for a pipeline
 - `nf-core licences` command is deprecated.
 - The structure of nf-core/tools pytests has been updated
 - The structure of the API docs has been updated

From f2b282c696ebfff78ac4e328dca3d9a25b258ec4 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 21 Aug 2024 16:12:58 +0200
Subject: [PATCH 313/414] add option to exclude fastqc from pipeline template

---
 nf_core/pipeline-template/CITATIONS.md                 |  7 +++----
 nf_core/pipeline-template/README.md                    |  4 ++--
 nf_core/pipeline-template/conf/modules.config          |  2 ++
 nf_core/pipeline-template/docs/output.md               |  9 ++++++---
 nf_core/pipeline-template/modules.json                 |  3 ++-
 .../local/utils_nfcore_pipeline_pipeline/main.nf       |  4 ++--
 nf_core/pipeline-template/workflows/pipeline.nf        |  4 +++-
 nf_core/pipelines/create/templatefeatures.yml          | 10 ++++++++++
 8 files changed, 30 insertions(+), 13 deletions(-)

diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md
index 7cf37e5018..2373f1de7f 100644
--- a/nf_core/pipeline-template/CITATIONS.md
+++ b/nf_core/pipeline-template/CITATIONS.md
@@ -12,11 +12,10 @@
 
 ## Pipeline tools
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+{% if fastqc %}- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
-
-{% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+> {% endif %} > {% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 > {%- endif %}
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index 7718d2e5f8..a618f87bf7 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -44,8 +44,8 @@
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-   {% if multiqc %}2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)){% endif %}
+{% if fastqc %}1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)){% endif %}
+{% if multiqc %}2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)){% endif %}
 
 ## Usage
 
diff --git a/nf_core/pipeline-template/conf/modules.config b/nf_core/pipeline-template/conf/modules.config
index 84972d8e24..078142fad0 100644
--- a/nf_core/pipeline-template/conf/modules.config
+++ b/nf_core/pipeline-template/conf/modules.config
@@ -18,9 +18,11 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
+    {%- if fastqc %}
     withName: FASTQC {
         ext.args = '--quiet'
     }
+    {%- endif %}
 
     {%- if multiqc %}
     withName: 'MULTIQC' {
diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md
index 76195a6825..5e42d50cc5 100644
--- a/nf_core/pipeline-template/docs/output.md
+++ b/nf_core/pipeline-template/docs/output.md
@@ -12,10 +12,13 @@ The directories listed below will be created in the results directory after the
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-- [FastQC](#fastqc) - Raw read QC
-  {% if multiqc %}- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline{% endif %}
+{% if fastqc %}- [FastQC](#fastqc) - Raw read QC{% endif %}
+{% if multiqc %}- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline{% endif %}
+
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
+{%- if fastqc %}
+
 ### FastQC
 
 <details markdown="1">
@@ -28,7 +31,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 </details>
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
-
+{%- endif %}
 {%- if multiqc %}
 
 ### MultiQC
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 8b156083f3..6ab68d0f2a 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -5,11 +5,12 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    {%- if fastqc %}
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["modules"]
-                    }{%- if multiqc %},
+                    }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %}
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 3db8f66cb6..fe9e558cfe 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -230,7 +230,7 @@ def toolCitationText() {
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def citation_text = [
             "Tools used in the workflow included:",
-            "FastQC (Andrews 2010),",
+            {% if fastqc %}"FastQC (Andrews 2010),",{% endif %}
             "MultiQC (Ewels et al. 2016)",
             "."
         ].join(' ').trim()
@@ -243,7 +243,7 @@ def toolBibliographyText() {
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
-            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
+            {% if fastqc %}"<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",{% endif %}
             "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
         ].join(' ').trim()
 
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index d98c392f0c..e15d32f977 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -4,7 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { FASTQC                 } from '../modules/nf-core/fastqc/main'
+{% if fastqc %}include { FASTQC                 } from '../modules/nf-core/fastqc/main'{% endif %}
 {% if multiqc %}include { MULTIQC                } from '../modules/nf-core/multiqc/main'{% endif %}
 include { paramsSummaryMap       } from 'plugin/nf-validation'
 {% if multiqc %}include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
@@ -27,6 +27,7 @@ workflow {{ short_name|upper }} {
     ch_versions = Channel.empty()
     {% if multiqc %}ch_multiqc_files = Channel.empty(){% endif %}
 
+    {%- if fastqc %}
     //
     // MODULE: Run FastQC
     //
@@ -35,6 +36,7 @@ workflow {{ short_name|upper }} {
     )
     {% if multiqc %}ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}){% endif %}
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+    {%- endif %}
 
     //
     // Collate and save software versions
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 6a5fac358d..9fb56d610f 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -228,6 +228,16 @@ multiqc:
     multiqc_config: False
   nfcore_pipelines: True
   custom_pipelines: True
+fastqc:
+  skippable_paths:
+    - "modules/nf-core/fastqc/"
+  short_description: "Use fastqc"
+  description: "The pipeline will include the FastQC module which performs quality control analysis of input FASTQ files."
+  help_text: |
+    FastQC is a tool which provides quality control checks on raw sequencing data.
+    The pipeline will include the FastQC module.
+  nfcore_pipelines: True
+  custom_pipelines: True
 changelog:
   skippable_paths:
     - "CHANGELOG.md"

From e4f685d90e48c9ba0d01312eeae4fb2238afb000 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 21 Aug 2024 14:34:56 +0000
Subject: [PATCH 314/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1527f5ba49..6415612bbf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -30,6 +30,7 @@
 - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104))
 - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125))
 - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126))
+- add option to exclude fastqc from pipeline template ([#3129](https://github.com/nf-core/tools/pull/3129))
 
 ### Linting
 

From 0e4a7d1393fbe944f39e6c38219c43d02831999a Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 26 Aug 2024 11:31:14 +0200
Subject: [PATCH 315/414] don't fail when no nf-core modules installed

---
 nf_core/components/lint/__init__.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index d0f6685365..0373170cfb 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -114,9 +114,7 @@ def __init__(
                         )
                     )
             if not self.all_remote_components:
-                raise LookupError(
-                    f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline."
-                )
+                log.debug(f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline.")
             local_component_dir = Path(self.directory, self.component_type, "local")
 
             if local_component_dir.exists():
@@ -146,7 +144,7 @@ def __init__(
             ]
             self.all_local_components = []
             if not self.all_remote_components:
-                raise LookupError(f"No {self.component_type} in '{self.component_type}' directory")
+                log.debug(f"No {self.component_type} in '{self.component_type}' directory")
 
             # This could be better, perhaps glob for all nextflow.config files in?
             self.config = nf_core.utils.fetch_wf_config(self.directory / "tests" / "config", cache_config=True)

From 92618ad8be8362ba5bece5eb82ab44fc08012c21 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 26 Aug 2024 11:46:39 +0200
Subject: [PATCH 316/414] fix versions yaml file name

---
 nf_core/pipeline-template/workflows/pipeline.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index e15d32f977..8c797ede38 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -44,7 +44,7 @@ workflow {{ short_name|upper }} {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            name: {% if is_nfcore %}'nf_core_' {% else %} '' {% endif %} + 'pipeline_software_' + {% if multiqc %} 'mqc_' {% else %} '' {% endif %} + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }

From d437582e632ad7bed1768a684eafdeba13cd16cf Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 26 Aug 2024 12:46:28 +0200
Subject: [PATCH 317/414] udpate bpipe and fix pytests

---
 nf_core/components/lint/__init__.py |  4 ++--
 nf_core/modules/lint/__init__.py    |  2 +-
 tests/modules/test_lint.py          | 11 +++++------
 tests/subworkflows/test_lint.py     | 10 ++++------
 tests/test_modules.py               |  4 ++--
 5 files changed, 14 insertions(+), 17 deletions(-)

diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index 0373170cfb..c1b1f24cb7 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -114,7 +114,7 @@ def __init__(
                         )
                     )
             if not self.all_remote_components:
-                log.debug(f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline.")
+                log.warning(f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline.")
             local_component_dir = Path(self.directory, self.component_type, "local")
 
             if local_component_dir.exists():
@@ -144,7 +144,7 @@ def __init__(
             ]
             self.all_local_components = []
             if not self.all_remote_components:
-                log.debug(f"No {self.component_type} in '{self.component_type}' directory")
+                log.warning(f"No {self.component_type} in '{self.component_type}' directory")
 
             # This could be better, perhaps glob for all nextflow.config files in?
             self.config = nf_core.utils.fetch_wf_config(self.directory / "tests" / "config", cache_config=True)
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index b75f7e7570..017b3965b4 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -110,7 +110,7 @@ def lint(
         """
         # TODO: consider unifying modules and subworkflows lint() function and add it to the ComponentLint class
         # Prompt for module or all
-        if module is None and not all_modules:
+        if module is None and not all_modules and len(self.all_remote_components) > 0:
             questions = [
                 {
                     "type": "list",
diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py
index dfe288a6ee..cc7e0565e0 100644
--- a/tests/modules/test_lint.py
+++ b/tests/modules/test_lint.py
@@ -2,7 +2,6 @@
 from pathlib import Path
 from typing import Union
 
-import pytest
 import yaml
 from git.repo import Repo
 
@@ -191,8 +190,8 @@ def test_modules_lint_empty(self):
         """Test linting a pipeline with no modules installed"""
         self.mods_remove.remove("fastqc", force=True)
         self.mods_remove.remove("multiqc", force=True)
-        with pytest.raises(LookupError):
-            nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
+        nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
+        assert "No modules from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text
 
     def test_modules_lint_new_modules(self):
         """lint a new module"""
@@ -206,8 +205,8 @@ def test_modules_lint_no_gitlab(self):
         """Test linting a pipeline with no modules installed"""
         self.mods_remove.remove("fastqc", force=True)
         self.mods_remove.remove("multiqc", force=True)
-        with pytest.raises(LookupError):
-            nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
+        nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
+        assert f"No modules from {GITLAB_URL} installed in pipeline" in self.caplog.text
 
     def test_modules_lint_gitlab_modules(self):
         """Lint modules from a different remote"""
@@ -566,7 +565,7 @@ def test_modules_meta_yml_input_mismatch(self):
             fh.write(main_nf)
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) >= 0
-        assert len(module_lint.warned) == 2
+        assert len(module_lint.warned) == 2, f"Linting warning with {[x.__dict__ for x in module_lint.warned]}"
         lint_tests = [x.lint_test for x in module_lint.warned]
         # check that it is there twice:
         assert lint_tests.count("meta_input_meta_only") == 1
diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py
index 2693008707..c8b97fd0b0 100644
--- a/tests/subworkflows/test_lint.py
+++ b/tests/subworkflows/test_lint.py
@@ -2,8 +2,6 @@
 import shutil
 from pathlib import Path
 
-import pytest
-
 import nf_core.subworkflows
 
 from ..test_subworkflows import TestSubworkflows
@@ -25,8 +23,8 @@ def test_subworkflows_lint_empty(self):
         self.subworkflow_remove.remove("utils_nextflow_pipeline", force=True)
         self.subworkflow_remove.remove("utils_nfcore_pipeline", force=True)
         self.subworkflow_remove.remove("utils_nfvalidation_plugin", force=True)
-        with pytest.raises(LookupError):
-            nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
+        nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
+        assert "No subworkflows from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text
 
     def test_subworkflows_lint_new_subworkflow(self):
         """lint a new subworkflow"""
@@ -39,8 +37,8 @@ def test_subworkflows_lint_new_subworkflow(self):
 
     def test_subworkflows_lint_no_gitlab(self):
         """Test linting a pipeline with no subworkflows installed"""
-        with pytest.raises(LookupError):
-            nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
+        nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
+        assert f"No subworkflows from {GITLAB_URL} installed in pipeline" in self.caplog.text
 
     def test_subworkflows_lint_gitlab_subworkflows(self):
         """Lint subworkflows from a different remote"""
diff --git a/tests/test_modules.py b/tests/test_modules.py
index 9ce74fd4e1..0e16497176 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -44,8 +44,8 @@ def create_modules_repo_dummy(tmp_dir):
         yaml.dump(nf_core_yml.model_dump(), fh)
     # mock biocontainers and anaconda response
     with responses.RequestsMock() as rsps:
-        mock_anaconda_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0")
-        mock_biocontainers_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0")
+        mock_anaconda_api_calls(rsps, "bpipe", "0.9.13--hdfd78af_0")
+        mock_biocontainers_api_calls(rsps, "bpipe", "0.9.13--hdfd78af_0")
         # bpipe is a valid package on bioconda that is very unlikely to ever be added to nf-core/modules
         module_create = nf_core.modules.create.ModuleCreate(
             root_dir, "bpipe/test", "@author", "process_single", False, False

From 9551cdc3467dca4b4cd1bc3d3bf735340b9ee7bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Mon, 26 Aug 2024 14:21:37 +0200
Subject: [PATCH 318/414] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 nf_core/pipeline-template/conf/modules.config                 | 2 +-
 .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/conf/modules.config b/nf_core/pipeline-template/conf/modules.config
index 078142fad0..35e861d9b1 100644
--- a/nf_core/pipeline-template/conf/modules.config
+++ b/nf_core/pipeline-template/conf/modules.config
@@ -18,7 +18,7 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    {%- if fastqc %}
+    {% if fastqc -%}
     withName: FASTQC {
         ext.args = '--quiet'
     }
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index fe9e558cfe..b130b7f88a 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -231,7 +231,7 @@ def toolCitationText() {
     def citation_text = [
             "Tools used in the workflow included:",
             {% if fastqc %}"FastQC (Andrews 2010),",{% endif %}
-            "MultiQC (Ewels et al. 2016)",
+            {% if multiqc %}"MultiQC (Ewels et al. 2016)",{% endif %}
             "."
         ].join(' ').trim()
 
@@ -244,7 +244,7 @@ def toolBibliographyText() {
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
             {% if fastqc %}"<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",{% endif %}
-            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
+            {% if multiqc %}"<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"{% endif %}
         ].join(' ').trim()
 
     return reference_text

From 9d29e9342b5258b8c08f495d49409761707493c9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Mon, 26 Aug 2024 12:25:34 +0000
Subject: [PATCH 319/414] update textual snapshots

---
 .../__snapshots__/test_create_app.ambr        | 764 +++++++++---------
 .../pytest-0/test_github_details0             |   1 -
 .../pytest-0/test_github_exit_message0        |   1 -
 .../pytest-0/test_github_question0            |   1 -
 .../pytest-1/test_github_details0             |   1 -
 .../pytest-1/test_github_exit_message0        |   1 -
 .../pytest-1/test_github_question0            |   1 -
 7 files changed, 382 insertions(+), 388 deletions(-)
 delete mode 160000 tmp/pytest-of-gitpod/pytest-0/test_github_details0
 delete mode 160000 tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0
 delete mode 160000 tmp/pytest-of-gitpod/pytest-0/test_github_question0
 delete mode 160000 tmp/pytest-of-gitpod/pytest-1/test_github_details0
 delete mode 160000 tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0
 delete mode 160000 tmp/pytest-of-gitpod/pytest-1/test_github_question0

diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index ee470c915c..f5a19837b6 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
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diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_details0 b/tmp/pytest-of-gitpod/pytest-0/test_github_details0
deleted file mode 160000
index ee82f320cb..0000000000
--- a/tmp/pytest-of-gitpod/pytest-0/test_github_details0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit ee82f320cb567b302e7328c1cacab94a98dae787
diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0
deleted file mode 160000
index f7fe48cf9d..0000000000
--- a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit f7fe48cf9d00ab24581686a6d4226d2e9005c607
diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_question0 b/tmp/pytest-of-gitpod/pytest-0/test_github_question0
deleted file mode 160000
index dce3324acb..0000000000
--- a/tmp/pytest-of-gitpod/pytest-0/test_github_question0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit dce3324acbbe32f905afae8553e042f39404b37e
diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_details0 b/tmp/pytest-of-gitpod/pytest-1/test_github_details0
deleted file mode 160000
index e2638dca91..0000000000
--- a/tmp/pytest-of-gitpod/pytest-1/test_github_details0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit e2638dca91b137a96b491008b1eeef2bfd791bec
diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0
deleted file mode 160000
index 74cda800a8..0000000000
--- a/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 74cda800a86fd07e93bbf8e00e4890516e3d838d
diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_question0 b/tmp/pytest-of-gitpod/pytest-1/test_github_question0
deleted file mode 160000
index 444ebc5370..0000000000
--- a/tmp/pytest-of-gitpod/pytest-1/test_github_question0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 444ebc5370bf91ea808f5d65c5788064f0480045

From 52da9e369598bc69ad356b25c38d6c09fed940cf Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 21 Aug 2024 15:05:24 +0000
Subject: [PATCH 320/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6415612bbf..45d4fc18bd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,7 @@
 - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125))
 - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126))
 - add option to exclude fastqc from pipeline template ([#3129](https://github.com/nf-core/tools/pull/3129))
+- add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130))
 
 ### Linting
 

From a8cb9408d16ce47eda65baee2f73354b7566b72e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Mon, 26 Aug 2024 14:10:30 +0200
Subject: [PATCH 321/414] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 nf_core/pipelines/create/templatefeatures.yml | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 9fb56d610f..ab5f262374 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -310,3 +310,23 @@ slackreport:
       - ".prettierignore"
   nfcore_pipelines: False
   custom_pipelines: True
+documentation:
+  skippable_paths:
+    - "docs"
+  short_description: "Add documentation"
+  description: "Add documentation to the pipeline"
+  help_text: |
+    This will add documentation markdown files where you can describe your pipeline.
+    It includes:
+    - docs/README.md: A README file where you can describe the structure of your documentation.
+    - docs/output.md: A file where you can explain the output generated by the pipeline
+    - docs/usage.md: A file where you can explain the usage of the pipeline and its parameters.
+
+    These files come with an exemplary documentation structure written.
+  linting:
+    files_exist:
+      - "docs/output.md"
+      - "docs/README.md"
+      - "docs/usage.md"
+  nfcore_pipelines: False
+  custom_pipelines: True

From bcbed0567441c2e5d62f2525da1a2ebebc7d5a23 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 26 Aug 2024 15:55:44 +0200
Subject: [PATCH 322/414] update textual snapshots

---
 .../__snapshots__/test_create_app.ambr        | 512 +++++++++---------
 1 file changed, 256 insertions(+), 256 deletions(-)

diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index f5a19837b6..0015728fda 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
           font-weight: 700;
       }
   
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+      .terminal-3611359904-matrix {
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           font-size: 20px;
           line-height: 24.4px;
           font-variant-east-asian: full-width;
       }
   
-      .terminal-1136262003-title {
+      .terminal-3611359904-title {
           font-size: 18px;
           font-weight: bold;
           font-family: arial;
       }
   
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-  .terminal-1136262003-r4 { fill: #e1e1e1 }
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-  .terminal-1136262003-r7 { fill: #507bb3 }
-  .terminal-1136262003-r8 { fill: #e2e2e2 }
-  .terminal-1136262003-r9 { fill: #808080 }
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-  .terminal-1136262003-r18 { fill: #7ae998 }
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-  .terminal-1136262003-r22 { fill: #a7a9ab }
-  .terminal-1136262003-r23 { fill: #e2e3e3 }
+      .terminal-3611359904-r1 { fill: #c5c8c6 }
+  .terminal-3611359904-r2 { fill: #e3e3e3 }
+  .terminal-3611359904-r3 { fill: #989898 }
+  .terminal-3611359904-r4 { fill: #e1e1e1 }
+  .terminal-3611359904-r5 { fill: #4ebf71;font-weight: bold }
+  .terminal-3611359904-r6 { fill: #1e1e1e }
+  .terminal-3611359904-r7 { fill: #507bb3 }
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+  .terminal-3611359904-r9 { fill: #808080 }
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+  .terminal-3611359904-r12 { fill: #0178d4 }
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+  .terminal-3611359904-r14 { fill: #e2e3e3;font-weight: bold }
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+  .terminal-3611359904-r16 { fill: #e4e4e4 }
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+  .terminal-3611359904-r20 { fill: #008139 }
+  .terminal-3611359904-r21 { fill: #fea62b;font-weight: bold }
+  .terminal-3611359904-r22 { fill: #a7a9ab }
+  .terminal-3611359904-r23 { fill: #e2e3e3 }
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From d3d6345b5bc1519dd9426b66319043d05d0c2a85 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 22 Aug 2024 10:54:18 +0200
Subject: [PATCH 323/414] add option to exclude test configs from pipeline
 template

---
 .../create-test-lint-wf-template.yml          |  1 +
 .../pipeline-template/.github/CONTRIBUTING.md |  7 ++++-
 .../.github/PULL_REQUEST_TEMPLATE.md          |  2 ++
 .../.github/workflows/download_pipeline.yml   |  4 +--
 nf_core/pipeline-template/README.md           |  2 +-
 nf_core/pipeline-template/docs/usage.md       |  3 ++
 nf_core/pipeline-template/nextflow.config     |  4 ++-
 .../pipeline-template/nextflow_schema.json    |  4 +--
 nf_core/pipelines/create/templatefeatures.yml | 28 +++++++++++++++++++
 9 files changed, 48 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 70125a10f3..46f55a4b64 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -70,6 +70,7 @@ jobs:
           - TEMPLATE: is_nfcore
           - TEMPLATE: nf_core_configs
             profile: "self_hosted_runner"
+          - TEMPLATE: test_config
       fail-fast: false
 
     steps:
diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md
index 5a58501bb2..f331d38673 100644
--- a/nf_core/pipeline-template/.github/CONTRIBUTING.md
+++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md
@@ -30,16 +30,18 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
+{%- if test_config %}
 You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
 
 ```bash
 nf-test test --profile debug,test,docker --verbose
 ```
 
+{% endif %}
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 
-There are typically two types of tests that run:
+{% if test_config %}There are typically two types of tests that run:{% endif %}
 
 ### Lint tests
 
@@ -48,12 +50,15 @@ To enforce these and ensure that all pipelines stay in sync, we have developed a
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
+{%- if test_config %}
+
 ### Pipeline tests
 
 Each `nf-core` pipeline should be set up with a minimal set of test-data.
 `GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
 If there are any failures then the automated tests fail.
 These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
+{%- endif %}
 
 ## Patch
 
diff --git a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
index dee23ccab1..c96f2dd4c2 100644
--- a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
+++ b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
@@ -20,8 +20,10 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/t
 - [ ] If necessary, also make a PR on the {{ name }} _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
       {%- endif %}
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
+      {%- if test_config %}
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
+      {%- endif %}
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.
diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
index 99a42d86d2..e7a28e5ac4 100644
--- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
+++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -68,7 +68,7 @@ jobs:
           --download-configuration
 
       - name: Inspect download
-        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+        run: tree ./${{ env.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %}
 
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
@@ -83,4 +83,4 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %}
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %}{% endif %}
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index a618f87bf7..c8ed828d38 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -50,7 +50,7 @@
 ## Usage
 
 > [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. {% if test_config %}Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.{% endif %}
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md
index 1dc033eea5..ae2761797a 100644
--- a/nf_core/pipeline-template/docs/usage.md
+++ b/nf_core/pipeline-template/docs/usage.md
@@ -148,9 +148,12 @@ They are loaded in sequence, so later profiles can overwrite earlier profiles.
 
 If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment.
 
+{%- if test_config %}
+
 - `test`
   - A profile with a complete configuration for automated testing
   - Includes links to test data so needs no other parameters
+    {%- endif %}
 - `docker`
   - A generic configuration profile to be used with [Docker](https://docker.com/)
 - `singularity`
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 4a06efc984..b366884199 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -41,7 +41,7 @@ params {
     hook_url                     = null
     help                         = false
     version                      = false
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+    {% if test_config %}pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'{% endif %}
 
     {%- if nf_core_configs %}
     // Config options
@@ -189,8 +189,10 @@ profiles {
         executor.memory         = 8.GB
     }
     {%- endif %}
+    {%- if test_config %}
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
+    {%- endif %}
 }
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 4a376330bd..758689e89e 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -273,14 +273,14 @@
                     "description": "Validation of parameters in lenient more.",
                     "hidden": true,
                     "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
-                },
+                }{% if test_config %},
                 "pipelines_testdata_base_path": {
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
                     "description": "Base URL or local path to location of pipeline test dataset files",
                     "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                     "hidden": true
-                }
+                }{% endif %}
             }
         }
     },
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index ab5f262374..b795663e4e 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -330,3 +330,31 @@ documentation:
       - "docs/usage.md"
   nfcore_pipelines: False
   custom_pipelines: True
+test_config:
+  skippable_paths:
+    - "conf/test.config"
+    - "conf/test_full.config"
+    - ".github/workflows/awsfulltest.yml"
+    - ".github/workflows/awstest.yml"
+    - ".github/workflows/ci.yml"
+  short_description: "Add testing profiles"
+  description: "Add two default testing profiles"
+  help_text: |
+    This will add two default testing profiles to run the pipeline with different inputs.
+    You can customise them and add other test profiles.
+
+    These profiles can be used to run the pipeline with a minimal testing dataset with `nextflow run <your_pipeline> -profile test`.
+
+    The pipeline will include two profiles: `test` and `test_full`.
+    In nf-core, we typically use the `test` profile to run the pipeline with a minimal dataset and the `test_full` to run the pipeline with a larger dataset that simulates a real-world scenario.
+  linting:
+    files_exist:
+      - "conf/test.config"
+      - "conf/test_full.config"
+      - ".github/workflows/ci.yml"
+    nextflow_config: False
+    files_unchanged:
+      - ".github/CONTRIBUTING.md"
+      - ".github/PULL_REQUEST_TEMPLATE.md"
+  nfcore_pipelines: False
+  custom_pipelines: True

From b301c5c0d8ea2441b6037cfe90dcc9ed7ed43292 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 22 Aug 2024 08:59:49 +0000
Subject: [PATCH 324/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 45d4fc18bd..3d2f47a2d1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -32,6 +32,7 @@
 - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126))
 - add option to exclude fastqc from pipeline template ([#3129](https://github.com/nf-core/tools/pull/3129))
 - add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130))
+- add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133))
 
 ### Linting
 

From 4552219367be87b359fdc248cb81e58a0958a94d Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 26 Aug 2024 16:18:06 +0200
Subject: [PATCH 325/414] update textual snapshots

---
 .../__snapshots__/test_create_app.ambr        | 508 +++++++++---------
 1 file changed, 254 insertions(+), 254 deletions(-)

diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index 0015728fda..d8d5edbaf3 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
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From 25030e3389fa5b3f712420a902ca6ddadc01213d Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 26 Aug 2024 16:33:50 +0200
Subject: [PATCH 326/414] filter generated matrix with yq

---
 .github/workflows/create-test-lint-wf-template.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 46f55a4b64..85ce2230ab 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -44,7 +44,7 @@ jobs:
       - name: Create Matrix
         id: create_matrix
         run: |
-          echo "matrix=$(yq 'keys | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
+          echo "matrix=$(yq 'keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
 
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}
@@ -66,11 +66,8 @@ jobs:
             runner: ubuntu-latest
             profile: "docker"
         exclude:
-          - TEMPLATE: github
-          - TEMPLATE: is_nfcore
           - TEMPLATE: nf_core_configs
             profile: "self_hosted_runner"
-          - TEMPLATE: test_config
       fail-fast: false
 
     steps:

From 498435b68d266b085003d0958a4ce86ed47d7850 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 22 Aug 2024 11:11:46 +0200
Subject: [PATCH 327/414] add option to exclude tower.yml from pipeline
 template

---
 nf_core/pipelines/create/templatefeatures.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index b795663e4e..82ec111e42 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -358,3 +358,15 @@ test_config:
       - ".github/PULL_REQUEST_TEMPLATE.md"
   nfcore_pipelines: False
   custom_pipelines: True
+seqera_platform:
+  skippable_paths:
+    - "tower.yml"
+  short_description: "Add Seqera Platform output"
+  description: "Add a YAML file to specify which output files to upload when launching a pipeline from the Seqera Platform"
+  help_text: |
+    When launching a pipeline with the Seqera Platform, a `tower.yml` file can be used to add configuration options.
+
+    In the pipeline template, this file is used to specify the output files of you pipeline which will be shown on the reports tab of Seqera Platform.
+    You can extend this file adding any other desired configuration.
+  nfcore_pipelines: False
+  custom_pipelines: True

From 0f96bb3366637f4cc248ba89470a1d2a5eb6be6c Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 22 Aug 2024 09:13:54 +0000
Subject: [PATCH 328/414] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3d2f47a2d1..99e2f2427d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -33,6 +33,7 @@
 - add option to exclude fastqc from pipeline template ([#3129](https://github.com/nf-core/tools/pull/3129))
 - add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130))
 - add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133))
+- add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
 
 ### Linting
 

From b85ea4da6e8287aef01993009cfeac2e2c71b0cd Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 26 Aug 2024 17:21:14 +0200
Subject: [PATCH 329/414] update nf-schema subwf

---
 nf_core/pipeline-template/modules.json        |  2 +-
 .../utils_nfcore_pipeline_pipeline/main.nf    | 11 ++++++++--
 .../nf-core/utils_nfschema_plugin/main.nf     | 20 ++++++++++++++++---
 3 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 0a883b60b7..666546b6fb 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -32,7 +32,7 @@
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "a3e87febb28bd0461c22a917c5b2c1492053ef85",
+                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
                         "installed_by": ["subworkflows"]
                     }{% endif %}
                 }
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 0867a0a4c9..16f5784683 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -56,7 +56,9 @@ workflow PIPELINE_INITIALISATION {
     // Validate parameters and generate parameter summary to stdout
     //
     UTILS_NFSCHEMA_PLUGIN (
-        validate_params
+        workflow,
+        validate_params,
+        null
     )
     {% endif %}
 
@@ -128,6 +130,11 @@ workflow PIPELINE_COMPLETION {
     {% if multiqc %}multiqc_report  //  string: Path to MultiQC report{% endif %}
 
     main:
+    {% if nf_schema %}
+    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    {% else %}
+    summary_params = [:]
+    {% endif %}
 
     //
     // Completion email and summary
@@ -136,7 +143,7 @@ workflow PIPELINE_COMPLETION {
         {%- if email %}
         if (email || email_on_fail) {
             completionEmail(
-                {% if nf_schema %}paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json"){% else %}{}{% endif %},
+                summary_params,
                 email,
                 email_on_fail,
                 plaintext_email,
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
index 5d1dc7c928..4994303ea0 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -8,7 +8,13 @@ include { validateParameters } from 'plugin/nf-schema'
 workflow UTILS_NFSCHEMA_PLUGIN {
 
     take:
-    validate_params // boolean: validate the parameters
+    input_workflow      // workflow: the workflow object used by nf-schema to get metadata from the workflow
+    validate_params     // boolean:  validate the parameters
+    parameters_schema   // string:   path to the parameters JSON schema.
+                        //           this has to be the same as the schema given to `validation.parametersSchema`
+                        //           when this input is empty it will automatically use the configured schema or
+                        //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
+                        //           for meta pipelines
 
     main:
 
@@ -16,14 +22,22 @@ workflow UTILS_NFSCHEMA_PLUGIN {
     // Print parameter summary to stdout. This will display the parameters
     // that differ from the default given in the JSON schema
     //
-    log.info paramsSummaryLog(workflow)
+    if(parameters_schema) {
+        log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
+    } else {
+        log.info paramsSummaryLog(input_workflow)
+    }
 
     //
     // Validate the parameters using nextflow_schema.json or the schema
     // given via the validation.parametersSchema configuration option
     //
     if(validate_params) {
-        validateParameters()
+        if(parameters_schema) {
+            validateParameters(parameters_schema:parameters_schema)
+        } else {
+            validateParameters()
+        }
     }
 
     emit:

From 0dd8d6fc338b8cadac5f64e43812fc9b33efaa15 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 26 Aug 2024 17:23:59 +0200
Subject: [PATCH 330/414] update textual snapshots

---
 .../__snapshots__/test_create_app.ambr        | 512 +++++++++---------
 1 file changed, 256 insertions(+), 256 deletions(-)

diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index d8d5edbaf3..08676899a1 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
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From 0fb97db609f912b91b89129d423634b162dc4538 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 26 Aug 2024 17:27:44 +0200
Subject: [PATCH 331/414] fix some issues

---
 nf_core/pipeline-template/nextflow.config    | 2 +-
 tests/pipelines/lint/test_plugin_includes.py | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 3c238ee0ce..b4c7f41134 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -297,7 +297,7 @@ validation {
     summary {
         beforeText = validation.help.beforeText
         afterText = validation.help.afterText
-    }[% endif %]
+    }{% endif %}
 }
 {% endif -%}
 
diff --git a/tests/pipelines/lint/test_plugin_includes.py b/tests/pipelines/lint/test_plugin_includes.py
index 21e6107c14..ca14d5456d 100644
--- a/tests/pipelines/lint/test_plugin_includes.py
+++ b/tests/pipelines/lint/test_plugin_includes.py
@@ -2,11 +2,12 @@
 
 from ..test_lint import TestLint
 
+
 class TestLintNextflowConfig(TestLint):
     def setUp(self) -> None:
         super().setUp()
         self.new_pipeline = self._make_pipeline_copy()
-    
+
     def test_default_values_match(self):
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
         result = lint_obj.plugin_includes()
@@ -20,4 +21,4 @@ def test_wrong_include(self):
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
         result = lint_obj.plugin_includes()
         assert len(result["failed"]) == 1
-        assert len(result["warned"]) == 0
\ No newline at end of file
+        assert len(result["warned"]) == 0

From 7dee4476669957b3b53cd3e77dd7cdbc7b544a1a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 26 Aug 2024 17:33:20 +0200
Subject: [PATCH 332/414] fix linting utils_nfschema_plugin

---
 .../nf-core/utils_nfschema_plugin/meta.yml    | 13 ++++
 .../utils_nfschema_plugin/tests/main.nf.test  | 63 +++++++++++++++++--
 2 files changed, 72 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
index 90b8cb1898..f7d9f02885 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -9,9 +9,22 @@ keywords:
   - summary
 components: []
 input:
+  - input_workflow:
+      type: object
+      description: |
+        The workflow object of the used pipeline.
+        This object contains meta data used to create the params summary log
   - validate_params:
       type: boolean
       description: Validate the parameters and error if invalid.
+  - parameters_schema:
+      type: string
+      description: |
+        Path to the parameters JSON schema.
+        This has to be the same as the schema given to the `validation.parametersSchema` config
+        option. When this input is empty it will automatically use the configured schema or
+        "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
+        for meta pipelines.
 output:
   - dummy_emit:
       type: boolean
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 703d3a9b86..842dc432af 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -1,5 +1,3 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core subworkflows test utils_nfschema_plugin
 nextflow_workflow {
 
     name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
@@ -9,6 +7,7 @@ nextflow_workflow {
     tag "subworkflows"
     tag "subworkflows_nfcore"
     tag "subworkflows/utils_nfschema_plugin"
+    tag "plugin/nf-schema"
 
     config "./nextflow.config"
 
@@ -23,7 +22,9 @@ nextflow_workflow {
             workflow {
                 """
                 validate_params = false
-                input[0] = validate_params
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
                 """
             }
         }
@@ -47,7 +48,61 @@ nextflow_workflow {
             workflow {
                 """
                 validate_params = true
-                input[0] = validate_params
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+
+    test("Should run nothing - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = 1
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
                 """
             }
         }

From 6d01b0faf3c1f62dcc22724197bcf599089a8b3b Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 26 Aug 2024 17:36:32 +0200
Subject: [PATCH 333/414] update utils subwfs

---
 nf_core/pipeline-template/modules.json        |  4 +-
 .../nf-core/utils_nextflow_pipeline/main.nf   | 24 +++++-----
 .../tests/nextflow.config                     |  2 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     | 45 +++++++++----------
 .../tests/nextflow.config                     |  2 +-
 5 files changed, 37 insertions(+), 40 deletions(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 19df47df2e..ec1cf1d963 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -23,12 +23,12 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "20c03aede5a80ff520a905cea1f8ca121b5bb661",
+                        "git_sha": "2aacc9ef22bfc627b18eca17e9a3bb13c58aab64",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
+                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
                         "installed_by": ["subworkflows"]
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index e770d91b97..b54fc16c71 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -2,10 +2,6 @@
 // Subworkflow with functionality that may be useful for any Nextflow pipeline
 //
 
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 // Generate version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) {
     def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
     def filename   = "params_${timestamp}.json"
     def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
-    def jsonStr    = JsonOutput.toJson(params)
-    temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+    def jsonStr    = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text   = groovy.json.JsonOutput.prettyPrint(jsonStr)
 
-    FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
 }
 
@@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) {
 // When running with -profile conda, warn if channels have not been set-up appropriately
 //
 def checkCondaChannels() {
-    Yaml parser = new Yaml()
+    def parser = new org.yaml.snakeyaml.Yaml()
     def channels = []
     try {
         def config = parser.load("conda config --show channels".execute().text)
@@ -102,14 +98,16 @@ def checkCondaChannels() {
 
     // Check that all channels are present
     // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda']
+    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
     def channel_priority_violation = false
-    def n = required_channels_in_order.size()
-    for (int i = 0; i < n - 1; i++) {
-        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+
+    required_channels_in_order.eachWithIndex { channel, index ->
+        if (index < required_channels_in_order.size() - 1) {
+            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+        }
     }
 
     if (channels_missing | channel_priority_violation) {
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index 0fa4abaf43..a09572e5bb 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.10.0'
+    nextflowVersion = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 14558c3927..cbd8495bb6 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,9 +2,6 @@
 // Subworkflow with utility functions specific to the nf-core pipeline template
 //
 
-import org.yaml.snakeyaml.Yaml
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE {
 //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
 //
 def checkConfigProvided() {
-    valid_config = true
+    def valid_config = true as Boolean
     if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
         log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
             "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
@@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) {
 //
 def workflowCitation() {
     def temp_doi_ref = ""
-    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    def manifest_doi = workflow.manifest.doi.tokenize(",")
     // Using a loop to handle multiple DOIs
     // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
     // Removing ` ` since the manifest.doi is a string and not a proper list
-    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    manifest_doi.each { doi_ref ->
+        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    }
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
         temp_doi_ref + "\n" +
@@ -84,7 +83,7 @@ def workflowCitation() {
 // Generate workflow version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -102,8 +101,8 @@ def getWorkflowVersion() {
 // Get software versions for pipeline
 //
 def processVersionsFromYAML(yaml_file) {
-    Yaml yaml = new Yaml()
-    versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    def yaml = new org.yaml.snakeyaml.Yaml()
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -124,7 +123,7 @@ def workflowVersionToYAML() {
 def softwareVersionsToYAML(ch_versions) {
     return ch_versions
                 .unique()
-                .map { processVersionsFromYAML(it) }
+                .map { version -> processVersionsFromYAML(version) }
                 .unique()
                 .mix(Channel.of(workflowVersionToYAML()))
 }
@@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().each { group ->
         def group_params = summary_params.get(group)  // This gets the parameters of that particular group
         if (group_params) {
             summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
             summary_section += "    <dl class=\"dl-horizontal\">\n"
-            for (param in group_params.keySet()) {
+            group_params.keySet().sort().each { param ->
                 summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
             }
             summary_section += "    </dl>\n"
         }
     }
 
-    String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+    def yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
     yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
     yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
     yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
@@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) {
 // nf-core logo
 //
 def nfCoreLogo(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     String.format(
         """\n
         ${dashedLine(monochrome_logs)}
@@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) {
 // Return dashed line
 //
 def dashedLine(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     return "-${colors.dim}----------------------------------------------------${colors.reset}-"
 }
 
@@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) {
 // ANSII colours used for terminal logging
 //
 def logColours(monochrome_logs=true) {
-    Map colorcodes = [:]
+    def colorcodes = [:] as Map
 
     // Reset / Meta
     colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
@@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     }
 
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
@@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def sendmail_html          = sendmail_template.toString()
 
     // Send the HTML e-mail
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
@@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     // Write summary e-mail HTML to a file
     def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
     output_hf.delete()
 
     // Write summary e-mail TXT to a file
     def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
-    FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
     output_tf.delete()
 }
 
@@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 // Print pipeline summary on completion
 //
 def completionSummary(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (workflow.success) {
         if (workflow.stats.ignoredCount == 0) {
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
@@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
index 0fa4abaf43..d0a926bf6d 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.10.0'
+    nextflowVersion  = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }

From a7dcdd7b6a02a8cd4a4876a0b888d43de3252f66 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 09:19:09 +0200
Subject: [PATCH 334/414] fix some linting issues

---
 nf_core/pipelines/lint/files_exist.py     |  4 +-
 nf_core/pipelines/lint/nextflow_config.py | 67 +++++++++++------------
 nf_core/pipelines/schema.py               |  2 +-
 3 files changed, 35 insertions(+), 38 deletions(-)

diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index ad0605dcf7..e944882187 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -200,9 +200,7 @@ def files_exist(self) -> Dict[str, List[str]]:
         Path("Singularity"),
     ]
     files_warn_ifexists = [Path(".travis.yml")]
-    files_fail_ifinconfig: List[Tuple[Path, List[Dict[str, str]]]] = [
-        (Path("lib", "nfcore_external_java_deps.jar"), [{"plugins": "nf-validation"}, {"plugins": "nf-schema"}]),
-    ]
+    files_fail_ifinconfig: List[Tuple[Path, List[Dict[str, str]]]] = []
 
     # Remove files that should be ignored according to the linting config
     ignore_files = self.lint_config.get("files_exist", []) if self.lint_config is not None else []
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 71eb6f118f..2159d7939a 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -160,48 +160,47 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     # Lint for plugins
     config_plugins = ast.literal_eval(self.nf_config.get("plugins", "[]"))
     found_plugins = []
-    if len(config_plugins) == 0:
-        warned.append("nextflow.config contains an empty plugins scope")
     for plugin in config_plugins:
         if "@" not in plugin:
             failed.append(f"Plugin '{plugin}' does not have a pinned version")
         found_plugins.append(plugin.split("@")[0])
 
-    if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
-        failed.append("nextflow.config contains both nf-validation and nf-schema")
-    if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
-        warned.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
+    if "nf-validation" in found_plugins or "nf-schema" in found_plugins:
+        if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
+            failed.append("nextflow.config contains both nf-validation and nf-schema")
+        if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
+            warned.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
 
-    if "nf-schema" in found_plugins:
-        passed.append("Found nf-schema plugin")
-        if self.nf_config.get("validation.help.enabled", "false") == "false":
-            failed.append(
-                "The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages"
+        if "nf-schema" in found_plugins:
+            passed.append("Found nf-schema plugin")
+            if self.nf_config.get("validation.help.enabled", "false") == "false":
+                failed.append(
+                    "The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages"
+                )
+            config_fail.extend([["validation.help.enabled"]])
+            config_warn.extend(
+                [
+                    ["validation.help.beforeText"],
+                    ["validation.help.afterText"],
+                    ["validation.help.command"],
+                    ["validation.summary.beforeText"],
+                    ["validation.summary.afterText"],
+                ]
+            )
+            config_fail_ifdefined.extend(
+                [
+                    "params.validationFailUnrecognisedParams",
+                    "params.validationLenientMode",
+                    "params.validationSchemaIgnoreParams",
+                    "params.validationShowHiddenParams",
+                ]
             )
-        config_fail.extend([["validation.help.enabled"]])
-        config_warn.extend(
-            [
-                ["validation.help.beforeText"],
-                ["validation.help.afterText"],
-                ["validation.help.command"],
-                ["validation.summary.beforeText"],
-                ["validation.summary.afterText"],
-            ]
-        )
-        config_fail_ifdefined.extend(
-            [
-                "params.validationFailUnrecognisedParams",
-                "params.validationLenientMode",
-                "params.validationSchemaIgnoreParams",
-                "params.validationShowHiddenParams",
-            ]
-        )
 
-    if "nf-validation" in found_plugins:
-        passed.append("Found nf-validation plugin")
-        warned.append(
-            "nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/"
-        )
+        if "nf-validation" in found_plugins:
+            passed.append("Found nf-validation plugin")
+            warned.append(
+                "nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/"
+            )
 
     # Remove field that should be ignored according to the linting config
     ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else []
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index dbe851415f..13b8f62641 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -83,7 +83,7 @@ def _update_validation_plugin_from_config(self, config: str) -> None:
                 break
 
         if not plugin_found:
-            log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema")
+            log.info("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema notation for the JSON schema.")
 
         self.validation_plugin = plugin
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"

From fcdf65be8eef12b7f2c94f7e575c1fbaef8f51da Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 09:21:38 +0200
Subject: [PATCH 335/414] ruff

---
 nf_core/pipelines/schema.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 13b8f62641..76f085a49d 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -83,7 +83,9 @@ def _update_validation_plugin_from_config(self, config: str) -> None:
                 break
 
         if not plugin_found:
-            log.info("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema notation for the JSON schema.")
+            log.info(
+                "Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema notation for the JSON schema."
+            )
 
         self.validation_plugin = plugin
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"

From 56150dc2e95f0cd99752f263d56a649e5a9822b0 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 09:23:59 +0200
Subject: [PATCH 336/414] add linting doc for plugin_includes

---
 docs/api/_src/pipeline_lint_tests/plugin_includes.md | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 docs/api/_src/pipeline_lint_tests/plugin_includes.md

diff --git a/docs/api/_src/pipeline_lint_tests/plugin_includes.md b/docs/api/_src/pipeline_lint_tests/plugin_includes.md
new file mode 100644
index 0000000000..48bddadc80
--- /dev/null
+++ b/docs/api/_src/pipeline_lint_tests/plugin_includes.md
@@ -0,0 +1,5 @@
+# plugin_includes
+
+```{eval-rst}
+.. automethod:: nf_core.pipelines.lint.PipelineLint.plugin_includes
+```

From 5a29c4ef39faefc7f50e30f55c093411adb3f5e0 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 09:38:47 +0200
Subject: [PATCH 337/414] readd file exists check

---
 nf_core/pipelines/lint/files_exist.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index e944882187..7bfbae8ec9 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -198,6 +198,7 @@ def files_exist(self) -> Dict[str, List[str]]:
         Path("parameters.settings.json"),
         Path("pipeline_template.yml"),  # saving information in .nf-core.yml
         Path("Singularity"),
+        Path("lib", "nfcore_external_java_deps.jar"),
     ]
     files_warn_ifexists = [Path(".travis.yml")]
     files_fail_ifinconfig: List[Tuple[Path, List[Dict[str, str]]]] = []

From 18738ef7292891c4f7cd29676af2d4457769822c Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 09:50:58 +0200
Subject: [PATCH 338/414] fix launch command

---
 nf_core/pipelines/launch.py    | 23 ++++++++++++++++-------
 tests/pipelines/test_launch.py | 10 +++++-----
 2 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/nf_core/pipelines/launch.py b/nf_core/pipelines/launch.py
index e03982a25a..a14a8d6d72 100644
--- a/nf_core/pipelines/launch.py
+++ b/nf_core/pipelines/launch.py
@@ -263,15 +263,22 @@ def set_schema_inputs(self):
 
     def merge_nxf_flag_schema(self):
         """Take the Nextflow flag schema and merge it with the pipeline schema"""
+        if "allOf" not in self.schema_obj.schema:
+            self.schema_obj.schema["allOf"] = []
         # Add the coreNextflow subschema to the schema definitions
-        if "definitions" not in self.schema_obj.schema:
+        if "$defs" in self.schema_obj.schema or "definitions" not in self.schema_obj.schema:
+            if "$defs" not in self.schema_obj.schema:
+                self.schema_obj["$defs"] = {}
+            self.schema_obj.schema["$defs"].update(self.nxf_flag_schema)
+            self.schema_obj.schema["allOf"].insert(0, {"$ref": "#/$defs/coreNextflow"})
+
+        if "definitions" in self.schema_obj.schema:
             self.schema_obj.schema["definitions"] = {}
-        self.schema_obj.schema["definitions"].update(self.nxf_flag_schema)
+            self.schema_obj.schema["definitions"].update(self.nxf_flag_schema)
+            self.schema_obj.schema["allOf"].insert(0, {"$ref": "#/definitions/coreNextflow"})
         # Add the new defintion to the allOf key so that it's included in validation
         # Put it at the start of the list so that it comes first
-        if "allOf" not in self.schema_obj.schema:
-            self.schema_obj.schema["allOf"] = []
-        self.schema_obj.schema["allOf"].insert(0, {"$ref": "#/definitions/coreNextflow"})
+
 
     def prompt_web_gui(self):
         """Ask whether to use the web-based or cli wizard to collect params"""
@@ -379,7 +386,8 @@ def sanitise_web_response(self):
         for param_id, param_obj in self.schema_obj.schema.get("properties", {}).items():
             questionary_objects[param_id] = self.single_param_to_questionary(param_id, param_obj, print_help=False)
 
-        for _, definition in self.schema_obj.schema.get("definitions", {}).items():
+        definitions_schemas = self.schema_obj.schema.get("$defs", self.schema_obj.schema.get("definitions", {})).items()
+        for _, definition in definitions_schemas:
             for param_id, param_obj in definition.get("properties", {}).items():
                 questionary_objects[param_id] = self.single_param_to_questionary(param_id, param_obj, print_help=False)
 
@@ -399,9 +407,10 @@ def prompt_schema(self):
         """Go through the pipeline schema and prompt user to change defaults"""
         answers = {}
         # Start with the subschema in the definitions - use order of allOf
+        definitions_schemas = self.schema_obj.schema.get("$defs", self.schema_obj.schema.get("definitions", {})).items()
         for allOf in self.schema_obj.schema.get("allOf", []):
             d_key = allOf["$ref"][14:]
-            answers.update(self.prompt_group(d_key, self.schema_obj.schema["definitions"][d_key]))
+            answers.update(self.prompt_group(d_key, definitions_schemas[d_key]))
 
         # Top level schema params
         for param_id, param_obj in self.schema_obj.schema.get("properties", {}).items():
diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py
index 7c6e3d6196..d63e7b6dc5 100644
--- a/tests/pipelines/test_launch.py
+++ b/tests/pipelines/test_launch.py
@@ -47,7 +47,7 @@ def test_launch_file_exists_overwrite(self, mock_webbrowser, mock_lauch_web_gui,
     def test_get_pipeline_schema(self):
         """Test loading the params schema from a pipeline"""
         self.launcher.get_pipeline_schema()
-        assert len(self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]) > 2
+        assert len(self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]) > 2
 
     @with_temporary_folder
     def test_make_pipeline_schema(self, tmp_path):
@@ -60,8 +60,8 @@ def test_make_pipeline_schema(self, tmp_path):
         Path(test_pipeline_dir, "nextflow_schema.json").unlink()
         self.launcher = nf_core.pipelines.launch.Launch(test_pipeline_dir, params_out=self.nf_params_fn)
         self.launcher.get_pipeline_schema()
-        assert len(self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]) >= 2
-        assert self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]["outdir"] == {
+        assert len(self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]) >= 2
+        assert self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]["outdir"] == {
             "type": "string",
             "format": "directory-path",
             "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
@@ -91,8 +91,8 @@ def test_nf_merge_schema(self):
         self.launcher.get_pipeline_schema()
         self.launcher.set_schema_inputs()
         self.launcher.merge_nxf_flag_schema()
-        assert self.launcher.schema_obj.schema["allOf"][0] == {"$ref": "#/definitions/coreNextflow"}
-        assert "-resume" in self.launcher.schema_obj.schema["definitions"]["coreNextflow"]["properties"]
+        assert self.launcher.schema_obj.schema["allOf"][0] == {"$ref": "#/$defs/coreNextflow"}
+        assert "-resume" in self.launcher.schema_obj.schema["$defs"]["coreNextflow"]["properties"]
 
     def test_ob_to_questionary_string(self):
         """Check converting a python dict to a pyenquirer format - simple strings"""

From ebf6a27c7d9869e19d8bf5c67467bf59cb7d543c Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 10:26:00 +0200
Subject: [PATCH 339/414] fix schema tests

---
 nf_core/pipelines/schema.py    | 13 ++++++-----
 tests/pipelines/test_schema.py | 41 ++++++++++++++++++----------------
 2 files changed, 29 insertions(+), 25 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 76f085a49d..6c1c198bb8 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -54,9 +54,7 @@ def __init__(self):
     # Update the validation plugin code everytime the schema gets changed
     def set_schema_filename(self, schema: str) -> None:
         self._schema_filename = schema
-        basepath = "/".join(str(schema).split("/")[:-1])
-        config = f"{basepath}/nextflow.config" if basepath != "" else "nextflow.config"
-        self._update_validation_plugin_from_config(config)
+        self._update_validation_plugin_from_config()
 
     def get_schema_filename(self) -> str:
         return self._schema_filename
@@ -66,9 +64,12 @@ def del_schema_filename(self) -> None:
 
     schema_filename = property(get_schema_filename, set_schema_filename, del_schema_filename)
 
-    def _update_validation_plugin_from_config(self, config: str) -> None:
+    def _update_validation_plugin_from_config(self) -> None:
         plugin = "nf-schema"
-        conf = nf_core.utils.fetch_wf_config(Path(self.schema_filename).parent)
+        if self.schema_filename:
+            conf = nf_core.utils.fetch_wf_config(Path(self.schema_filename).parent)
+        else:
+            conf = nf_core.utils.fetch_wf_config(Path(self.pipeline_dir))
 
         plugins = str(conf.get("plugins", "")).strip('"').strip("'").strip(" ").split(",")
         plugin_found = False
@@ -464,7 +465,7 @@ def validate_schema(self, schema=None):
             for d_param_id in d_schema.get("properties", {}):
                 # Check that we don't have any duplicate parameter IDs in different definitions
                 if d_param_id in param_keys:
-                    raise AssertionError(f"Duplicate parameter found in schema `definitions`: `{d_param_id}`")
+                    raise AssertionError(f"Duplicate parameter found in schema `{self.defs_notation}`: `{d_param_id}`")
                 param_keys.append(d_param_id)
                 num_params += 1
 
diff --git a/tests/pipelines/test_schema.py b/tests/pipelines/test_schema.py
index 777d959e66..2abaf07bd2 100644
--- a/tests/pipelines/test_schema.py
+++ b/tests/pipelines/test_schema.py
@@ -24,6 +24,9 @@ class TestSchema(unittest.TestCase):
     def setUp(self):
         """Create a new PipelineSchema object"""
         self.schema_obj = nf_core.pipelines.schema.PipelineSchema()
+        self.schema_obj.schema_draft = "https://json-schema.org/draft/2020-12/schema"
+        self.schema_obj.defs_notation = "$defs"
+        self.schema_obj.validation_plugin = "nf-schema"
         self.root_repo_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
 
         # Create a test pipeline in temp directory
@@ -105,7 +108,7 @@ def test_schema_docs(self):
         docs = self.schema_obj.print_documentation()
         assert self.schema_obj.schema["title"] in docs
         assert self.schema_obj.schema["description"] in docs
-        for definition in self.schema_obj.schema.get("definitions", {}).values():
+        for definition in self.schema_obj.schema.get("$defs", {}).values():
             assert definition["title"] in docs
             assert definition["description"] in docs
 
@@ -175,43 +178,43 @@ def test_validate_schema_fail_duplicate_ids(self):
         Check that the schema validation fails when we have duplicate IDs in definition subschema
         """
         self.schema_obj.schema = {
-            "$schema": "http://json-schema.org/draft-07/schema",
-            "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"foo": {}}}},
-            "allOf": [{"$ref": "#/definitions/groupOne"}, {"$ref": "#/definitions/groupTwo"}],
+            "$schema": "https://json-schema.org/draft/2020-12/schema",
+            "$defs": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"foo": {}}}},
+            "allOf": [{"$ref": "#/$defs/groupOne"}, {"$ref": "#/$defs/groupTwo"}],
         }
         with pytest.raises(AssertionError) as exc_info:
             self.schema_obj.validate_schema(self.schema_obj.schema)
-        assert exc_info.value.args[0] == "Duplicate parameter found in schema `definitions`: `foo`"
+        assert exc_info.value.args[0] == "Duplicate parameter found in schema `$defs`: `foo`"
 
     def test_validate_schema_fail_missing_def(self):
         """
-        Check that the schema validation fails when we a definition in allOf is not in definitions
+        Check that the schema validation fails when we a definition in allOf is not in $defs
         """
         self.schema_obj.schema = {
-            "$schema": "http://json-schema.org/draft-07/schema",
-            "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
-            "allOf": [{"$ref": "#/definitions/groupOne"}],
+            "$schema": "https://json-schema.org/draft/2020-12/schema",
+            "$defs": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
+            "allOf": [{"$ref": "#/$defs/groupOne"}],
         }
         with pytest.raises(AssertionError) as exc_info:
             self.schema_obj.validate_schema(self.schema_obj.schema)
-        assert exc_info.value.args[0] == "Definition subschema `#/definitions/groupTwo` not included in schema `allOf`"
+        assert exc_info.value.args[0] == "Definition subschema `#/$defs/groupTwo` not included in schema `allOf`"
 
     def test_validate_schema_fail_unexpected_allof(self):
         """
         Check that the schema validation fails when we an unrecognised definition is in allOf
         """
         self.schema_obj.schema = {
-            "$schema": "http://json-schema.org/draft-07/schema",
-            "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
+            "$schema": "https://json-schema.org/draft/2020-12/schema",
+            "$defs": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
             "allOf": [
-                {"$ref": "#/definitions/groupOne"},
-                {"$ref": "#/definitions/groupTwo"},
-                {"$ref": "#/definitions/groupThree"},
+                {"$ref": "#/$defs/groupOne"},
+                {"$ref": "#/$defs/groupTwo"},
+                {"$ref": "#/$defs/groupThree"},
             ],
         }
         with pytest.raises(AssertionError) as exc_info:
             self.schema_obj.validate_schema(self.schema_obj.schema)
-        assert exc_info.value.args[0] == "Subschema `groupThree` found in `allOf` but not `definitions`"
+        assert exc_info.value.args[0] == "Subschema `groupThree` found in `allOf` but not `$defs`"
 
     def test_make_skeleton_schema(self):
         """Test making a new schema skeleton"""
@@ -267,7 +270,7 @@ def test_remove_schema_notfound_configs_childschema(self):
         even when they're in a group
         """
         self.schema_obj.schema = {
-            "definitions": {
+            "$defs": {
                 "subSchemaId": {
                     "properties": {"foo": {"type": "string"}, "bar": {"type": "string"}},
                     "required": ["foo"],
@@ -277,8 +280,8 @@ def test_remove_schema_notfound_configs_childschema(self):
         self.schema_obj.pipeline_params = {"bar": True}
         self.schema_obj.no_prompts = True
         params_removed = self.schema_obj.remove_schema_notfound_configs()
-        assert len(self.schema_obj.schema["definitions"]["subSchemaId"]["properties"]) == 1
-        assert "required" not in self.schema_obj.schema["definitions"]["subSchemaId"]
+        assert len(self.schema_obj.schema["$defs"]["subSchemaId"]["properties"]) == 1
+        assert "required" not in self.schema_obj.schema["$defs"]["subSchemaId"]
         assert len(params_removed) == 1
         assert "foo" in params_removed
 

From 04fabe5d38eb2b948903645137d98a37cd532567 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 10:26:47 +0200
Subject: [PATCH 340/414] ruff

---
 nf_core/pipelines/launch.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nf_core/pipelines/launch.py b/nf_core/pipelines/launch.py
index a14a8d6d72..a80639ea94 100644
--- a/nf_core/pipelines/launch.py
+++ b/nf_core/pipelines/launch.py
@@ -279,7 +279,6 @@ def merge_nxf_flag_schema(self):
         # Add the new defintion to the allOf key so that it's included in validation
         # Put it at the start of the list so that it comes first
 
-
     def prompt_web_gui(self):
         """Ask whether to use the web-based or cli wizard to collect params"""
         log.info(

From 0649a756bd4727926951be3a17b6bf643ea93dae Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 10:31:07 +0200
Subject: [PATCH 341/414] readd file exists check

---
 tests/pipelines/lint/test_files_exist.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/pipelines/lint/test_files_exist.py b/tests/pipelines/lint/test_files_exist.py
index 85ba817536..65217903f8 100644
--- a/tests/pipelines/lint/test_files_exist.py
+++ b/tests/pipelines/lint/test_files_exist.py
@@ -62,7 +62,7 @@ def test_files_exist_pass_conditional(self):
         lib_dir.mkdir()
         (lib_dir / "nfcore_external_java_deps.jar").touch()
         results = lint_obj.files_exist()
-        assert results["failed"] == []
+        assert results["failed"] == ["File must be removed: `lib/nfcore_external_java_deps.jar`"]
         assert results["ignored"] == []
 
     def test_files_exist_fail_conditional(self):

From 9fd98692e9eb22514f9a107509b12c4cfc2df14e Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 10:41:23 +0200
Subject: [PATCH 342/414] fix lint test

---
 tests/subworkflows/test_lint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py
index c8b97fd0b0..56574b865c 100644
--- a/tests/subworkflows/test_lint.py
+++ b/tests/subworkflows/test_lint.py
@@ -22,7 +22,7 @@ def test_subworkflows_lint_empty(self):
         """Test linting a pipeline with no subworkflows installed"""
         self.subworkflow_remove.remove("utils_nextflow_pipeline", force=True)
         self.subworkflow_remove.remove("utils_nfcore_pipeline", force=True)
-        self.subworkflow_remove.remove("utils_nfvalidation_plugin", force=True)
+        self.subworkflow_remove.remove("utils_nfschema_plugin", force=True)
         nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
         assert "No subworkflows from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text
 

From 6cccc1e8aa650ccc13f4e9159265d42f84f9f9e5 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 11:16:07 +0200
Subject: [PATCH 343/414] update textual snapshots

---
 .../__snapshots__/test_create_app.ambr        | 762 +++++++++---------
 1 file changed, 381 insertions(+), 381 deletions(-)

diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index 08676899a1..3ed8349ee1 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
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From 2ccbdd9b64bd9e3cb2792408a3920c6bc314dba4 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 11:37:05 +0200
Subject: [PATCH 344/414] skip linting before and after Text params for custom
 pipelines

---
 nf_core/pipelines/create/templatefeatures.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 7fd7880cba..057b5a6f33 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -141,6 +141,10 @@ is_nfcore:
     nextflow_config:
       - "manifest.name"
       - "manifest.homePage"
+      - "validation.help.beforeText"
+      - "validation.help.afterText"
+      - "validation.sumary.beforeText"
+      - "validation.sumary.afterText"
     multiqc_config:
       - "report_comment"
   nfcore_pipelines: False

From ed01eba16b92d98db06eaa10bfe6282cd41821df Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 11:42:50 +0200
Subject: [PATCH 345/414] typo

---
 nf_core/pipelines/create/templatefeatures.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 057b5a6f33..940d124085 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -143,8 +143,8 @@ is_nfcore:
       - "manifest.homePage"
       - "validation.help.beforeText"
       - "validation.help.afterText"
-      - "validation.sumary.beforeText"
-      - "validation.sumary.afterText"
+      - "validation.summary.beforeText"
+      - "validation.summary.afterText"
     multiqc_config:
       - "report_comment"
   nfcore_pipelines: False

From 1b597f17c3ea20e5932f1b92b72887190a5a9a9c Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 12:38:04 +0200
Subject: [PATCH 346/414] Update nf_core/pipeline-template/nextflow.config
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 nf_core/pipeline-template/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index b4c7f41134..c9437d45f2 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -275,7 +275,7 @@ validation {
     help {
         enabled = true
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-        {% if is_nfcore %}
+        {%- if is_nfcore %}
         beforeText = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m

From 93cc41be471cd4e50eb83ed5547e4d65496b65fc Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 12:40:36 +0200
Subject: [PATCH 347/414] Update
 nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 4fcda5a7da..92aaa52a11 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -130,7 +130,7 @@ workflow PIPELINE_COMPLETION {
     {% if multiqc %}multiqc_report  //  string: Path to MultiQC report{% endif %}
 
     main:
-    {% if nf_schema %}
+    {%- if nf_schema %}
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
     {% else %}
     summary_params = [:]

From 6e358f3fdb2e2a893a87e7a642e61d788d4c8d8c Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 12:40:44 +0200
Subject: [PATCH 348/414] Update
 nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 92aaa52a11..71c96dea1c 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -132,7 +132,7 @@ workflow PIPELINE_COMPLETION {
     main:
     {%- if nf_schema %}
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-    {% else %}
+    {%- else %}
     summary_params = [:]
     {% endif %}
 

From dbe9318ac9eb698f6c4d53c2768217289574ba47 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 12:40:53 +0200
Subject: [PATCH 349/414] Update
 nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 71c96dea1c..ae66f3674c 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -134,7 +134,7 @@ workflow PIPELINE_COMPLETION {
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
     {%- else %}
     summary_params = [:]
-    {% endif %}
+    {%- endif %}
 
     //
     // Completion email and summary

From 4025b546d6a9090099636fe821e489d1fd07ba45 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 12:41:26 +0200
Subject: [PATCH 350/414] Update nf_core/pipelines/create/templatefeatures.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 nf_core/pipelines/create/templatefeatures.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 940d124085..8d31852ab9 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -260,7 +260,7 @@ nf_schema:
   skippable_paths:
     - "subworkflows/nf-core/utils_nfschema_plugin"
   short_description: "Use nf-schema"
-  description: "Use nf-schema for this pipeline."
+  description: "Use the nf-schema Nextflow plugin for this pipeline."
   help_text: |
     nf-schema is used to validate input parameters based on a JSON schema.
     It also provides helper functionality to create help messages, get a summary

From 679de826cfd3e6526d718e2d95a8ba2da057d512 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 12:42:58 +0200
Subject: [PATCH 351/414] Update tests/pipelines/lint/test_plugin_includes.py
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 tests/pipelines/lint/test_plugin_includes.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/pipelines/lint/test_plugin_includes.py b/tests/pipelines/lint/test_plugin_includes.py
index ca14d5456d..8eb31e2671 100644
--- a/tests/pipelines/lint/test_plugin_includes.py
+++ b/tests/pipelines/lint/test_plugin_includes.py
@@ -3,7 +3,7 @@
 from ..test_lint import TestLint
 
 
-class TestLintNextflowConfig(TestLint):
+class TestLintPluginIncludes(TestLint):
     def setUp(self) -> None:
         super().setUp()
         self.new_pipeline = self._make_pipeline_copy()

From 3ac1bd8e42a986381c12941b94ce786f8fb393f4 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 12:46:56 +0200
Subject: [PATCH 352/414] review suggestions

---
 nf_core/pipeline-template/modules.json        |  2 +-
 .../nf-core/utils_nextflow_pipeline/main.nf   |  2 +-
 nf_core/pipelines/lint/files_exist.py         | 22 ++-----------------
 tests/pipelines/lint/test_files_exist.py      | 21 ------------------
 4 files changed, 4 insertions(+), 43 deletions(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index ec1cf1d963..9f44a4a672 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -23,7 +23,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "2aacc9ef22bfc627b18eca17e9a3bb13c58aab64",
+                        "git_sha": "0710581f16d6f4e6b27ab6f410757c8259fdd6f4",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index b54fc16c71..28e32b200e 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -98,7 +98,7 @@ def checkCondaChannels() {
 
     // Check that all channels are present
     // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    def required_channels_in_order = ['conda-forge', 'bioconda']
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index 7bfbae8ec9..99f2d1b937 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -1,6 +1,6 @@
 import logging
 from pathlib import Path
-from typing import Dict, List, Tuple, Union
+from typing import Dict, List, Union
 
 log = logging.getLogger(__name__)
 
@@ -201,7 +201,6 @@ def files_exist(self) -> Dict[str, List[str]]:
         Path("lib", "nfcore_external_java_deps.jar"),
     ]
     files_warn_ifexists = [Path(".travis.yml")]
-    files_fail_ifinconfig: List[Tuple[Path, List[Dict[str, str]]]] = []
 
     # Remove files that should be ignored according to the linting config
     ignore_files = self.lint_config.get("files_exist", []) if self.lint_config is not None else []
@@ -240,24 +239,7 @@ def pf(file_path: Union[str, Path]) -> Path:
             failed.append(f"File must be removed: {self._wrap_quotes(file)}")
         else:
             passed.append(f"File not found check: {self._wrap_quotes(file)}")
-    # Files that cause an error if they exists together with a certain entry in nextflow.config
-    for file_cond in files_fail_ifinconfig:
-        if str(file_cond[0]) in ignore_files:
-            continue
-        in_config = False
-        for condition in file_cond[1]:
-            config_key, config_value = list(condition.items())[0]
-            if config_key in self.nf_config and config_value in self.nf_config[config_key]:
-                log.debug(f"Found {config_key} in nextflow.config with value {config_value}")
-                in_config = True
-        if pf(file_cond[0]).is_file() and in_config:
-            failed.append(f"File must be removed: {self._wrap_quotes(file_cond[0])}")
-        elif pf(file_cond[0]).is_file() and not in_config:
-            passed.append(f"File found check: {self._wrap_quotes(file_cond[0])}")
-        elif not pf(file_cond[0]).is_file() and not in_config:
-            failed.append(f"File not found check: {self._wrap_quotes(file_cond[0])}")
-        elif not pf(file_cond[0]).is_file() and in_config:
-            passed.append(f"File not found check: {self._wrap_quotes(file_cond[0])}")
+
     # Files that cause a warning if they exist
     for file in files_warn_ifexists:
         if str(file) in ignore_files:
diff --git a/tests/pipelines/lint/test_files_exist.py b/tests/pipelines/lint/test_files_exist.py
index 65217903f8..97dd346cdf 100644
--- a/tests/pipelines/lint/test_files_exist.py
+++ b/tests/pipelines/lint/test_files_exist.py
@@ -54,27 +54,6 @@ def test_files_exist_pass(self):
         results = lint_obj.files_exist()
         assert results["failed"] == []
 
-    def test_files_exist_pass_conditional(self):
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
-        lint_obj.nf_config["plugins"] = []
-        lib_dir = Path(self.new_pipeline, "lib")
-        lib_dir.mkdir()
-        (lib_dir / "nfcore_external_java_deps.jar").touch()
-        results = lint_obj.files_exist()
-        assert results["failed"] == ["File must be removed: `lib/nfcore_external_java_deps.jar`"]
-        assert results["ignored"] == []
-
-    def test_files_exist_fail_conditional(self):
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
-        lib_dir = Path(self.new_pipeline, "lib")
-        lib_dir.mkdir()
-        (lib_dir / "nfcore_external_java_deps.jar").touch()
-        results = lint_obj.files_exist()
-        assert results["failed"] == ["File must be removed: `lib/nfcore_external_java_deps.jar`"]
-        assert results["ignored"] == []
-
     def test_files_exist_pass_conditional_nfschema(self):
         # replace nf-validation with nf-schema in nextflow.config
         with open(Path(self.new_pipeline, "nextflow.config")) as f:

From d4266c0bb19027db883107d47a50ace106affff7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 13:32:53 +0200
Subject: [PATCH 353/414] use latest version of utils_nextflow_pipeline

---
 nf_core/pipeline-template/modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 9f44a4a672..caeaac2fdf 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -23,7 +23,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "0710581f16d6f4e6b27ab6f410757c8259fdd6f4",
+                        "git_sha": "16f913a1ea8bb2cc48ccfc0b3b9406c5b3333799",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {

From bc20099658a5a66e2ca3cc982b2e7cc4735bbab8 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 13:52:18 +0200
Subject: [PATCH 354/414] make help params snake_case

---
 nf_core/pipeline-template/nextflow.config | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index c9437d45f2..8818ec54db 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -40,8 +40,8 @@ params {
     monochrome_logs              = false
     hook_url                     = null
     {% if nf_schema %}help                         = false
-    helpFull                     = false
-    showHidden                   = false{% endif %}
+    help_full                    = false
+    show_hidden                  = false{% endif %}
     version                      = false
     {% if test_config %}pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'{% endif %}
 
@@ -275,6 +275,8 @@ validation {
     help {
         enabled = true
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        fullParameter = "help_full"
+        showHiddenParameter = "show_hidden"
         {%- if is_nfcore %}
         beforeText = """
 -\033[2m----------------------------------------------------\033[0m-

From 829d594be396edd5a2d54d8536972689b64b5fe6 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 14:33:58 +0200
Subject: [PATCH 355/414] Update nf_core/pipelines/create/templatefeatures.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 nf_core/pipelines/create/templatefeatures.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 8d31852ab9..7388ecc7ba 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -262,7 +262,7 @@ nf_schema:
   short_description: "Use nf-schema"
   description: "Use the nf-schema Nextflow plugin for this pipeline."
   help_text: |
-    nf-schema is used to validate input parameters based on a JSON schema.
+    [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) is used to validate input parameters based on a JSON schema.
     It also provides helper functionality to create help messages, get a summary
     of changed parameters and validate and convert a samplesheet to a channel.
   nfcore_pipelines: True

From 1ff7cbcfe58015b636c8edd852ac422e74598770 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 14:34:25 +0200
Subject: [PATCH 356/414] Update nf_core/pipelines/lint/plugin_includes.py
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 nf_core/pipelines/lint/plugin_includes.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py
index 6a57b1d280..4fc40ae26c 100644
--- a/nf_core/pipelines/lint/plugin_includes.py
+++ b/nf_core/pipelines/lint/plugin_includes.py
@@ -16,10 +16,10 @@ def plugin_includes(self) -> Dict[str, List[str]]:
     config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", "[]"))]
     validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema"
 
-    passed: list[str] = []
-    warned: list[str] = []
-    failed: list[str] = []
-    ignored: list[str] = []
+    passed: List[str] = []
+    warned: List[str] = []
+    failed: List[str] = []
+    ignored: List[str] = []
 
     plugin_include_pattern = re.compile(r"^include\s*{[^}]+}\s*from\s*[\"']plugin/([^\"']+)[\"']\s*$", re.MULTILINE)
     workflow_files = [

From aed94601c7241546def06c226758c96688587cb2 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 14:37:03 +0200
Subject: [PATCH 357/414] apply review suggestions

---
 nf_core/pipelines/lint/nextflow_config.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 2159d7939a..790fc21797 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -168,8 +168,6 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     if "nf-validation" in found_plugins or "nf-schema" in found_plugins:
         if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
             failed.append("nextflow.config contains both nf-validation and nf-schema")
-        if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
-            warned.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
 
         if "nf-schema" in found_plugins:
             passed.append("Found nf-schema plugin")

From 4407901d8c7a039d97ee45390ead386611de42e2 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 14:41:53 +0200
Subject: [PATCH 358/414] update utils_nextflow_pipeline commit messages

---
 nf_core/pipeline-template/modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index caeaac2fdf..367202155a 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -23,7 +23,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "16f913a1ea8bb2cc48ccfc0b3b9406c5b3333799",
+                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {

From 330e43c76109f500ee88bdeddd0ef578751d8376 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 14:48:37 +0200
Subject: [PATCH 359/414] update ignoring of help params

---
 nf_core/pipelines/schema.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 6c1c198bb8..95ed5e5b6e 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -92,7 +92,11 @@ def _update_validation_plugin_from_config(self) -> None:
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
         if plugin == "nf-schema":
             self.defs_notation = "$defs"
-            ignored_params = ["help", "helpFull", "showHidden"]  # Help parameter should be ignored by default
+            ignored_params = [
+                conf.get("validation.help.shortParameter", "help"),
+                conf.get("validation.help.fullParameter", "helpFull"),
+                conf.get("validation.help.showHiddenParameter", "showHidden"),
+            ]  # Help parameter should be ignored by default
             ignored_params_config = conf.get("validation", {}).get("defaultIgnoreParams", [])
             if len(ignored_params_config) > 0:
                 ignored_params.extend(ignored_params_config)

From 3600db75edf62709fcd48c6174c6b698c95c93f3 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 14:57:12 +0200
Subject: [PATCH 360/414] update file exists docstring

---
 nf_core/pipelines/lint/files_exist.py | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index 99f2d1b937..bd25ff33d0 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -87,6 +87,7 @@ def files_exist(self) -> Dict[str, List[str]]:
         lib/Workflow.groovy
         lib/WorkflowMain.groovy
         lib/WorkflowPIPELINE.groovy
+        lib/nfcore_external_java_deps.jar
         parameters.settings.json
         pipeline_template.yml # saving information in .nf-core.yml
         Singularity
@@ -98,12 +99,6 @@ def files_exist(self) -> Dict[str, List[str]]:
 
         .travis.yml
 
-    Files that *must not* be present if a certain entry is present in ``nextflow.config``:
-
-    .. code-block:: bash
-
-        lib/nfcore_external_java_deps.jar # if "nf-validation" is in nextflow.config
-
     .. tip:: You can configure the ``nf-core pipelines lint`` tests to ignore any of these checks by setting
             the ``files_exist`` key as follows in your ``.nf-core.yml`` config file. For example:
 

From e816fafe8a1c984bf54b7f78979c35f494b1a2d9 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 15:32:20 +0200
Subject: [PATCH 361/414] update snapshot

---
 .../__snapshots__/test_create_app.ambr        | 504 +++++++++---------
 1 file changed, 252 insertions(+), 252 deletions(-)

diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index 3ed8349ee1..af88080668 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -2233,255 +2233,255 @@
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+  </text><text class="terminal-3384959394-r1" x="1220" y="800.8" textLength="12.2" clip-path="url(#terminal-3384959394-line-32)">
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From deb7186e6f354ac00d1da0a58ec4b63e77d21f67 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 15:15:44 +0200
Subject: [PATCH 362/414] fix sync pipeline from current directory

---
 nf_core/pipelines/create/create.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 05b04a5422..8e1d46c690 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -70,6 +70,8 @@ def __init__(
                     self.config = CreateConfig(**config_yml["template"].model_dump())
                 else:
                     raise UserWarning("The template configuration was not provided in '.nf-core.yml'.")
+                # Update the output directory
+                self.config.outdir = outdir if outdir else Path().cwd()
             except (FileNotFoundError, UserWarning):
                 log.debug("The '.nf-core.yml' configuration file was not found.")
         elif (name and description and author) or (

From a1e2c15da1234b666354c505a42c8d6c8c724949 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 16:29:30 +0200
Subject: [PATCH 363/414] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 91b348faea..84a3018fed 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -80,6 +80,7 @@
 - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074))
 - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102))
 - Update gitpod setup ([#3136](https://github.com/nf-core/tools/pull/3136))
+- fix syncing a pipeline from current directory ([#3143](https://github.com/nf-core/tools/pull/3143))
 
 ## Version updates
 

From 21b81ef755422af889f685e9fb54e659b8b64d49 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 21 Aug 2024 12:47:00 +0200
Subject: [PATCH 364/414] add option to exclude nf-core components from
 pipeline template

---
 nf_core/pipeline-template/.editorconfig         |  2 ++
 nf_core/pipeline-template/main.nf               | 14 +++++++++++---
 nf_core/pipeline-template/nextflow.config       | 10 +++++-----
 nf_core/pipeline-template/workflows/pipeline.nf |  4 ++++
 nf_core/pipelines/create/templatefeatures.yml   | 14 ++++++++++++++
 5 files changed, 36 insertions(+), 8 deletions(-)

diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig
index 5efa586109..5145366e50 100644
--- a/nf_core/pipeline-template/.editorconfig
+++ b/nf_core/pipeline-template/.editorconfig
@@ -11,6 +11,7 @@ indent_style = space
 [*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
+{%- if modules %}
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset
@@ -24,6 +25,7 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
+{%- endif %}
 
 {%- if email %}
 [/assets/email*]
diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index 5a7de44a53..dd87c9a93a 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -18,6 +18,7 @@
 */
 
 include { {{ short_name|upper }}  } from './workflows/{{ short_name }}'
+{%- if modules %}
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 {%- if igenomes %}
@@ -33,7 +34,7 @@ include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_{{ s
 //   This is an example of how to use getGenomeAttribute() to fetch parameters
 //   from igenomes.config using `--genome`
 params.fasta = getGenomeAttribute('fasta')
-{% endif %}
+{% endif %}{% endif %}
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
@@ -56,7 +57,7 @@ workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
     {{ short_name|upper }} (
         samplesheet
     )
-{%- if multiqc %}
+{%- if multiqc or modules %}
     emit:
     multiqc_report = {{ short_name|upper }}.out.multiqc_report // channel: /path/to/multiqc_report.html
 {%- endif %}
@@ -71,6 +72,7 @@ workflow {
 
     main:
 
+    {%- modules %}
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
@@ -82,14 +84,19 @@ workflow {
         params.outdir,
         params.input
     )
-
+    {% endif %}
     //
     // WORKFLOW: Run main workflow
     //
     {{ prefix_nodash|upper }}_{{ short_name|upper }} (
+        {%- if modules %}
         PIPELINE_INITIALISATION.out.samplesheet
+        {%- else %}
+        params.input
+        {%- endif %}
     )
 
+    {%- if modules %}
     //
     // SUBWORKFLOW: Run completion tasks
     //
@@ -104,6 +111,7 @@ workflow {
         {% if adaptivecard or slackreport %}params.hook_url,{% endif %}
         {% if multiqc %}{{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %}
     )
+    {%- endif %}
 }
 
 /*
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 8818ec54db..6aa89cbe5d 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -66,10 +66,10 @@ params {
     validate_params            = true
 
 }
-
+{% if modules %}
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
-
+{% endif %}
 {% if nf_core_configs -%}
 // Load nf-core custom profiles from different Institutions
 try {
@@ -289,7 +289,7 @@ validation {
 -\033[2m----------------------------------------------------\033[0m-
 """
         afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
-* The nf-core framework 
+* The nf-core framework
   https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
@@ -302,10 +302,10 @@ validation {
     }{% endif %}
 }
 {% endif -%}
-
+{%- if modules %}
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
-
+{% endif %}
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 def check_max(obj, type) {
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 2aef42a864..5635c192bc 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -4,12 +4,14 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
+{%- if modules %}
 {% if fastqc %}include { FASTQC                 } from '../modules/nf-core/fastqc/main'{% endif %}
 {% if multiqc %}include { MULTIQC                } from '../modules/nf-core/multiqc/main'{% endif %}
 {% if nf_schema %}include { paramsSummaryMap       } from 'plugin/nf-schema'{% endif %}
 {% if multiqc %}include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 {% if citations or multiqc %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
+{%- endif %}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -24,6 +26,7 @@ workflow {{ short_name|upper }} {
 
     main:
 
+    {%- if modules %}
     ch_versions = Channel.empty()
     {% if multiqc %}ch_multiqc_files = Channel.empty(){% endif %}
 
@@ -98,6 +101,7 @@ workflow {{ short_name|upper }} {
     emit:
     {%- if multiqc %}multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html{% endif %}
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
+{% endif %}
 }
 
 /*
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 7388ecc7ba..8f2cd3454b 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -300,6 +300,20 @@ email:
       - ".prettierignore"
   nfcore_pipelines: False
   custom_pipelines: True
+modules:
+  skippable_paths:
+    - "conf/base.config"
+    - "conf/modules.config"
+    - "conf/modules.json"
+    - "modules"
+    - "subworkflows"
+  short_description: "Use nf-core components"
+  description: "Include all required files to use nf-core modules and subworkflows"
+  help_text: |
+    It is *recommended* to use this feature if you want to use modules and subworkflows in your pipeline.
+    This will add all required files to use nf-core components or any compatible components from private repos by using `nf-core modules` and `nf-core subworkflows` commands.
+  nfcore_pipelines: False
+  custom_pipelines: True
 adaptivecard:
   skippable_paths:
     - "assets/adaptivecard.json"

From a552e13f684808bd0251e319b102c5746a759fd1 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 21 Aug 2024 12:47:00 +0200
Subject: [PATCH 365/414] add option to exclude nf-core components from
 pipeline template

---
 nf_core/pipeline-template/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index dd87c9a93a..280a8b537f 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -19,6 +19,7 @@
 
 include { {{ short_name|upper }}  } from './workflows/{{ short_name }}'
 {%- if modules %}
+{%- if modules %}
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 {%- if igenomes %}
@@ -72,6 +73,7 @@ workflow {
 
     main:
 
+    {%- if modules %}
     {%- modules %}
     //
     // SUBWORKFLOW: Run initialisation tasks

From 36b559ecffb296c3ecb3297e87c3c65dae1c42d4 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 11:06:25 +0200
Subject: [PATCH 366/414] allow linting a pipeline without nf-core components

---
 nf_core/commands_pipelines.py                 |   5 +-
 nf_core/pipeline-template/main.nf             |   6 +-
 .../pipeline-template/nextflow_schema.json    |   2 +
 .../pipeline-template/workflows/pipeline.nf   |   2 +-
 nf_core/pipelines/create/templatefeatures.yml |  41 ++++---
 nf_core/pipelines/lint/__init__.py            | 105 ++++++++++--------
 6 files changed, 92 insertions(+), 69 deletions(-)

diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py
index 4b6fa75f3e..23affb1d27 100644
--- a/nf_core/commands_pipelines.py
+++ b/nf_core/commands_pipelines.py
@@ -144,9 +144,12 @@ def pipelines_lint(
             ctx.obj["hide_progress"],
         )
         swf_failed = 0
+        module_failed = 0
         if subworkflow_lint_obj is not None:
             swf_failed = len(subworkflow_lint_obj.failed)
-        if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0:
+        if module_lint_obj is not None:
+            module_failed = len(module_lint_obj.failed)
+        if len(lint_obj.failed) + module_failed + swf_failed > 0:
             sys.exit(1)
     except AssertionError as e:
         log.critical(e)
diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index 280a8b537f..6516ebf90e 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -19,7 +19,6 @@
 
 include { {{ short_name|upper }}  } from './workflows/{{ short_name }}'
 {%- if modules %}
-{%- if modules %}
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 {%- if igenomes %}
@@ -58,10 +57,10 @@ workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
     {{ short_name|upper }} (
         samplesheet
     )
-{%- if multiqc or modules %}
+{%- if multiqc %}{%- if modules %}
     emit:
     multiqc_report = {{ short_name|upper }}.out.multiqc_report // channel: /path/to/multiqc_report.html
-{%- endif %}
+{%- endif %}{%- endif %}
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -74,7 +73,6 @@ workflow {
     main:
 
     {%- if modules %}
-    {%- modules %}
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 39bf0d0da3..c84f652d07 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -56,6 +56,7 @@
                     "fa_icon": "fas fa-book",
                     "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
                 },
+                {%- if modules %}
                 "fasta": {
                     "type": "string",
                     "format": "file-path",
@@ -66,6 +67,7 @@
                     "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                     "fa_icon": "far fa-file-code"
                 },
+                {%- endif %}
                 "igenomes_ignore": {
                     "type": "boolean",
                     "description": "Do not load the iGenomes reference config.",
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 5635c192bc..5b7e0ff143 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -24,9 +24,9 @@ workflow {{ short_name|upper }} {
     take:
     ch_samplesheet // channel: samplesheet read in from --input
 
+    {%- if modules %}
     main:
 
-    {%- if modules %}
     ch_versions = Channel.empty()
     {% if multiqc %}ch_multiqc_files = Channel.empty(){% endif %}
 
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 8f2cd3454b..0409f812f6 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -242,6 +242,33 @@ fastqc:
     The pipeline will include the FastQC module.
   nfcore_pipelines: True
   custom_pipelines: True
+modules:
+  skippable_paths:
+    - "conf/base.config"
+    - "conf/modules.config"
+    - "conf/modules.json"
+    - "modules"
+    - "subworkflows"
+  short_description: "Use nf-core components"
+  description: "Include all required files to use nf-core modules and subworkflows"
+  help_text: |
+    It is *recommended* to use this feature if you want to use modules and subworkflows in your pipeline.
+    This will add all required files to use nf-core components or any compatible components from private repos by using `nf-core modules` and `nf-core subworkflows` commands.
+  linting:
+    nfcore_components: False
+    modules_json: False
+    base_config: False
+    modules_config: False
+    files_exist:
+      - "conf/base.config"
+      - "conf/modules.config"
+      - "conf/modules.json"
+    nextflow_config:
+      - "process.cpus"
+      - "process.memory"
+      - "process.time"
+  nfcore_pipelines: False
+  custom_pipelines: True
 changelog:
   skippable_paths:
     - "CHANGELOG.md"
@@ -300,20 +327,6 @@ email:
       - ".prettierignore"
   nfcore_pipelines: False
   custom_pipelines: True
-modules:
-  skippable_paths:
-    - "conf/base.config"
-    - "conf/modules.config"
-    - "conf/modules.json"
-    - "modules"
-    - "subworkflows"
-  short_description: "Use nf-core components"
-  description: "Include all required files to use nf-core modules and subworkflows"
-  help_text: |
-    It is *recommended* to use this feature if you want to use modules and subworkflows in your pipeline.
-    This will add all required files to use nf-core components or any compatible components from private repos by using `nf-core modules` and `nf-core subworkflows` commands.
-  nfcore_pipelines: False
-  custom_pipelines: True
 adaptivecard:
   skippable_paths:
     - "assets/adaptivecard.json"
diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
index 219cdd8f5c..3ddb60ab5e 100644
--- a/nf_core/pipelines/lint/__init__.py
+++ b/nf_core/pipelines/lint/__init__.py
@@ -152,6 +152,7 @@ def _get_all_lint_tests(release_mode):
             "base_config",
             "modules_config",
             "nfcore_yml",
+            "nfcore_components",
         ] + (["version_consistency"] if release_mode else [])
 
     def _load(self) -> bool:
@@ -546,7 +547,7 @@ def run_linting(
     md_fn=None,
     json_fn=None,
     hide_progress: bool = False,
-) -> Tuple[PipelineLint, ComponentLint, Union[ComponentLint, None]]:
+) -> Tuple[PipelineLint, Union[ComponentLint, None], Union[ComponentLint, None]]:
     """Runs all nf-core linting checks on a given Nextflow pipeline project
     in either `release` mode or `normal` mode (default). Returns an object
     of type :class:`PipelineLint` after finished.
@@ -591,41 +592,45 @@ def run_linting(
     lint_obj._load_lint_config()
     lint_obj.load_pipeline_config()
 
-    # Create the modules lint object
-    module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress)
-    # Create the subworkflows lint object
-    try:
-        subworkflow_lint_obj = nf_core.subworkflows.lint.SubworkflowLint(pipeline_dir, hide_progress=hide_progress)
-    except LookupError:
-        subworkflow_lint_obj = None
-
-    # Verify that the pipeline is correctly configured and has  a modules.json file
-    module_lint_obj.has_valid_directory()
-    module_lint_obj.has_modules_file()
-    # Run only the tests we want
-    if key:
-        # Select only the module lint tests
-        module_lint_tests = list(
-            set(key).intersection(set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)))
-        )
-        # Select only the subworkflow lint tests
-        subworkflow_lint_tests = list(
-            set(key).intersection(
-                set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True))
+    if "nfcore_components" in lint_obj.lint_config and not lint_obj.lint_config:
+        # Create the modules lint object
+        module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress)
+        # Create the subworkflows lint object
+        try:
+            subworkflow_lint_obj = nf_core.subworkflows.lint.SubworkflowLint(pipeline_dir, hide_progress=hide_progress)
+        except LookupError:
+            subworkflow_lint_obj = None
+
+        # Verify that the pipeline is correctly configured and has  a modules.json file
+        module_lint_obj.has_valid_directory()
+        module_lint_obj.has_modules_file()
+        # Run only the tests we want
+        if key:
+            # Select only the module lint tests
+            module_lint_tests = list(
+                set(key).intersection(set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)))
             )
-        )
+            # Select only the subworkflow lint tests
+            subworkflow_lint_tests = list(
+                set(key).intersection(
+                    set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True))
+                )
+            )
+        else:
+            # If no key is supplied, run the default modules tests
+            module_lint_tests = list(("module_changes", "module_version"))
+            subworkflow_lint_tests = list(("subworkflow_changes", "subworkflow_version"))
+        module_lint_obj.filter_tests_by_key(module_lint_tests)
+        if subworkflow_lint_obj is not None:
+            subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)
+
+        # Set up files for component linting test
+        module_lint_obj.set_up_pipeline_files()
+        if subworkflow_lint_obj is not None:
+            subworkflow_lint_obj.set_up_pipeline_files()
     else:
-        # If no key is supplied, run the default modules tests
-        module_lint_tests = list(("module_changes", "module_version"))
-        subworkflow_lint_tests = list(("subworkflow_changes", "subworkflow_version"))
-    module_lint_obj.filter_tests_by_key(module_lint_tests)
-    if subworkflow_lint_obj is not None:
-        subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)
-
-    # Set up files for component linting test
-    module_lint_obj.set_up_pipeline_files()
-    if subworkflow_lint_obj is not None:
-        subworkflow_lint_obj.set_up_pipeline_files()
+        module_lint_obj = None
+        subworkflow_lint_obj = None
 
     # Run the pipeline linting tests
     try:
@@ -635,24 +640,26 @@ def run_linting(
         log.info("Stopping tests...")
         return lint_obj, module_lint_obj, subworkflow_lint_obj
 
-    # Run the module lint tests
-    if len(module_lint_obj.all_local_components) > 0:
-        module_lint_obj.lint_modules(module_lint_obj.all_local_components, local=True)
-    if len(module_lint_obj.all_remote_components) > 0:
-        module_lint_obj.lint_modules(module_lint_obj.all_remote_components, local=False)
-    # Run the subworkflows lint tests
-    if subworkflow_lint_obj is not None:
-        if len(subworkflow_lint_obj.all_local_components) > 0:
-            subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_local_components, local=True)
-        if len(subworkflow_lint_obj.all_remote_components) > 0:
-            subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_remote_components, local=False)
+    if module_lint_obj is not None and subworkflow_lint_obj is not None:
+        # Run the module lint tests
+        if len(module_lint_obj.all_local_components) > 0:
+            module_lint_obj.lint_modules(module_lint_obj.all_local_components, local=True)
+        if len(module_lint_obj.all_remote_components) > 0:
+            module_lint_obj.lint_modules(module_lint_obj.all_remote_components, local=False)
+        # Run the subworkflows lint tests
+        if subworkflow_lint_obj is not None:
+            if len(subworkflow_lint_obj.all_local_components) > 0:
+                subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_local_components, local=True)
+            if len(subworkflow_lint_obj.all_remote_components) > 0:
+                subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_remote_components, local=False)
 
     # Print the results
     lint_obj._print_results(show_passed)
-    module_lint_obj._print_results(show_passed, sort_by=sort_by)
-    if subworkflow_lint_obj is not None:
-        subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by)
-    nf_core.pipelines.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj)
+    if module_lint_obj is not None and subworkflow_lint_obj is not None:
+        module_lint_obj._print_results(show_passed, sort_by=sort_by)
+        if subworkflow_lint_obj is not None:
+            subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by)
+        nf_core.pipelines.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj)
     nf_core.pipelines.lint_utils.print_fixes(lint_obj)
 
     # Save results to Markdown file

From cb3e9e695259f7f00f984e439f2892500652c40b Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 12:34:56 +0200
Subject: [PATCH 367/414] don't detect nfcore_components as a linting test

---
 nf_core/pipelines/create/templatefeatures.yml | 2 +-
 nf_core/pipelines/lint/__init__.py            | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 0409f812f6..635a3c4845 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -262,7 +262,7 @@ modules:
     files_exist:
       - "conf/base.config"
       - "conf/modules.config"
-      - "conf/modules.json"
+      - "modules.json"
     nextflow_config:
       - "process.cpus"
       - "process.memory"
diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
index 3ddb60ab5e..0cdc594ca0 100644
--- a/nf_core/pipelines/lint/__init__.py
+++ b/nf_core/pipelines/lint/__init__.py
@@ -152,7 +152,6 @@ def _get_all_lint_tests(release_mode):
             "base_config",
             "modules_config",
             "nfcore_yml",
-            "nfcore_components",
         ] + (["version_consistency"] if release_mode else [])
 
     def _load(self) -> bool:
@@ -178,7 +177,8 @@ def _load_lint_config(self) -> bool:
         # Check if we have any keys that don't match lint test names
         if self.lint_config is not None:
             for k in self.lint_config:
-                if k not in self.lint_tests:
+                if k != "nfcore_components" and k not in self.lint_tests:
+                    # nfcore_components is an exception to allow custom pipelines without nf-core components
                     log.warning(f"Found unrecognised test name '{k}' in pipeline lint config")
                     is_correct = False
 

From 3403f2e0a9a1671420dfd82b9e694bf404e8de97 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 13:56:54 +0200
Subject: [PATCH 368/414] apply review comments from @mashehu

---
 nf_core/pipelines/create/templatefeatures.yml |  2 +-
 nf_core/pipelines/lint/__init__.py            | 32 +++++++++----------
 nf_core/pipelines/lint_utils.py               | 13 ++++++--
 3 files changed, 27 insertions(+), 20 deletions(-)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 635a3c4845..40f25e3977 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -246,7 +246,7 @@ modules:
   skippable_paths:
     - "conf/base.config"
     - "conf/modules.config"
-    - "conf/modules.json"
+    - "modules.json"
     - "modules"
     - "subworkflows"
   short_description: "Use nf-core components"
diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
index 0cdc594ca0..6d27351b62 100644
--- a/nf_core/pipelines/lint/__init__.py
+++ b/nf_core/pipelines/lint/__init__.py
@@ -9,7 +9,7 @@
 import logging
 import os
 from pathlib import Path
-from typing import List, Tuple, Union
+from typing import List, Optional, Tuple, Union
 
 import git
 import rich
@@ -547,7 +547,7 @@ def run_linting(
     md_fn=None,
     json_fn=None,
     hide_progress: bool = False,
-) -> Tuple[PipelineLint, Union[ComponentLint, None], Union[ComponentLint, None]]:
+) -> Tuple[PipelineLint, Optional[ComponentLint], Optional[ComponentLint]]:
     """Runs all nf-core linting checks on a given Nextflow pipeline project
     in either `release` mode or `normal` mode (default). Returns an object
     of type :class:`PipelineLint` after finished.
@@ -592,7 +592,10 @@ def run_linting(
     lint_obj._load_lint_config()
     lint_obj.load_pipeline_config()
 
-    if "nfcore_components" in lint_obj.lint_config and not lint_obj.lint_config:
+    if "nfcore_components" in lint_obj.lint_config and not lint_obj.lint_config["nfcore_components"]:
+        module_lint_obj = None
+        subworkflow_lint_obj = None
+    else:
         # Create the modules lint object
         module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress)
         # Create the subworkflows lint object
@@ -628,9 +631,6 @@ def run_linting(
         module_lint_obj.set_up_pipeline_files()
         if subworkflow_lint_obj is not None:
             subworkflow_lint_obj.set_up_pipeline_files()
-    else:
-        module_lint_obj = None
-        subworkflow_lint_obj = None
 
     # Run the pipeline linting tests
     try:
@@ -640,26 +640,26 @@ def run_linting(
         log.info("Stopping tests...")
         return lint_obj, module_lint_obj, subworkflow_lint_obj
 
-    if module_lint_obj is not None and subworkflow_lint_obj is not None:
+    if module_lint_obj is not None:
         # Run the module lint tests
         if len(module_lint_obj.all_local_components) > 0:
             module_lint_obj.lint_modules(module_lint_obj.all_local_components, local=True)
         if len(module_lint_obj.all_remote_components) > 0:
             module_lint_obj.lint_modules(module_lint_obj.all_remote_components, local=False)
+    if subworkflow_lint_obj is not None:
         # Run the subworkflows lint tests
-        if subworkflow_lint_obj is not None:
-            if len(subworkflow_lint_obj.all_local_components) > 0:
-                subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_local_components, local=True)
-            if len(subworkflow_lint_obj.all_remote_components) > 0:
-                subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_remote_components, local=False)
+        if len(subworkflow_lint_obj.all_local_components) > 0:
+            subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_local_components, local=True)
+        if len(subworkflow_lint_obj.all_remote_components) > 0:
+            subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_remote_components, local=False)
 
     # Print the results
     lint_obj._print_results(show_passed)
-    if module_lint_obj is not None and subworkflow_lint_obj is not None:
+    if module_lint_obj is not None:
         module_lint_obj._print_results(show_passed, sort_by=sort_by)
-        if subworkflow_lint_obj is not None:
-            subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by)
-        nf_core.pipelines.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj)
+    if subworkflow_lint_obj is not None:
+        subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by)
+    nf_core.pipelines.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj)
     nf_core.pipelines.lint_utils.print_fixes(lint_obj)
 
     # Save results to Markdown file
diff --git a/nf_core/pipelines/lint_utils.py b/nf_core/pipelines/lint_utils.py
index ccab76295f..ff65fb0e56 100644
--- a/nf_core/pipelines/lint_utils.py
+++ b/nf_core/pipelines/lint_utils.py
@@ -22,15 +22,22 @@ def print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj):
     swf_passed = 0
     swf_warned = 0
     swf_failed = 0
+    module_passed = 0
+    module_warned = 0
+    module_failed = 0
     if subworkflow_lint_obj is not None:
         swf_passed = len(subworkflow_lint_obj.passed)
         swf_warned = len(subworkflow_lint_obj.warned)
         swf_failed = len(subworkflow_lint_obj.failed)
-    nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed) + swf_passed
+    if module_lint_obj is not None:
+        module_passed = len(module_lint_obj.passed)
+        module_warned = len(module_lint_obj.warned)
+        module_failed = len(module_lint_obj.failed)
+    nbr_passed = len(lint_obj.passed) + module_passed + swf_passed
     nbr_ignored = len(lint_obj.ignored)
     nbr_fixed = len(lint_obj.fixed)
-    nbr_warned = len(lint_obj.warned) + len(module_lint_obj.warned) + swf_warned
-    nbr_failed = len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed
+    nbr_warned = len(lint_obj.warned) + module_warned + swf_warned
+    nbr_failed = len(lint_obj.failed) + module_failed + swf_failed
 
     summary_colour = "red" if nbr_failed > 0 else "green"
     table = Table(box=rich.box.ROUNDED, style=summary_colour)

From bed7b37195015203de439fd96cc5ca6859a85c9f Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 14:00:29 +0200
Subject: [PATCH 369/414] don't remove base.config when removing nf-core
 components

---
 nf_core/pipeline-template/nextflow.config     | 2 --
 nf_core/pipelines/create/templatefeatures.yml | 2 --
 2 files changed, 4 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 6aa89cbe5d..d1b83ce3f9 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -66,10 +66,8 @@ params {
     validate_params            = true
 
 }
-{% if modules %}
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
-{% endif %}
 {% if nf_core_configs -%}
 // Load nf-core custom profiles from different Institutions
 try {
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 40f25e3977..8d8186f323 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -244,7 +244,6 @@ fastqc:
   custom_pipelines: True
 modules:
   skippable_paths:
-    - "conf/base.config"
     - "conf/modules.config"
     - "modules.json"
     - "modules"
@@ -260,7 +259,6 @@ modules:
     base_config: False
     modules_config: False
     files_exist:
-      - "conf/base.config"
       - "conf/modules.config"
       - "modules.json"
     nextflow_config:

From 6a5d830f67bc38f22c5655b2cc70e9d1bbb9ea8b Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 16:48:00 +0200
Subject: [PATCH 370/414] Revert "don't remove base.config when removing
 nf-core components"

This reverts commit 68dab6e621aa689e104443f3c0f2c85f416574af.
---
 nf_core/pipeline-template/nextflow.config     | 2 ++
 nf_core/pipelines/create/templatefeatures.yml | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index d1b83ce3f9..6aa89cbe5d 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -66,8 +66,10 @@ params {
     validate_params            = true
 
 }
+{% if modules %}
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
+{% endif %}
 {% if nf_core_configs -%}
 // Load nf-core custom profiles from different Institutions
 try {
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 8d8186f323..40f25e3977 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -244,6 +244,7 @@ fastqc:
   custom_pipelines: True
 modules:
   skippable_paths:
+    - "conf/base.config"
     - "conf/modules.config"
     - "modules.json"
     - "modules"
@@ -259,6 +260,7 @@ modules:
     base_config: False
     modules_config: False
     files_exist:
+      - "conf/base.config"
       - "conf/modules.config"
       - "modules.json"
     nextflow_config:

From 1b8cce2cbe16fbdaa1bc293f2a52bc0b538972d4 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 16:52:20 +0200
Subject: [PATCH 371/414] update textual snapshots

---
 .../__snapshots__/test_create_app.ambr        | 511 +++++++++---------
 1 file changed, 255 insertions(+), 256 deletions(-)

diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index af88080668..8a0f4dd68d 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
           font-weight: 700;
       }
   
-      .terminal-2541420365-matrix {
+      .terminal-2784035137-matrix {
           font-family: Fira Code, monospace;
           font-size: 20px;
           line-height: 24.4px;
           font-variant-east-asian: full-width;
       }
   
-      .terminal-2541420365-title {
+      .terminal-2784035137-title {
           font-size: 18px;
           font-weight: bold;
           font-family: arial;
       }
   
-      .terminal-2541420365-r1 { fill: #c5c8c6 }
-  .terminal-2541420365-r2 { fill: #e3e3e3 }
-  .terminal-2541420365-r3 { fill: #989898 }
-  .terminal-2541420365-r4 { fill: #e1e1e1 }
-  .terminal-2541420365-r5 { fill: #4ebf71;font-weight: bold }
-  .terminal-2541420365-r6 { fill: #1e1e1e }
-  .terminal-2541420365-r7 { fill: #507bb3 }
-  .terminal-2541420365-r8 { fill: #e2e2e2 }
-  .terminal-2541420365-r9 { fill: #808080 }
-  .terminal-2541420365-r10 { fill: #dde6ed;font-weight: bold }
-  .terminal-2541420365-r11 { fill: #001541 }
-  .terminal-2541420365-r12 { fill: #0178d4 }
-  .terminal-2541420365-r13 { fill: #454a50 }
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From 8351e0c9326a28ab1f4eb2d5bdb947fd0d96c26d Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 17:05:32 +0200
Subject: [PATCH 372/414] add process cpus, memory and time to nextflow.config
 if we remove base.config

---
 nf_core/pipeline-template/nextflow.config     | 11 +++++++++++
 nf_core/pipelines/create/templatefeatures.yml |  4 ----
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 6aa89cbe5d..7776bc03f1 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -69,6 +69,17 @@ params {
 {% if modules %}
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
+{%- else %}
+process {
+    // TODO nf-core: Check the defaults for all processes
+    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
+    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
+    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    maxRetries    = 1
+    maxErrors     = '-1'
+}
 {% endif %}
 {% if nf_core_configs -%}
 // Load nf-core custom profiles from different Institutions
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 40f25e3977..d72e2cff77 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -263,10 +263,6 @@ modules:
       - "conf/base.config"
       - "conf/modules.config"
       - "modules.json"
-    nextflow_config:
-      - "process.cpus"
-      - "process.memory"
-      - "process.time"
   nfcore_pipelines: False
   custom_pipelines: True
 changelog:

From d295defdd9e7a4b8d3d1da1ae026437ab274ee54 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 5 Aug 2024 11:20:39 +0200
Subject: [PATCH 373/414] add tests to ensure all files are part of a template
 customisation group

---
 tests/pipelines/test_create.py | 39 ++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py
index 13fd3b24cd..0d93afb117 100644
--- a/tests/pipelines/test_create.py
+++ b/tests/pipelines/test_create.py
@@ -7,6 +7,7 @@
 import git
 import jinja2
 import yaml
+import itertools
 
 import nf_core.pipelines.create.create
 from nf_core.pipelines.create.utils import load_features_yaml
@@ -15,6 +16,7 @@
 
 PIPELINE_TEMPLATE_YML = TEST_DATA_DIR / "pipeline_create_template.yml"
 PIPELINE_TEMPLATE_YML_SKIP = TEST_DATA_DIR / "pipeline_create_template_skip.yml"
+PIPELINE_TEMPLATE = Path(nf_core.__file__).parent / "pipeline-template"
 
 
 class NfcoreCreateTest(unittest.TestCase):
@@ -134,3 +136,40 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path):
         assert not (pipeline.outdir / ".github").exists()
         assert not (pipeline.outdir / "conf" / "igenomes.config").exists()
         assert not (pipeline.outdir / ".editorconfig").exists()
+
+    def test_template_customisation_all_files_grouping(self):
+        """Test that all pipeline template files are included in a pipeline customisation group."""
+        create_obj = nf_core.pipelines.create.create.PipelineCreate(
+            template_config=PIPELINE_TEMPLATE_YML_SKIP,
+            default_branch=self.default_branch,
+        )
+        all_skippable_paths = itertools.chain(*[sp for sp in create_obj.skippable_paths.values()])
+        for _, _, files in PIPELINE_TEMPLATE.walk():
+            for file in files:
+                str_path = str(Path(file).relative_to(PIPELINE_TEMPLATE))
+                assert str_path in all_skippable_paths, f"Template file `{str_path}` not present in a group for pipeline customisation `PipelineCreate.skippable_paths`."
+
+    def test_template_customisation_all_template_areas(self):
+        """Check that all groups in `skippable_paths` are template areas."""
+        create_obj = nf_core.pipelines.create.create.PipelineCreate(
+            template_config=PIPELINE_TEMPLATE_YML_SKIP,
+            default_branch=self.default_branch,
+        )
+        for area in create_obj.skippable_paths.keys():
+            if area != "is_nfcore":
+                assert area in create_obj.template_areas.keys(), f"Customisation template group `{area}` not present in `PipelineCreate.template_areas`."
+
+    def test_template_customisation_all_features_tested(self):
+        "Check that all customisation groups are tested on CI."
+        create_obj = nf_core.pipelines.create.create.PipelineCreate(
+            template_config=PIPELINE_TEMPLATE_YML_SKIP,
+            default_branch=self.default_branch,
+        )
+        with open(PIPELINE_TEMPLATE_YML_SKIP) as fh:
+            skip_yaml = yaml.safe_load(fh)
+        with open(Path(nf_core.__file__).parent.parent / ".github" / "workflows" / "create-test-lint-wf-template.yml") as fh:
+            ci_workflow = yaml.safe_load(fh)
+        for area in create_obj.skippable_paths.keys():
+            assert area in skip_yaml["skip_features"], f"Customisation template group `{area}` not tested in `tests/data/pipeline_create_template_skip.yml`."
+            if area != "github":
+                assert f"template_skip_{area}.yml" in ci_workflow["jobs"]["RunTestWorkflow"]["strategy"]["matrix"]["TEMPLATE"], f"Customisation template group `{area}` not tested in `create-test-lint-wf-template.yml` github workflow."

From f700e61932f0ff3bb0b40e0570145ad389a86cab Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 5 Aug 2024 11:28:46 +0200
Subject: [PATCH 374/414] fix linting

---
 tests/pipelines/test_create.py | 23 +++++++++++++++++------
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py
index 0d93afb117..cb8151849d 100644
--- a/tests/pipelines/test_create.py
+++ b/tests/pipelines/test_create.py
@@ -1,5 +1,6 @@
 """Some tests covering the pipeline creation sub command."""
 
+import itertools
 import os
 import unittest
 from pathlib import Path
@@ -7,7 +8,6 @@
 import git
 import jinja2
 import yaml
-import itertools
 
 import nf_core.pipelines.create.create
 from nf_core.pipelines.create.utils import load_features_yaml
@@ -147,7 +147,9 @@ def test_template_customisation_all_files_grouping(self):
         for _, _, files in PIPELINE_TEMPLATE.walk():
             for file in files:
                 str_path = str(Path(file).relative_to(PIPELINE_TEMPLATE))
-                assert str_path in all_skippable_paths, f"Template file `{str_path}` not present in a group for pipeline customisation `PipelineCreate.skippable_paths`."
+                assert (
+                    str_path in all_skippable_paths
+                ), f"Template file `{str_path}` not present in a group for pipeline customisation `PipelineCreate.skippable_paths`."
 
     def test_template_customisation_all_template_areas(self):
         """Check that all groups in `skippable_paths` are template areas."""
@@ -157,7 +159,9 @@ def test_template_customisation_all_template_areas(self):
         )
         for area in create_obj.skippable_paths.keys():
             if area != "is_nfcore":
-                assert area in create_obj.template_areas.keys(), f"Customisation template group `{area}` not present in `PipelineCreate.template_areas`."
+                assert (
+                    area in create_obj.template_areas.keys()
+                ), f"Customisation template group `{area}` not present in `PipelineCreate.template_areas`."
 
     def test_template_customisation_all_features_tested(self):
         "Check that all customisation groups are tested on CI."
@@ -167,9 +171,16 @@ def test_template_customisation_all_features_tested(self):
         )
         with open(PIPELINE_TEMPLATE_YML_SKIP) as fh:
             skip_yaml = yaml.safe_load(fh)
-        with open(Path(nf_core.__file__).parent.parent / ".github" / "workflows" / "create-test-lint-wf-template.yml") as fh:
+        with open(
+            Path(nf_core.__file__).parent.parent / ".github" / "workflows" / "create-test-lint-wf-template.yml"
+        ) as fh:
             ci_workflow = yaml.safe_load(fh)
         for area in create_obj.skippable_paths.keys():
-            assert area in skip_yaml["skip_features"], f"Customisation template group `{area}` not tested in `tests/data/pipeline_create_template_skip.yml`."
+            assert (
+                area in skip_yaml["skip_features"]
+            ), f"Customisation template group `{area}` not tested in `tests/data/pipeline_create_template_skip.yml`."
             if area != "github":
-                assert f"template_skip_{area}.yml" in ci_workflow["jobs"]["RunTestWorkflow"]["strategy"]["matrix"]["TEMPLATE"], f"Customisation template group `{area}` not tested in `create-test-lint-wf-template.yml` github workflow."
+                assert (
+                    f"template_skip_{area}.yml"
+                    in ci_workflow["jobs"]["RunTestWorkflow"]["strategy"]["matrix"]["TEMPLATE"]
+                ), f"Customisation template group `{area}` not tested in `create-test-lint-wf-template.yml` github workflow."

From b8812e8abc220d5022c81198d12f66b84b2fe265 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 5 Aug 2024 11:29:30 +0200
Subject: [PATCH 375/414] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 84a3018fed..88d6355693 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -36,6 +36,7 @@
 - add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130))
 - add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133))
 - add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
+- Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))
 
 ### Linting
 

From e6507ccd2c2e11a23ac5fcbacb7c5389deb7fbd8 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 28 Aug 2024 09:43:32 +0200
Subject: [PATCH 376/414] rename templatefeatures.yml to template_features.yml

---
 .github/workflows/create-test-lint-wf-template.yml              | 2 +-
 MANIFEST.in                                                     | 2 +-
 .../create/{templatefeatures.yml => template_features.yml}      | 0
 nf_core/pipelines/create/utils.py                               | 2 +-
 4 files changed, 3 insertions(+), 3 deletions(-)
 rename nf_core/pipelines/create/{templatefeatures.yml => template_features.yml} (100%)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 85ce2230ab..1fb521b4bb 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -44,7 +44,7 @@ jobs:
       - name: Create Matrix
         id: create_matrix
         run: |
-          echo "matrix=$(yq 'keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
+          echo "matrix=$(yq 'keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | tojson(0)' nf_core/pipelines/create/template_features.yml)" >> $GITHUB_OUTPUT
 
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}
diff --git a/MANIFEST.in b/MANIFEST.in
index 2bec403804..ce2e08c090 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -10,4 +10,4 @@ include nf_core/assets/logo/nf-core-repo-logo-base-darkbg.png
 include nf_core/assets/logo/placeholder_logo.svg
 include nf_core/assets/logo/MavenPro-Bold.ttf
 include nf_core/pipelines/create/create.tcss
-include nf_core/pipelines/create/templatefeatures.yml
+include nf_core/pipelines/create/template_features.yml
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/template_features.yml
similarity index 100%
rename from nf_core/pipelines/create/templatefeatures.yml
rename to nf_core/pipelines/create/template_features.yml
diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
index 0b72c2bcf5..9b331c2a3b 100644
--- a/nf_core/pipelines/create/utils.py
+++ b/nf_core/pipelines/create/utils.py
@@ -37,7 +37,7 @@ def init_context(value: Dict[str, Any]) -> Iterator[None]:
 NFCORE_PIPELINE_GLOBAL: bool = True
 
 # YAML file describing template features
-features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml"
+features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "template_features.yml"
 
 
 class CreateConfig(NFCoreTemplateConfig):

From fcfdbaf08031d94504e1ee7f14bea7b967101591 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 28 Aug 2024 10:12:34 +0200
Subject: [PATCH 377/414] update test to use template_features.yml and add
 missing files to a feature group

---
 .../pipelines/create/template_features.yml    |  6 +-
 tests/pipelines/test_create.py                | 78 ++++++++-----------
 2 files changed, 38 insertions(+), 46 deletions(-)

diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml
index d72e2cff77..a8300700ae 100644
--- a/nf_core/pipelines/create/template_features.yml
+++ b/nf_core/pipelines/create/template_features.yml
@@ -1,7 +1,8 @@
 github:
   skippable_paths:
-    - ".github/"
+    - ".github"
     - ".gitignore"
+    - ".gitattributes"
   short_description: "Skip the creation of a local Git repository."
   description: ""
   help_text: ""
@@ -282,6 +283,9 @@ changelog:
 nf_schema:
   skippable_paths:
     - "subworkflows/nf-core/utils_nfschema_plugin"
+    - "nextflow_schema.json"
+    - "assets/schema_input.json"
+    - "assets/samplesheet.csv"
   short_description: "Use nf-schema"
   description: "Use the nf-schema Nextflow plugin for this pipeline."
   help_text: |
diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py
index cb8151849d..cccd9643f2 100644
--- a/tests/pipelines/test_create.py
+++ b/tests/pipelines/test_create.py
@@ -1,6 +1,5 @@
 """Some tests covering the pipeline creation sub command."""
 
-import itertools
 import os
 import unittest
 from pathlib import Path
@@ -139,48 +138,37 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path):
 
     def test_template_customisation_all_files_grouping(self):
         """Test that all pipeline template files are included in a pipeline customisation group."""
-        create_obj = nf_core.pipelines.create.create.PipelineCreate(
-            template_config=PIPELINE_TEMPLATE_YML_SKIP,
-            default_branch=self.default_branch,
-        )
-        all_skippable_paths = itertools.chain(*[sp for sp in create_obj.skippable_paths.values()])
-        for _, _, files in PIPELINE_TEMPLATE.walk():
+        template_features_yml = load_features_yaml()
+        base_required_files = [
+            ".nf-core.yml",
+            "README.md",
+            "nextflow.config",
+            "CITATIONS.md",
+            "main.nf",
+            "workflows/pipeline.nf",
+        ]
+        all_skipped_files = []
+        for feature in template_features_yml.keys():
+            if template_features_yml[feature]["skippable_paths"]:
+                all_skipped_files.extend(template_features_yml[feature]["skippable_paths"])
+
+        for root, _, files in PIPELINE_TEMPLATE.walk():
             for file in files:
-                str_path = str(Path(file).relative_to(PIPELINE_TEMPLATE))
-                assert (
-                    str_path in all_skippable_paths
-                ), f"Template file `{str_path}` not present in a group for pipeline customisation `PipelineCreate.skippable_paths`."
-
-    def test_template_customisation_all_template_areas(self):
-        """Check that all groups in `skippable_paths` are template areas."""
-        create_obj = nf_core.pipelines.create.create.PipelineCreate(
-            template_config=PIPELINE_TEMPLATE_YML_SKIP,
-            default_branch=self.default_branch,
-        )
-        for area in create_obj.skippable_paths.keys():
-            if area != "is_nfcore":
-                assert (
-                    area in create_obj.template_areas.keys()
-                ), f"Customisation template group `{area}` not present in `PipelineCreate.template_areas`."
-
-    def test_template_customisation_all_features_tested(self):
-        "Check that all customisation groups are tested on CI."
-        create_obj = nf_core.pipelines.create.create.PipelineCreate(
-            template_config=PIPELINE_TEMPLATE_YML_SKIP,
-            default_branch=self.default_branch,
-        )
-        with open(PIPELINE_TEMPLATE_YML_SKIP) as fh:
-            skip_yaml = yaml.safe_load(fh)
-        with open(
-            Path(nf_core.__file__).parent.parent / ".github" / "workflows" / "create-test-lint-wf-template.yml"
-        ) as fh:
-            ci_workflow = yaml.safe_load(fh)
-        for area in create_obj.skippable_paths.keys():
-            assert (
-                area in skip_yaml["skip_features"]
-            ), f"Customisation template group `{area}` not tested in `tests/data/pipeline_create_template_skip.yml`."
-            if area != "github":
-                assert (
-                    f"template_skip_{area}.yml"
-                    in ci_workflow["jobs"]["RunTestWorkflow"]["strategy"]["matrix"]["TEMPLATE"]
-                ), f"Customisation template group `{area}` not tested in `create-test-lint-wf-template.yml` github workflow."
+                str_path = str((root / file).relative_to(PIPELINE_TEMPLATE))
+                if str_path not in base_required_files:
+                    try:
+                        assert (
+                            str_path in all_skipped_files
+                        ), f"Template file `{str_path}` not present in a group for pipeline customisation in `template_features.yml`."
+                    except AssertionError:
+                        if "/" in str_path:
+                            # Check if the parent directory is in the skipped files
+                            upper_dir_present = False
+                            for i in range(1, len(str_path.split("/"))):
+                                upper_dir = "/".join(str_path.split("/")[:i])
+                                if upper_dir in all_skipped_files:
+                                    upper_dir_present = True
+                                    break
+                            assert upper_dir_present, f"Template file `{str_path}` not present in a group for pipeline customisation in `template_features.yml`."
+                        else:
+                            raise

From ea52f9bf241c0f7302d385b74123624b65bbe11d Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 28 Aug 2024 10:27:39 +0200
Subject: [PATCH 378/414] fix pipeline linting when skipping nf_schema

---
 nf_core/pipelines/create/template_features.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml
index a8300700ae..b3b124f622 100644
--- a/nf_core/pipelines/create/template_features.yml
+++ b/nf_core/pipelines/create/template_features.yml
@@ -292,6 +292,13 @@ nf_schema:
     [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) is used to validate input parameters based on a JSON schema.
     It also provides helper functionality to create help messages, get a summary
     of changed parameters and validate and convert a samplesheet to a channel.
+  linting:
+    files_exist:
+      - "nextflow_schema.json"
+    schema_params: False
+    schema_lint: False
+    schema_description: False
+    nextflow_config: False
   nfcore_pipelines: True
   custom_pipelines: True
 license:

From fc7c1e810542aebf976fa10378c78637f9fa2788 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 28 Aug 2024 10:34:46 +0200
Subject: [PATCH 379/414] switch to os.walk to support <3.10 versions of Python

---
 tests/pipelines/test_create.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py
index cccd9643f2..d72b346903 100644
--- a/tests/pipelines/test_create.py
+++ b/tests/pipelines/test_create.py
@@ -152,9 +152,9 @@ def test_template_customisation_all_files_grouping(self):
             if template_features_yml[feature]["skippable_paths"]:
                 all_skipped_files.extend(template_features_yml[feature]["skippable_paths"])
 
-        for root, _, files in PIPELINE_TEMPLATE.walk():
+        for root, _, files in os.walk(PIPELINE_TEMPLATE):
             for file in files:
-                str_path = str((root / file).relative_to(PIPELINE_TEMPLATE))
+                str_path = str((Path(root) / file).relative_to(PIPELINE_TEMPLATE))
                 if str_path not in base_required_files:
                     try:
                         assert (

From aa2a41706281b504a16f2e74ea3e92a9851f5991 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 29 Aug 2024 09:35:52 +0200
Subject: [PATCH 380/414] handle cases where the directory path contains the
 name of the component

---
 nf_core/components/nfcore_component.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index db3196be91..5f29bea4eb 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -64,7 +64,12 @@ def __init__(
             self.process_name = ""
             self.environment_yml: Optional[Path] = Path(self.component_dir, "environment.yml")
 
-            repo_dir = self.component_dir.parts[: self.component_dir.parts.index(self.component_name.split("/")[0])][-1]
+            name_index = (
+                len(self.component_dir.parts)
+                - 1
+                - self.component_dir.parts[::-1].index(self.component_name.split("/")[0])
+            )
+            repo_dir = self.component_dir.parts[:name_index][-1]
             self.org = repo_dir
             self.nftest_testdir = Path(self.component_dir, "tests")
             self.nftest_main_nf = Path(self.nftest_testdir, "main.nf.test")

From 847fe0b98201402dff755d680459e414008ac16b Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 29 Aug 2024 09:44:27 +0200
Subject: [PATCH 381/414] udpate changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 84a3018fed..0e198caa50 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -48,6 +48,7 @@
 - Linting will now check if the schema is correct for the used validation plugin ([#3116])(https://github.com/nf-core/tools/pull/3116)
 - Linting will now check the use of the right validation plugin include statements in the workflow scripts ([#3116])(https://github.com/nf-core/tools/pull/3116)
 - Full linting for correct use of nf-schema and nf-validation ([#3116](https://github.com/nf-core/tools/pull/3116))
+- Handle cases where the directory path contains the name of the component ([#3147](https://github.com/nf-core/tools/pull/3147))
 
 ### Pipeline create command
 

From 283284c5ab705c032b6e75850d44fe8a61f7530c Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 29 Aug 2024 12:31:47 +0200
Subject: [PATCH 382/414] some more minimal template fixes

---
 nf_core/pipeline-template/README.md            |  6 ++++++
 nf_core/pipeline-template/nextflow.config      |  9 +++++----
 nf_core/pipeline-template/nextflow_schema.json | 12 +++++++-----
 nf_core/pipelines/create/template_features.yml |  2 +-
 4 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index 1fa210c0e0..f4cbce19c3 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -7,6 +7,12 @@
   </picture>
 </h1>
 
+{%- else %}
+
+<h1>
+  {{ name }}
+</h1>
+
 {% endif -%}
 {% if github_badges -%}
 [![GitHub Actions CI Status](https://github.com/{{ name }}/actions/workflows/ci.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/ci.yml)
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 7776bc03f1..8201916b3f 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -31,14 +31,14 @@ params {
 
     // Boilerplate options
     outdir                       = null
-    publish_dir_mode             = 'copy'
+    {% if modules %}publish_dir_mode             = 'copy'{% endif %}
     {%- if email %}
     email                        = null
     email_on_fail                = null
     plaintext_email              = false
     {%- endif %}
-    monochrome_logs              = false
-    hook_url                     = null
+    {% if modules %}monochrome_logs              = false{% endif %}
+    {% if slackreport or adaptivecard %}hook_url                     = null{% endif %}
     {% if nf_schema %}help                         = false
     help_full                    = false
     show_hidden                  = false{% endif %}
@@ -62,9 +62,10 @@ params {
     max_cpus                   = 16
     max_time                   = '240.h'
 
+    {%- if nf_schema %}
     // Schema validation default options
     validate_params            = true
-
+    {% endif %}
 }
 {% if modules %}
 // Load base.config by default for all pipelines
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index c84f652d07..446da25aed 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -184,6 +184,7 @@
                     "fa_icon": "fas fa-question-circle",
                     "hidden": true
                 },
+                {%- if modules %}
                 "publish_dir_mode": {
                     "type": "string",
                     "default": "copy",
@@ -192,7 +193,7 @@
                     "fa_icon": "fas fa-copy",
                     "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
-                },{% if email %}
+                },{% endif %}{% if email %}
                 "email_on_fail": {
                     "type": "string",
                     "description": "Email address for completion summary, only when pipeline fails.",
@@ -215,21 +216,22 @@
                     "default": "25.MB",
                     "fa_icon": "fas fa-file-upload",
                     "hidden": true
-                },
-                {% endif %}
+                },{% endif %}
+                {%- if modules %}
                 "monochrome_logs": {
                     "type": "boolean",
                     "description": "Do not use coloured log outputs.",
                     "fa_icon": "fas fa-palette",
                     "hidden": true
-                },
+                },{% endif %}
+                {%- if slackreport or adaptivecard %}
                 "hook_url": {
                     "type": "string",
                     "description": "Incoming hook URL for messaging service",
                     "fa_icon": "fas fa-people-group",
                     "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                     "hidden": true
-                },
+                },{% endif %}
                 {%- if multiqc %}
                 "multiqc_config": {
                     "type": "string",
diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml
index b3b124f622..744c054075 100644
--- a/nf_core/pipelines/create/template_features.yml
+++ b/nf_core/pipelines/create/template_features.yml
@@ -27,7 +27,7 @@ github:
     readme:
       - "nextflow_badge"
   nfcore_pipelines: False
-  custom_pipelines: False
+  custom_pipelines: True
 ci:
   skippable_paths:
     - ".github/workflows/"

From 43b35748a4d4078d080ffbe4f494cbb6f2aed1ff Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 29 Aug 2024 13:49:20 +0200
Subject: [PATCH 383/414] update textual snapshots

---
 .../__snapshots__/test_create_app.ambr        | 511 +++++++++---------
 1 file changed, 256 insertions(+), 255 deletions(-)

diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index 8a0f4dd68d..9a7e52288f 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
           font-weight: 700;
       }
   
-      .terminal-2784035137-matrix {
+      .terminal-1873624262-matrix {
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From a0682c3fa7c9bd2b2b3f16dd06097efa79943b36 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 29 Aug 2024 13:58:30 +0200
Subject: [PATCH 384/414] don't remove .gitignore when unselecting github

---
 nf_core/pipelines/create/template_features.yml | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml
index 744c054075..b59a2e51a6 100644
--- a/nf_core/pipelines/create/template_features.yml
+++ b/nf_core/pipelines/create/template_features.yml
@@ -1,11 +1,18 @@
 github:
   skippable_paths:
     - ".github"
-    - ".gitignore"
     - ".gitattributes"
-  short_description: "Skip the creation of a local Git repository."
-  description: ""
-  help_text: ""
+  short_description: "Use a GitHub repository."
+  description: "Create a GitHub repository for the pipeline."
+  help_text: |
+    This will create a GitHub repository for the pipeline.
+
+    The repository will include:
+    - Continuous Integration (CI) tests
+    - Issues and pull requests templates
+
+    The initialisation of a git repository is required to use the nf-core/tools.
+    This means that even if you unselect this option, your pipeline will still contain a `.git` directory and `.gitignore` file.
   linting:
     files_exist:
       - ".github/ISSUE_TEMPLATE/bug_report.yml"
@@ -13,7 +20,6 @@ github:
       - ".github/PULL_REQUEST_TEMPLATE.md"
       - ".github/CONTRIBUTING.md"
       - ".github/.dockstore.yml"
-      - ".gitignore"
     files_unchanged:
       - ".github/ISSUE_TEMPLATE/bug_report.yml"
       - ".github/ISSUE_TEMPLATE/config.yml"

From 825d7b68b928267c4cfcff6989907dc389165165 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 29 Aug 2024 14:07:59 +0200
Subject: [PATCH 385/414] update textual snapshots

---
 .../__snapshots__/test_create_app.ambr        | 512 +++++++++---------
 1 file changed, 256 insertions(+), 256 deletions(-)

diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index 9a7e52288f..6e3009e18e 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
           font-weight: 700;
       }
   
-      .terminal-1873624262-matrix {
+      .terminal-1208643741-matrix {
           font-family: Fira Code, monospace;
           font-size: 20px;
           line-height: 24.4px;
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+  </text><text class="terminal-3747616910-r19" x="0" y="1215.6" textLength="36.6" clip-path="url(#terminal-3747616910-line-49)">&#160;d&#160;</text><text class="terminal-3747616910-r20" x="36.6" y="1215.6" textLength="207.4" clip-path="url(#terminal-3747616910-line-49)">Toggle&#160;dark&#160;mode&#160;</text><text class="terminal-3747616910-r19" x="244" y="1215.6" textLength="36.6" clip-path="url(#terminal-3747616910-line-49)">&#160;q&#160;</text><text class="terminal-3747616910-r20" x="280.6" y="1215.6" textLength="61" clip-path="url(#terminal-3747616910-line-49)">Quit&#160;</text>
       </g>
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   </svg>

From 5b9eff5dfb1b579a334bd8b2903eb8bba25a46ce Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 29 Aug 2024 14:14:29 +0200
Subject: [PATCH 386/414] add .gitignore to base required files

---
 tests/pipelines/test_create.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py
index d72b346903..f83cc274fc 100644
--- a/tests/pipelines/test_create.py
+++ b/tests/pipelines/test_create.py
@@ -140,6 +140,7 @@ def test_template_customisation_all_files_grouping(self):
         """Test that all pipeline template files are included in a pipeline customisation group."""
         template_features_yml = load_features_yaml()
         base_required_files = [
+            ".gitignore",
             ".nf-core.yml",
             "README.md",
             "nextflow.config",

From 21e03ec5fd8effad4b48c8a269c2a248596f4086 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 30 Aug 2024 12:42:44 +0200
Subject: [PATCH 387/414] run nf-core lint --release on PRs to master

---
 nf_core/pipeline-template/.github/workflows/linting.yml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index ecd5e32f6c..00e8fd302a 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -58,6 +58,15 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+        if: ${{ github.base_ref == 'dev' }}
+
+      - name: Run nf-core pipelines lint --release
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+        if: ${{ github.base_ref == 'master' }}
 
       - name: Save PR number
         if: ${{ always() }}

From 424743eedb2cb6ed0e906e7682fd3e4107aa256f Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 30 Aug 2024 12:45:54 +0200
Subject: [PATCH 388/414] udpate changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0e198caa50..eb8b762b1e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -36,6 +36,7 @@
 - add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130))
 - add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133))
 - add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
+- run nf-core lint --release` on PRs to master`([#3148](https://github.com/nf-core/tools/pull/3148))
 
 ### Linting
 

From fef0829832068384635a7ea36b956cbf663938aa Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sun, 1 Sep 2024 08:34:03 +0200
Subject: [PATCH 389/414] markdown header

---
 nf_core/pipeline-template/README.md | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index f4cbce19c3..beb45ed511 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -9,9 +9,7 @@
 
 {%- else %}
 
-<h1>
-  {{ name }}
-</h1>
+# {{ name }}
 
 {% endif -%}
 {% if github_badges -%}

From 6482287913cfb0776fe1ca00b14e5589c3f1dcfb Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 3 Sep 2024 16:52:11 +0200
Subject: [PATCH 390/414] fix issue where tool and subtool have the same name

---
 nf_core/components/nfcore_component.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 5f29bea4eb..433dff438f 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -64,12 +64,19 @@ def __init__(
             self.process_name = ""
             self.environment_yml: Optional[Path] = Path(self.component_dir, "environment.yml")
 
+            component_list = self.component_name.split("/")
+
             name_index = (
                 len(self.component_dir.parts)
                 - 1
-                - self.component_dir.parts[::-1].index(self.component_name.split("/")[0])
+                - self.component_dir.parts[::-1].index(component_list[0])
             )
+            if len(component_list) != 1 and component_list[0] == component_list[1]:
+                # Handle cases where the subtool has the same name as the tool
+                name_index -= 1
+
             repo_dir = self.component_dir.parts[:name_index][-1]
+            
             self.org = repo_dir
             self.nftest_testdir = Path(self.component_dir, "tests")
             self.nftest_main_nf = Path(self.nftest_testdir, "main.nf.test")

From 05c238e6d0f9dbbf784c9e6bd0ba00dc711e998c Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 3 Sep 2024 17:46:09 +0200
Subject: [PATCH 391/414] pre commit

---
 nf_core/components/nfcore_component.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 433dff438f..0f3cdcdfbd 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -66,17 +66,13 @@ def __init__(
 
             component_list = self.component_name.split("/")
 
-            name_index = (
-                len(self.component_dir.parts)
-                - 1
-                - self.component_dir.parts[::-1].index(component_list[0])
-            )
+            name_index = len(self.component_dir.parts) - 1 - self.component_dir.parts[::-1].index(component_list[0])
             if len(component_list) != 1 and component_list[0] == component_list[1]:
                 # Handle cases where the subtool has the same name as the tool
                 name_index -= 1
 
             repo_dir = self.component_dir.parts[:name_index][-1]
-            
+
             self.org = repo_dir
             self.nftest_testdir = Path(self.component_dir, "tests")
             self.nftest_main_nf = Path(self.nftest_testdir, "main.nf.test")

From 736d5e8ce5764555020074cb03d11267fe4eef54 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 4 Sep 2024 11:51:11 +0200
Subject: [PATCH 392/414] Removes all remaining references to max_* params

---
 .github/workflows/create-test-wf.yml         |   2 +-
 CHANGELOG.md                                 |   2 +-
 nf_core/pipelines/lint/nextflow_config.py    |  16 ++-
 tests/pipelines/lint/test_nextflow_config.py |  87 ++------------
 tests/pipelines/test_launch.py               | 118 +++++++++++++++----
 5 files changed, 116 insertions(+), 109 deletions(-)

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 7d69cb7b7b..56c6c822a9 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -75,7 +75,7 @@ jobs:
           pwd
           # echo content of current directory
           ls -la
-          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results --max_cpus 4
+          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
 
       - name: Upload log file artifact
         if: ${{ always() }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index cd3e558153..c5e22af180 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,6 +37,7 @@
 - add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133))
 - add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
 - Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))
+- Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([#3037](https://github.com/nf-core/tools/pull/3037))
 
 ### Linting
 
@@ -98,7 +99,6 @@
 
 - Don't cache pip in `linting.yml` ([#2961](https://github.com/nf-core/tools/pull/2961))
 - Lint pipelines with the nf-core template version and post comment if it is outdated ([#2978](https://github.com/nf-core/tools/pull/2978))
-- Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([#3037](https://github.com/nf-core/tools/pull/3037))
 
 ### General
 
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index f694a1ab2c..4179517880 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -80,7 +80,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     * ``params.nf_required_version``: The old method for specifying the minimum Nextflow version. Replaced by ``manifest.nextflowVersion``
     * ``params.container``: The old method for specifying the dockerhub container address. Replaced by ``process.container``
     * ``igenomesIgnore``: Changed to ``igenomes_ignore``
-    * ``params.max_cpus``: Old method of specifying the maximum number of CPUs a process can request. Replaced by native Nextflow `resourceLimits`directive.
+    * ``params.max_cpus``: Old method of specifying the maximum number of CPUs a process can request. Replaced by native Nextflow `resourceLimits`directive in config files.
     * ``params.max_memory``: Old method of specifying the maximum number of memory can request. Replaced by native Nextflow `resourceLimits`directive.
     * ``params.max_time``: Old method of specifying the maximum number of CPUs can request. Replaced by native Nextflow `resourceLimits`directive.
 
@@ -149,7 +149,13 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["params.input"],
     ]
     # Throw a warning if these are missing
-    config_warn = [["manifest.mainScript"], ["timeline.file"], ["trace.file"], ["report.file"], ["dag.file"]]
+    config_warn = [
+        ["manifest.mainScript"],
+        ["timeline.file"],
+        ["trace.file"],
+        ["report.file"],
+        ["dag.file"],
+    ]
     # Old depreciated vars - fail if present
     config_fail_ifdefined = [
         "params.nf_required_version",
@@ -207,7 +213,11 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             )
 
     # Remove field that should be ignored according to the linting config
-    ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else []
+    ignore_configs = (
+        self.lint_config.get("nextflow_config", [])
+        if self.lint_config is not None
+        else []
+    )
 
     for cfs in config_fail:
         for cf in cfs:
diff --git a/tests/pipelines/lint/test_nextflow_config.py b/tests/pipelines/lint/test_nextflow_config.py
index 3cc9355452..88b5e4503e 100644
--- a/tests/pipelines/lint/test_nextflow_config.py
+++ b/tests/pipelines/lint/test_nextflow_config.py
@@ -30,8 +30,9 @@ def test_default_values_match(self):
         result = lint_obj.nextflow_config()
         assert len(result["failed"]) == 0
         assert len(result["warned"]) == 0
-        assert "Config default value correct: params.max_cpus" in str(result["passed"])
-        assert "Config default value correct: params.validate_params" in str(result["passed"])
+        assert "Config default value correct: params.validate_params" in str(
+            result["passed"]
+        )
 
     def test_nextflow_config_bad_name_fail(self):
         """Tests that config variable existence test fails with bad pipeline name"""
@@ -69,80 +70,6 @@ def test_nextflow_config_missing_test_profile_failed(self):
         assert len(result["failed"]) > 0
         assert len(result["warned"]) == 0
 
-    def test_default_values_fail(self):
-        """Test linting fails if the default values in nextflow.config do not match the ones defined in the nextflow_schema.json."""
-        # Change the default value of max_cpus in nextflow.config
-        nf_conf_file = Path(self.new_pipeline) / "nextflow.config"
-        with open(nf_conf_file) as f:
-            content = f.read()
-            fail_content = re.sub(r"\bmax_cpus\s*=\s*16\b", "max_cpus = 0", content)
-        with open(nf_conf_file, "w") as f:
-            f.write(fail_content)
-        # Change the default value of max_memory in nextflow_schema.json
-        nf_schema_file = Path(self.new_pipeline) / "nextflow_schema.json"
-        with open(nf_schema_file) as f:
-            content = f.read()
-            fail_content = re.sub(r'"default": "128.GB"', '"default": "18.GB"', content)
-        with open(nf_schema_file, "w") as f:
-            f.write(fail_content)
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj.load_pipeline_config()
-        result = lint_obj.nextflow_config()
-        assert len(result["failed"]) == 2
-        assert (
-            "Config default value incorrect: `params.max_cpus` is set as `16` in `nextflow_schema.json` but is `0` in `nextflow.config`."
-            in result["failed"]
-        )
-        assert (
-            "Config default value incorrect: `params.max_memory` is set as `18.GB` in `nextflow_schema.json` but is `128.GB` in `nextflow.config`."
-            in result["failed"]
-        )
-
-    def test_catch_params_assignment_in_main_nf(self):
-        """Test linting fails if main.nf contains an assignment to a parameter from nextflow_schema.json."""
-        # Add parameter assignment in main.nf
-        main_nf_file = Path(self.new_pipeline) / "main.nf"
-        with open(main_nf_file, "a") as f:
-            f.write("params.max_time = 42")
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj.load_pipeline_config()
-        result = lint_obj.nextflow_config()
-        assert len(result["failed"]) == 1
-        assert (
-            result["failed"][0]
-            == "Config default value incorrect: `params.max_time` is set as `240.h` in `nextflow_schema.json` but is `null` in `nextflow.config`."
-        )
-
-    def test_allow_params_reference_in_main_nf(self):
-        """Test linting allows for references like `params.aligner == 'bwa'` in main.nf. The test will detect if the bug mentioned in GitHub-issue #2833 reemerges."""
-        # Add parameter reference in main.nf
-        main_nf_file = Path(self.new_pipeline) / "main.nf"
-        with open(main_nf_file, "a") as f:
-            f.write("params.max_time == 42")
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj.load_pipeline_config()
-        result = lint_obj.nextflow_config()
-        assert len(result["failed"]) == 0
-
-    def test_default_values_ignored(self):
-        """Test ignoring linting of default values."""
-        # Add max_cpus to the ignore list
-        nf_core_yml_path = Path(self.new_pipeline) / ".nf-core.yml"
-        nf_core_yml = NFCoreYamlConfig(
-            repository_type="pipeline", lint={"nextflow_config": [{"config_defaults": ["params.max_cpus"]}]}
-        )
-        with open(nf_core_yml_path, "w") as f:
-            yaml.dump(nf_core_yml.model_dump(), f)
-
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj.load_pipeline_config()
-        lint_obj._load_lint_config()
-        result = lint_obj.nextflow_config()
-        assert len(result["failed"]) == 0
-        assert len(result["ignored"]) == 1
-        assert "Config default value correct: params.max_cpu" not in str(result["passed"])
-        assert "Config default ignored: params.max_cpus" in str(result["ignored"])
-
     def test_default_values_float(self):
         """Test comparing two float values."""
         # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params`
@@ -150,7 +77,9 @@ def test_default_values_float(self):
         with open(nf_conf_file) as f:
             content = f.read()
             fail_content = re.sub(
-                r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content
+                r"validate_params\s*=\s*true",
+                "params.validate_params = true\ndummy = 0.000000001",
+                content,
             )
         with open(nf_conf_file, "w") as f:
             f.write(fail_content)
@@ -180,7 +109,9 @@ def test_default_values_float_fail(self):
         with open(nf_conf_file) as f:
             content = f.read()
             fail_content = re.sub(
-                r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content
+                r"validate_params\s*=\s*true",
+                "params.validate_params = true\ndummy = 0.000000001",
+                content,
             )
         with open(nf_conf_file, "w") as f:
             f.write(fail_content)
diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py
index d63e7b6dc5..5598fc695b 100644
--- a/tests/pipelines/test_launch.py
+++ b/tests/pipelines/test_launch.py
@@ -17,9 +17,13 @@ class TestLaunch(TestPipelines):
     def setUp(self) -> None:
         super().setUp()
         self.nf_params_fn = Path(self.pipeline_dir, "nf-params.json")
-        self.launcher = nf_core.pipelines.launch.Launch(self.pipeline_dir, params_out=self.nf_params_fn)
+        self.launcher = nf_core.pipelines.launch.Launch(
+            self.pipeline_dir, params_out=self.nf_params_fn
+        )
 
-    @mock.patch.object(nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True])
+    @mock.patch.object(
+        nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True]
+    )
     @mock.patch.object(nf_core.pipelines.launch.Launch, "launch_web_gui")
     def test_launch_pipeline(self, mock_webbrowser, mock_lauch_web_gui):
         """Test the main launch function"""
@@ -34,10 +38,14 @@ def test_launch_file_exists(self, mock_confirm):
         # Try and to launch, return with error
         assert self.launcher.launch_pipeline() is False
 
-    @mock.patch.object(nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True])
+    @mock.patch.object(
+        nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True]
+    )
     @mock.patch.object(nf_core.pipelines.launch.Launch, "launch_web_gui")
     @mock.patch.object(nf_core.pipelines.launch.Confirm, "ask", side_effect=[False])
-    def test_launch_file_exists_overwrite(self, mock_webbrowser, mock_lauch_web_gui, mock_confirm):
+    def test_launch_file_exists_overwrite(
+        self, mock_webbrowser, mock_lauch_web_gui, mock_confirm
+    ):
         """Test that we detect an existing params file and we overwrite it"""
         # Make an empty params file to be overwritten
         open(self.nf_params_fn, "a").close()
@@ -47,7 +55,14 @@ def test_launch_file_exists_overwrite(self, mock_webbrowser, mock_lauch_web_gui,
     def test_get_pipeline_schema(self):
         """Test loading the params schema from a pipeline"""
         self.launcher.get_pipeline_schema()
-        assert len(self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]) > 2
+        assert (
+            len(
+                self.launcher.schema_obj.schema["$defs"]["input_output_options"][
+                    "properties"
+                ]
+            )
+            > 2
+        )
 
     @with_temporary_folder
     def test_make_pipeline_schema(self, tmp_path):
@@ -58,10 +73,21 @@ def test_make_pipeline_schema(self, tmp_path):
         )
         create_obj.init_pipeline()
         Path(test_pipeline_dir, "nextflow_schema.json").unlink()
-        self.launcher = nf_core.pipelines.launch.Launch(test_pipeline_dir, params_out=self.nf_params_fn)
+        self.launcher = nf_core.pipelines.launch.Launch(
+            test_pipeline_dir, params_out=self.nf_params_fn
+        )
         self.launcher.get_pipeline_schema()
-        assert len(self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]) >= 2
-        assert self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]["outdir"] == {
+        assert (
+            len(
+                self.launcher.schema_obj.schema["$defs"]["input_output_options"][
+                    "properties"
+                ]
+            )
+            >= 2
+        )
+        assert self.launcher.schema_obj.schema["$defs"]["input_output_options"][
+            "properties"
+        ]["outdir"] == {
             "type": "string",
             "format": "directory-path",
             "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
@@ -91,8 +117,13 @@ def test_nf_merge_schema(self):
         self.launcher.get_pipeline_schema()
         self.launcher.set_schema_inputs()
         self.launcher.merge_nxf_flag_schema()
-        assert self.launcher.schema_obj.schema["allOf"][0] == {"$ref": "#/$defs/coreNextflow"}
-        assert "-resume" in self.launcher.schema_obj.schema["$defs"]["coreNextflow"]["properties"]
+        assert self.launcher.schema_obj.schema["allOf"][0] == {
+            "$ref": "#/$defs/coreNextflow"
+        }
+        assert (
+            "-resume"
+            in self.launcher.schema_obj.schema["$defs"]["coreNextflow"]["properties"]
+        )
 
     def test_ob_to_questionary_string(self):
         """Check converting a python dict to a pyenquirer format - simple strings"""
@@ -101,14 +132,21 @@ def test_ob_to_questionary_string(self):
             "default": "data/*{1,2}.fastq.gz",
         }
         result = self.launcher.single_param_to_questionary("input", sc_obj)
-        assert result == {"type": "input", "name": "input", "message": "", "default": "data/*{1,2}.fastq.gz"}
+        assert result == {
+            "type": "input",
+            "name": "input",
+            "message": "",
+            "default": "data/*{1,2}.fastq.gz",
+        }
 
     @mock.patch("questionary.unsafe_prompt", side_effect=[{"use_web_gui": "Web based"}])
     def test_prompt_web_gui_true(self, mock_prompt):
         """Check the prompt to launch the web schema or use the cli"""
         assert self.launcher.prompt_web_gui() is True
 
-    @mock.patch("questionary.unsafe_prompt", side_effect=[{"use_web_gui": "Command line"}])
+    @mock.patch(
+        "questionary.unsafe_prompt", side_effect=[{"use_web_gui": "Command line"}]
+    )
     def test_prompt_web_gui_false(self, mock_prompt):
         """Check the prompt to launch the web schema or use the cli"""
         assert self.launcher.prompt_web_gui() is False
@@ -123,17 +161,23 @@ def test_launch_web_gui_missing_keys(self, mock_poll_nfcore_web_api):
         assert exc_info.value.args[0].startswith("Web launch response not recognised:")
 
     @mock.patch(
-        "nf_core.utils.poll_nfcore_web_api", side_effect=[{"api_url": "foo", "web_url": "bar", "status": "recieved"}]
+        "nf_core.utils.poll_nfcore_web_api",
+        side_effect=[{"api_url": "foo", "web_url": "bar", "status": "recieved"}],
     )
     @mock.patch("webbrowser.open")
     @mock.patch("nf_core.utils.wait_cli_function")
-    def test_launch_web_gui(self, mock_poll_nfcore_web_api, mock_webbrowser, mock_wait_cli_function):
+    def test_launch_web_gui(
+        self, mock_poll_nfcore_web_api, mock_webbrowser, mock_wait_cli_function
+    ):
         """Check the code that opens the web browser"""
         self.launcher.get_pipeline_schema()
         self.launcher.merge_nxf_flag_schema()
         assert self.launcher.launch_web_gui() is None
 
-    @mock.patch("nf_core.utils.poll_nfcore_web_api", side_effect=[{"status": "error", "message": "foo"}])
+    @mock.patch(
+        "nf_core.utils.poll_nfcore_web_api",
+        side_effect=[{"status": "error", "message": "foo"}],
+    )
     def test_get_web_launch_response_error(self, mock_poll_nfcore_web_api):
         """Test polling the website for a launch response - status error"""
         with pytest.raises(AssertionError) as exc_info:
@@ -145,14 +189,22 @@ def test_get_web_launch_response_unexpected(self, mock_poll_nfcore_web_api):
         """Test polling the website for a launch response - status error"""
         with pytest.raises(AssertionError) as exc_info:
             self.launcher.get_web_launch_response()
-        assert exc_info.value.args[0].startswith("Web launch GUI returned unexpected status (foo): ")
+        assert exc_info.value.args[0].startswith(
+            "Web launch GUI returned unexpected status (foo): "
+        )
 
-    @mock.patch("nf_core.utils.poll_nfcore_web_api", side_effect=[{"status": "waiting_for_user"}])
+    @mock.patch(
+        "nf_core.utils.poll_nfcore_web_api",
+        side_effect=[{"status": "waiting_for_user"}],
+    )
     def test_get_web_launch_response_waiting(self, mock_poll_nfcore_web_api):
         """Test polling the website for a launch response - status waiting_for_user"""
         assert self.launcher.get_web_launch_response() is False
 
-    @mock.patch("nf_core.utils.poll_nfcore_web_api", side_effect=[{"status": "launch_params_complete"}])
+    @mock.patch(
+        "nf_core.utils.poll_nfcore_web_api",
+        side_effect=[{"status": "launch_params_complete"}],
+    )
     def test_get_web_launch_response_missing_keys(self, mock_poll_nfcore_web_api):
         """Test polling the website for a launch response - complete, but missing keys"""
         with pytest.raises(AssertionError) as exc_info:
@@ -175,7 +227,9 @@ def test_get_web_launch_response_missing_keys(self, mock_poll_nfcore_web_api):
         ],
     )
     @mock.patch.object(nf_core.pipelines.launch.Launch, "sanitise_web_response")
-    def test_get_web_launch_response_valid(self, mock_poll_nfcore_web_api, mock_sanitise):
+    def test_get_web_launch_response_valid(
+        self, mock_poll_nfcore_web_api, mock_sanitise
+    ):
         """Test polling the website for a launch response - complete, valid response"""
         self.launcher.get_pipeline_schema()
         assert self.launcher.get_web_launch_response() is True
@@ -185,11 +239,9 @@ def test_sanitise_web_response(self):
         self.launcher.get_pipeline_schema()
         self.launcher.nxf_flags["-name"] = ""
         self.launcher.schema_obj.input_params["igenomes_ignore"] = "true"
-        self.launcher.schema_obj.input_params["max_cpus"] = "12"
         self.launcher.sanitise_web_response()
         assert "-name" not in self.launcher.nxf_flags
         assert self.launcher.schema_obj.input_params["igenomes_ignore"] is True
-        assert self.launcher.schema_obj.input_params["max_cpus"] == 12
 
     def test_ob_to_questionary_bool(self):
         """Check converting a python dict to a pyenquirer format - booleans"""
@@ -262,7 +314,10 @@ def test_ob_to_questionary_enum(self):
 
     def test_ob_to_questionary_pattern(self):
         """Check converting a python dict to a questionary format - with pattern"""
-        sc_obj = {"type": "string", "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"}
+        sc_obj = {
+            "type": "string",
+            "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
+        }
         result = self.launcher.single_param_to_questionary("email", sc_obj)
         assert result["type"] == "input"
         assert result["validate"]("test@email.com") is True
@@ -295,7 +350,10 @@ def test_build_command_nf(self):
         self.launcher.nxf_flags["-name"] = "Test_Workflow"
         self.launcher.nxf_flags["-resume"] = True
         self.launcher.build_command()
-        assert self.launcher.nextflow_cmd == f'nextflow run {self.pipeline_dir} -name "Test_Workflow" -resume'
+        assert (
+            self.launcher.nextflow_cmd
+            == f'nextflow run {self.pipeline_dir} -name "Test_Workflow" -resume'
+        )
 
     def test_build_command_params(self):
         """Test the functionality to build a nextflow command - params supplied"""
@@ -303,13 +361,18 @@ def test_build_command_params(self):
         self.launcher.schema_obj.input_params.update({"input": "custom_input"})
         self.launcher.build_command()
         # Check command
-        assert self.launcher.nextflow_cmd == f'nextflow run {self.pipeline_dir} -params-file "{self.nf_params_fn}"'
+        assert (
+            self.launcher.nextflow_cmd
+            == f'nextflow run {self.pipeline_dir} -params-file "{self.nf_params_fn}"'
+        )
         # Check saved parameters file
         with open(self.nf_params_fn) as fh:
             try:
                 saved_json = json.load(fh)
             except json.JSONDecodeError as e:
-                raise UserWarning(f"Unable to load JSON file '{self.nf_params_fn}' due to error {e}")
+                raise UserWarning(
+                    f"Unable to load JSON file '{self.nf_params_fn}' due to error {e}"
+                )
 
         assert saved_json == {"input": "custom_input"}
 
@@ -319,4 +382,7 @@ def test_build_command_params_cl(self):
         self.launcher.get_pipeline_schema()
         self.launcher.schema_obj.input_params.update({"input": "custom_input"})
         self.launcher.build_command()
-        assert self.launcher.nextflow_cmd == f'nextflow run {self.pipeline_dir} --input "custom_input"'
+        assert (
+            self.launcher.nextflow_cmd
+            == f'nextflow run {self.pipeline_dir} --input "custom_input"'
+        )

From 556336034ffc1107a2c212fc2cd326a57953e150 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 4 Sep 2024 09:57:17 +0000
Subject: [PATCH 393/414] [automated] Fix code linting

---
 nf_core/pipelines/lint/nextflow_config.py    | 89 +++++---------------
 tests/pipelines/lint/test_nextflow_config.py |  7 +-
 tests/pipelines/test_launch.py               | 86 ++++---------------
 3 files changed, 40 insertions(+), 142 deletions(-)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 4179517880..14e91cc609 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -213,11 +213,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             )
 
     # Remove field that should be ignored according to the linting config
-    ignore_configs = (
-        self.lint_config.get("nextflow_config", [])
-        if self.lint_config is not None
-        else []
-    )
+    ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else []
 
     for cfs in config_fail:
         for cf in cfs:
@@ -244,13 +240,9 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             ignored.append(f"Config variable ignored: {self._wrap_quotes(cf)}")
             break
         if cf not in self.nf_config.keys():
-            passed.append(
-                f"Config variable (correctly) not found: {self._wrap_quotes(cf)}"
-            )
+            passed.append(f"Config variable (correctly) not found: {self._wrap_quotes(cf)}")
         else:
-            failed.append(
-                f"Config variable (incorrectly) found: {self._wrap_quotes(cf)}"
-            )
+            failed.append(f"Config variable (incorrectly) found: {self._wrap_quotes(cf)}")
 
     # Check and warn if the process configuration is done with deprecated syntax
 
@@ -271,13 +263,9 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         if k in ignore_configs:
             continue
         if self.nf_config.get(k) == "true":
-            passed.append(
-                f"Config ``{k}`` had correct value: ``{self.nf_config.get(k)}``"
-            )
+            passed.append(f"Config ``{k}`` had correct value: ``{self.nf_config.get(k)}``")
         else:
-            failed.append(
-                f"Config ``{k}`` did not have correct value: ``{self.nf_config.get(k)}``"
-            )
+            failed.append(f"Config ``{k}`` did not have correct value: ``{self.nf_config.get(k)}``")
 
     if "manifest.name" not in ignore_configs:
         # Check that the pipeline name starts with nf-core
@@ -286,9 +274,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             if not manifest_name.startswith("nf-core/"):
                 raise AssertionError()
         except (AssertionError, IndexError):
-            failed.append(
-                f"Config ``manifest.name`` did not begin with ``nf-core/``:\n    {manifest_name}"
-            )
+            failed.append(f"Config ``manifest.name`` did not begin with ``nf-core/``:\n    {manifest_name}")
         else:
             passed.append("Config ``manifest.name`` began with ``nf-core/``")
 
@@ -304,9 +290,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             )
 
         else:
-            passed.append(
-                "Config variable ``manifest.homePage`` began with https://github.com/nf-core/"
-            )
+            passed.append("Config variable ``manifest.homePage`` began with https://github.com/nf-core/")
 
     # Check that the DAG filename ends in ``.svg``
     if "dag.file" in self.nf_config:
@@ -314,21 +298,12 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         if self.nf_config["dag.file"].strip("'\"").endswith(default_dag_format):
             passed.append(f"Config ``dag.file`` ended with ``{default_dag_format}``")
         else:
-            failed.append(
-                f"Config ``dag.file`` did not end with ``{default_dag_format}``"
-            )
+            failed.append(f"Config ``dag.file`` did not end with ``{default_dag_format}``")
 
     # Check that the minimum nextflowVersion is set properly
     if "manifest.nextflowVersion" in self.nf_config:
-        if (
-            self.nf_config.get("manifest.nextflowVersion", "")
-            .strip("\"'")
-            .lstrip("!")
-            .startswith(">=")
-        ):
-            passed.append(
-                "Config variable ``manifest.nextflowVersion`` started with >= or !>="
-            )
+        if self.nf_config.get("manifest.nextflowVersion", "").strip("\"'").lstrip("!").startswith(">="):
+            passed.append("Config variable ``manifest.nextflowVersion`` started with >= or !>=")
         else:
             failed.append(
                 "Config ``manifest.nextflowVersion`` did not start with ``>=`` or ``!>=`` : "
@@ -338,9 +313,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     # Check that the pipeline version contains ``dev``
     if not self.release_mode and "manifest.version" in self.nf_config:
         if self.nf_config["manifest.version"].strip(" '\"").endswith("dev"):
-            passed.append(
-                f"Config ``manifest.version`` ends in ``dev``: ``{self.nf_config['manifest.version']}``"
-            )
+            passed.append(f"Config ``manifest.version`` ends in ``dev``: ``{self.nf_config['manifest.version']}``")
         else:
             warned.append(
                 f"Config ``manifest.version`` should end in ``dev``: ``{self.nf_config['manifest.version']}``"
@@ -359,32 +332,18 @@ def nextflow_config(self) -> Dict[str, List[str]]:
 
     if "custom_config" not in ignore_configs:
         # Check if custom profile params are set correctly
-        if (
-            self.nf_config.get("params.custom_config_version", "").strip("'")
-            == "master"
-        ):
+        if self.nf_config.get("params.custom_config_version", "").strip("'") == "master":
             passed.append("Config `params.custom_config_version` is set to `master`")
         else:
-            failed.append(
-                "Config `params.custom_config_version` is not set to `master`"
-            )
+            failed.append("Config `params.custom_config_version` is not set to `master`")
 
-        custom_config_base = (
-            "https://raw.githubusercontent.com/nf-core/configs/{}".format(
-                self.nf_config.get("params.custom_config_version", "").strip("'")
-            )
+        custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/{}".format(
+            self.nf_config.get("params.custom_config_version", "").strip("'")
         )
-        if (
-            self.nf_config.get("params.custom_config_base", "").strip("'")
-            == custom_config_base
-        ):
-            passed.append(
-                f"Config `params.custom_config_base` is set to `{custom_config_base}`"
-            )
+        if self.nf_config.get("params.custom_config_base", "").strip("'") == custom_config_base:
+            passed.append(f"Config `params.custom_config_base` is set to `{custom_config_base}`")
         else:
-            failed.append(
-                f"Config `params.custom_config_base` is not set to `{custom_config_base}`"
-            )
+            failed.append(f"Config `params.custom_config_base` is not set to `{custom_config_base}`")
 
         # Check that lines for loading custom profiles exist
         lines = [
@@ -426,9 +385,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
 
         match = re.search(r"\bprofiles\s*{", cleaned_content)
         if not match:
-            failed.append(
-                "nextflow.config does not contain `profiles` scope, but `test` profile is required"
-            )
+            failed.append("nextflow.config does not contain `profiles` scope, but `test` profile is required")
         else:
             # Extract profiles scope content and check for test profile
             start = match.end()
@@ -444,9 +401,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             if re.search(r"\btest\s*{", profiles_content):
                 passed.append("nextflow.config contains configuration profile `test`")
             else:
-                failed.append(
-                    "nextflow.config does not contain configuration profile `test`"
-                )
+                failed.append("nextflow.config does not contain configuration profile `test`")
 
     # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json
     ignore_defaults = []
@@ -490,9 +445,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
                 schema_default = str(schema.schema_defaults[param_name])
                 config_default = str(self.nf_config[param])
             if config_default is not None and config_default == schema_default:
-                passed.append(
-                    f"Config default value correct: {param}= {schema_default}"
-                )
+                passed.append(f"Config default value correct: {param}= {schema_default}")
             else:
                 failed.append(
                     f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`."
diff --git a/tests/pipelines/lint/test_nextflow_config.py b/tests/pipelines/lint/test_nextflow_config.py
index 88b5e4503e..4c3893f4c4 100644
--- a/tests/pipelines/lint/test_nextflow_config.py
+++ b/tests/pipelines/lint/test_nextflow_config.py
@@ -2,11 +2,8 @@
 import re
 from pathlib import Path
 
-import yaml
-
 import nf_core.pipelines.create.create
 import nf_core.pipelines.lint
-from nf_core.utils import NFCoreYamlConfig
 
 from ..test_lint import TestLint
 
@@ -30,9 +27,7 @@ def test_default_values_match(self):
         result = lint_obj.nextflow_config()
         assert len(result["failed"]) == 0
         assert len(result["warned"]) == 0
-        assert "Config default value correct: params.validate_params" in str(
-            result["passed"]
-        )
+        assert "Config default value correct: params.validate_params" in str(result["passed"])
 
     def test_nextflow_config_bad_name_fail(self):
         """Tests that config variable existence test fails with bad pipeline name"""
diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py
index 5598fc695b..5e230528a7 100644
--- a/tests/pipelines/test_launch.py
+++ b/tests/pipelines/test_launch.py
@@ -17,13 +17,9 @@ class TestLaunch(TestPipelines):
     def setUp(self) -> None:
         super().setUp()
         self.nf_params_fn = Path(self.pipeline_dir, "nf-params.json")
-        self.launcher = nf_core.pipelines.launch.Launch(
-            self.pipeline_dir, params_out=self.nf_params_fn
-        )
+        self.launcher = nf_core.pipelines.launch.Launch(self.pipeline_dir, params_out=self.nf_params_fn)
 
-    @mock.patch.object(
-        nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True]
-    )
+    @mock.patch.object(nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True])
     @mock.patch.object(nf_core.pipelines.launch.Launch, "launch_web_gui")
     def test_launch_pipeline(self, mock_webbrowser, mock_lauch_web_gui):
         """Test the main launch function"""
@@ -38,14 +34,10 @@ def test_launch_file_exists(self, mock_confirm):
         # Try and to launch, return with error
         assert self.launcher.launch_pipeline() is False
 
-    @mock.patch.object(
-        nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True]
-    )
+    @mock.patch.object(nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True])
     @mock.patch.object(nf_core.pipelines.launch.Launch, "launch_web_gui")
     @mock.patch.object(nf_core.pipelines.launch.Confirm, "ask", side_effect=[False])
-    def test_launch_file_exists_overwrite(
-        self, mock_webbrowser, mock_lauch_web_gui, mock_confirm
-    ):
+    def test_launch_file_exists_overwrite(self, mock_webbrowser, mock_lauch_web_gui, mock_confirm):
         """Test that we detect an existing params file and we overwrite it"""
         # Make an empty params file to be overwritten
         open(self.nf_params_fn, "a").close()
@@ -55,14 +47,7 @@ def test_launch_file_exists_overwrite(
     def test_get_pipeline_schema(self):
         """Test loading the params schema from a pipeline"""
         self.launcher.get_pipeline_schema()
-        assert (
-            len(
-                self.launcher.schema_obj.schema["$defs"]["input_output_options"][
-                    "properties"
-                ]
-            )
-            > 2
-        )
+        assert len(self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]) > 2
 
     @with_temporary_folder
     def test_make_pipeline_schema(self, tmp_path):
@@ -73,21 +58,10 @@ def test_make_pipeline_schema(self, tmp_path):
         )
         create_obj.init_pipeline()
         Path(test_pipeline_dir, "nextflow_schema.json").unlink()
-        self.launcher = nf_core.pipelines.launch.Launch(
-            test_pipeline_dir, params_out=self.nf_params_fn
-        )
+        self.launcher = nf_core.pipelines.launch.Launch(test_pipeline_dir, params_out=self.nf_params_fn)
         self.launcher.get_pipeline_schema()
-        assert (
-            len(
-                self.launcher.schema_obj.schema["$defs"]["input_output_options"][
-                    "properties"
-                ]
-            )
-            >= 2
-        )
-        assert self.launcher.schema_obj.schema["$defs"]["input_output_options"][
-            "properties"
-        ]["outdir"] == {
+        assert len(self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]) >= 2
+        assert self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]["outdir"] == {
             "type": "string",
             "format": "directory-path",
             "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
@@ -117,13 +91,8 @@ def test_nf_merge_schema(self):
         self.launcher.get_pipeline_schema()
         self.launcher.set_schema_inputs()
         self.launcher.merge_nxf_flag_schema()
-        assert self.launcher.schema_obj.schema["allOf"][0] == {
-            "$ref": "#/$defs/coreNextflow"
-        }
-        assert (
-            "-resume"
-            in self.launcher.schema_obj.schema["$defs"]["coreNextflow"]["properties"]
-        )
+        assert self.launcher.schema_obj.schema["allOf"][0] == {"$ref": "#/$defs/coreNextflow"}
+        assert "-resume" in self.launcher.schema_obj.schema["$defs"]["coreNextflow"]["properties"]
 
     def test_ob_to_questionary_string(self):
         """Check converting a python dict to a pyenquirer format - simple strings"""
@@ -144,9 +113,7 @@ def test_prompt_web_gui_true(self, mock_prompt):
         """Check the prompt to launch the web schema or use the cli"""
         assert self.launcher.prompt_web_gui() is True
 
-    @mock.patch(
-        "questionary.unsafe_prompt", side_effect=[{"use_web_gui": "Command line"}]
-    )
+    @mock.patch("questionary.unsafe_prompt", side_effect=[{"use_web_gui": "Command line"}])
     def test_prompt_web_gui_false(self, mock_prompt):
         """Check the prompt to launch the web schema or use the cli"""
         assert self.launcher.prompt_web_gui() is False
@@ -166,9 +133,7 @@ def test_launch_web_gui_missing_keys(self, mock_poll_nfcore_web_api):
     )
     @mock.patch("webbrowser.open")
     @mock.patch("nf_core.utils.wait_cli_function")
-    def test_launch_web_gui(
-        self, mock_poll_nfcore_web_api, mock_webbrowser, mock_wait_cli_function
-    ):
+    def test_launch_web_gui(self, mock_poll_nfcore_web_api, mock_webbrowser, mock_wait_cli_function):
         """Check the code that opens the web browser"""
         self.launcher.get_pipeline_schema()
         self.launcher.merge_nxf_flag_schema()
@@ -189,9 +154,7 @@ def test_get_web_launch_response_unexpected(self, mock_poll_nfcore_web_api):
         """Test polling the website for a launch response - status error"""
         with pytest.raises(AssertionError) as exc_info:
             self.launcher.get_web_launch_response()
-        assert exc_info.value.args[0].startswith(
-            "Web launch GUI returned unexpected status (foo): "
-        )
+        assert exc_info.value.args[0].startswith("Web launch GUI returned unexpected status (foo): ")
 
     @mock.patch(
         "nf_core.utils.poll_nfcore_web_api",
@@ -227,9 +190,7 @@ def test_get_web_launch_response_missing_keys(self, mock_poll_nfcore_web_api):
         ],
     )
     @mock.patch.object(nf_core.pipelines.launch.Launch, "sanitise_web_response")
-    def test_get_web_launch_response_valid(
-        self, mock_poll_nfcore_web_api, mock_sanitise
-    ):
+    def test_get_web_launch_response_valid(self, mock_poll_nfcore_web_api, mock_sanitise):
         """Test polling the website for a launch response - complete, valid response"""
         self.launcher.get_pipeline_schema()
         assert self.launcher.get_web_launch_response() is True
@@ -350,10 +311,7 @@ def test_build_command_nf(self):
         self.launcher.nxf_flags["-name"] = "Test_Workflow"
         self.launcher.nxf_flags["-resume"] = True
         self.launcher.build_command()
-        assert (
-            self.launcher.nextflow_cmd
-            == f'nextflow run {self.pipeline_dir} -name "Test_Workflow" -resume'
-        )
+        assert self.launcher.nextflow_cmd == f'nextflow run {self.pipeline_dir} -name "Test_Workflow" -resume'
 
     def test_build_command_params(self):
         """Test the functionality to build a nextflow command - params supplied"""
@@ -361,18 +319,13 @@ def test_build_command_params(self):
         self.launcher.schema_obj.input_params.update({"input": "custom_input"})
         self.launcher.build_command()
         # Check command
-        assert (
-            self.launcher.nextflow_cmd
-            == f'nextflow run {self.pipeline_dir} -params-file "{self.nf_params_fn}"'
-        )
+        assert self.launcher.nextflow_cmd == f'nextflow run {self.pipeline_dir} -params-file "{self.nf_params_fn}"'
         # Check saved parameters file
         with open(self.nf_params_fn) as fh:
             try:
                 saved_json = json.load(fh)
             except json.JSONDecodeError as e:
-                raise UserWarning(
-                    f"Unable to load JSON file '{self.nf_params_fn}' due to error {e}"
-                )
+                raise UserWarning(f"Unable to load JSON file '{self.nf_params_fn}' due to error {e}")
 
         assert saved_json == {"input": "custom_input"}
 
@@ -382,7 +335,4 @@ def test_build_command_params_cl(self):
         self.launcher.get_pipeline_schema()
         self.launcher.schema_obj.input_params.update({"input": "custom_input"})
         self.launcher.build_command()
-        assert (
-            self.launcher.nextflow_cmd
-            == f'nextflow run {self.pipeline_dir} --input "custom_input"'
-        )
+        assert self.launcher.nextflow_cmd == f'nextflow run {self.pipeline_dir} --input "custom_input"'

From 6633769fa4cf5c6f9a84745a9424fb07443b5a90 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 4 Sep 2024 12:06:55 +0200
Subject: [PATCH 394/414] Fix linting fail

---
 nf_core/pipeline-template/nextflow_schema.json | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index f75354d4e1..818adf9619 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -135,6 +135,7 @@
                 }
             }
         },
+        {%- endif %}
         "generic_options": {
             "title": "Generic options",
             "type": "object",

From d819232314df5ef888ea84ed366253f0f3ddf3ae Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 4 Sep 2024 12:10:36 +0200
Subject: [PATCH 395/414] Fix schema error

---
 nf_core/pipeline-template/nextflow_schema.json | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 818adf9619..4136a0b490 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -243,9 +243,6 @@
         {% if nf_core_configs %}{
             "$ref": "#/$defs/institutional_config_options"
         },{% endif %}
-        {
-            "$ref": "#/$defs/max_job_request_options"
-        },
         {
             "$ref": "#/$defs/generic_options"
         }

From b6e19d8a750c2fdcb63851d81a2337852f43e84f Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 5 Sep 2024 09:36:45 +0200
Subject: [PATCH 396/414] add a tabix tabix test

---
 tests/modules/test_lint.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py
index cc7e0565e0..144d163b27 100644
--- a/tests/modules/test_lint.py
+++ b/tests/modules/test_lint.py
@@ -186,6 +186,15 @@ def test_modules_lint_trimgalore(self):
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
 
+    def test_modules_lint_tabix_tabix(self):
+        """Test linting the tabix/tabix module"""
+        self.mods_install.install("tabix/tabix")
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
+        module_lint.lint(print_results=False, module="tabix/tabix")
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
     def test_modules_lint_empty(self):
         """Test linting a pipeline with no modules installed"""
         self.mods_remove.remove("fastqc", force=True)

From dad359cc43a17e587eb97213350f46dffa5c1021 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Thu, 5 Sep 2024 09:08:49 +0000
Subject: [PATCH 397/414] Add --update-all flag to remove defaults channels
 dependents

---
 nf_core/gitpod/gitpod.Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
index 849729966b..c462c6a47e 100644
--- a/nf_core/gitpod/gitpod.Dockerfile
+++ b/nf_core/gitpod/gitpod.Dockerfile
@@ -45,7 +45,7 @@ USER gitpod
 RUN conda config --add channels bioconda && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
-    conda install --quiet --yes --name base \
+    conda install --quiet --yes --update-all --name base \
     nextflow \
     nf-test \
     prettier \

From 1c6b5776187d4410ffe584cb3fd748335cc760d6 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Thu, 5 Sep 2024 09:20:23 +0000
Subject: [PATCH 398/414] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8858c89bb3..80e94dfaa3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -83,6 +83,7 @@
 - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102))
 - Update gitpod setup ([#3136](https://github.com/nf-core/tools/pull/3136))
 - fix syncing a pipeline from current directory ([#3143](https://github.com/nf-core/tools/pull/3143))
+- Patch gitpod conda setup to not use defaults channel ([#3159](https://github.com/nf-core/tools/pull/3159))
 
 ## Version updates
 

From 4f930c19b8c5086f713a8040507aca1e30674432 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Fri, 6 Sep 2024 14:55:38 +0200
Subject: [PATCH 399/414] Don't test conda `environment.yml` `name` attribute
 (which should no longer be there)

---
 CHANGELOG.md                            |  1 +
 nf_core/modules/lint/environment_yml.py | 39 -------------------------
 2 files changed, 1 insertion(+), 39 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 80e94dfaa3..ad84fb3978 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -50,6 +50,7 @@
 - Linting will now check the use of the right validation plugin include statements in the workflow scripts ([#3116])(https://github.com/nf-core/tools/pull/3116)
 - Full linting for correct use of nf-schema and nf-validation ([#3116](https://github.com/nf-core/tools/pull/3116))
 - Handle cases where the directory path contains the name of the component ([#3147](https://github.com/nf-core/tools/pull/3147))
+- Don't test conda `environment.yml` `name` attribute (which should no longer be there) ([#3161](https://github.com/nf-core/tools/pull/3161))
 
 ### Pipeline create command
 
diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py
index 341b9cd730..4488b0befa 100644
--- a/nf_core/modules/lint/environment_yml.py
+++ b/nf_core/modules/lint/environment_yml.py
@@ -90,42 +90,3 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
                 env_yml["dependencies"].sort()
                 with open(Path(module.component_dir, "environment.yml"), "w") as fh:
                     yaml.dump(env_yml, fh, Dumper=custom_yaml_dumper())
-
-            # Check that the name in the environment.yml file matches the name in the meta.yml file
-            with open(Path(module.component_dir, "meta.yml")) as fh:
-                meta_yml = yaml.safe_load(fh)
-
-            if env_yml["name"] == meta_yml["name"]:
-                module.passed.append(
-                    (
-                        "environment_yml_name",
-                        "The module's `environment.yml` name matches module name",
-                        module.environment_yml,
-                    )
-                )
-            else:
-                module.failed.append(
-                    (
-                        "environment_yml_name",
-                        f"Conflicting process name between environment.yml (`{env_yml['name']}`) and meta.yml (`{module.component_name}`)",
-                        module.environment_yml,
-                    )
-                )
-
-            # Check that the name is lowercase
-            if env_yml["name"] == env_yml["name"].lower():
-                module.passed.append(
-                    (
-                        "environment_yml_name_lowercase",
-                        "The module's `environment.yml` name is lowercase",
-                        module.environment_yml,
-                    )
-                )
-            else:
-                module.failed.append(
-                    (
-                        "environment_yml_name_lowercase",
-                        "The module's `environment.yml` name is not lowercase",
-                        module.environment_yml,
-                    )
-                )

From 0593114791f5a96304f27ad4070e4ea47c3936a2 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Fri, 6 Sep 2024 15:50:50 +0200
Subject: [PATCH 400/414] Remove name from conda enviroment.yml in module
 template

---
 nf_core/module-template/environment.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nf_core/module-template/environment.yml b/nf_core/module-template/environment.yml
index f234f85422..a8a40a8e03 100644
--- a/nf_core/module-template/environment.yml
+++ b/nf_core/module-template/environment.yml
@@ -1,6 +1,5 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "{{ component_name_underscore }}"
 channels:
   - conda-forge
   - bioconda

From ac88c16e187eba7ea607b904c35c521189970222 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Fri, 6 Sep 2024 16:20:49 +0200
Subject: [PATCH 401/414] Remove tests involving environment.yml with 'name'

---
 tests/modules/test_lint.py | 86 --------------------------------------
 1 file changed, 86 deletions(-)

diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py
index 144d163b27..51c814b88c 100644
--- a/tests/modules/test_lint.py
+++ b/tests/modules/test_lint.py
@@ -487,54 +487,6 @@ def test_modules_environment_yml_file_not_array(self):
         assert len(module_lint.warned) >= 0
         assert module_lint.failed[0].lint_test == "environment_yml_valid"
 
-    def test_modules_environment_yml_file_name_mismatch(self):
-        """Test linting a module with a different name in the environment.yml file"""
-        with open(
-            Path(
-                self.nfcore_modules,
-                "modules",
-                "nf-core",
-                "bpipe",
-                "test",
-                "environment.yml",
-            )
-        ) as fh:
-            yaml_content = yaml.safe_load(fh)
-        yaml_content["name"] = "bpipe-test"
-        with open(
-            Path(
-                self.nfcore_modules,
-                "modules",
-                "nf-core",
-                "bpipe",
-                "test",
-                "environment.yml",
-            ),
-            "w",
-        ) as fh:
-            fh.write(yaml.dump(yaml_content))
-        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
-        module_lint.lint(print_results=False, module="bpipe/test")
-        # reset changes
-        yaml_content["name"] = "bpipe_test"
-        with open(
-            Path(
-                self.nfcore_modules,
-                "modules",
-                "nf-core",
-                "bpipe",
-                "test",
-                "environment.yml",
-            ),
-            "w",
-        ) as fh:
-            fh.write(yaml.dump(yaml_content))
-
-        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-        assert len(module_lint.passed) > 0
-        assert len(module_lint.warned) >= 0
-        assert module_lint.failed[0].lint_test == "environment_yml_name"
-
     def test_modules_meta_yml_incorrect_licence_field(self):
         """Test linting a module with an incorrect Licence field in meta.yml"""
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh:
@@ -604,36 +556,11 @@ def test_modules_meta_yml_incorrect_name(self):
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh:
             meta_yml = yaml.safe_load(fh)
         meta_yml["name"] = "bpipe/test"
-        # need to make the same change to the environment.yml file
-        with open(
-            Path(
-                self.nfcore_modules,
-                "modules",
-                "nf-core",
-                "bpipe",
-                "test",
-                "environment.yml",
-            )
-        ) as fh:
-            environment_yml = yaml.safe_load(fh)
-        environment_yml["name"] = "bpipe/test"
         with open(
             Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"),
             "w",
         ) as fh:
             fh.write(yaml.dump(meta_yml))
-        with open(
-            Path(
-                self.nfcore_modules,
-                "modules",
-                "nf-core",
-                "bpipe",
-                "test",
-                "environment.yml",
-            ),
-            "w",
-        ) as fh:
-            fh.write(yaml.dump(environment_yml))
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
 
@@ -644,19 +571,6 @@ def test_modules_meta_yml_incorrect_name(self):
             "w",
         ) as fh:
             fh.write(yaml.dump(meta_yml))
-        environment_yml["name"] = "bpipe_test"
-        with open(
-            Path(
-                self.nfcore_modules,
-                "modules",
-                "nf-core",
-                "bpipe",
-                "test",
-                "environment.yml",
-            ),
-            "w",
-        ) as fh:
-            fh.write(yaml.dump(environment_yml))
 
         assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) >= 0

From 6b3e8489190084b8fdd4014fae527eb70cd4d80e Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 6 Sep 2024 17:07:05 +0200
Subject: [PATCH 402/414] Don't look for dev, look for not master

Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>
---
 nf_core/pipeline-template/.github/workflows/linting.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 00e8fd302a..826c66763f 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -58,7 +58,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
-        if: ${{ github.base_ref == 'dev' }}
+        if: ${{ github.base_ref != 'master' }}
 
       - name: Run nf-core pipelines lint --release
         env:

From 3e020cf2c5d08d0e4c53cc1e64e26cd989b8a745 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Fri, 6 Sep 2024 17:07:52 +0200
Subject: [PATCH 403/414] Move if statements to top of YAML blocks

---
 nf_core/pipeline-template/.github/workflows/linting.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 826c66763f..dbba830ec1 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -53,20 +53,20 @@ jobs:
           pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
+        if: ${{ github.base_ref != 'master' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
-        if: ${{ github.base_ref != 'master' }}
 
       - name: Run nf-core pipelines lint --release
+        if: ${{ github.base_ref == 'master' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
-        if: ${{ github.base_ref == 'master' }}
 
       - name: Save PR number
         if: ${{ always() }}

From 559903976a9dd5d81ed58df81f13bd8523de3618 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 16 Sep 2024 16:49:39 +0200
Subject: [PATCH 404/414] add tests back

---
 tests/pipelines/lint/test_nextflow_config.py | 78 ++++++++++++++++++++
 1 file changed, 78 insertions(+)

diff --git a/tests/pipelines/lint/test_nextflow_config.py b/tests/pipelines/lint/test_nextflow_config.py
index 4c3893f4c4..d2296618b0 100644
--- a/tests/pipelines/lint/test_nextflow_config.py
+++ b/tests/pipelines/lint/test_nextflow_config.py
@@ -2,8 +2,11 @@
 import re
 from pathlib import Path
 
+import yaml
+
 import nf_core.pipelines.create.create
 import nf_core.pipelines.lint
+from nf_core.utils import NFCoreYamlConfig
 
 from ..test_lint import TestLint
 
@@ -65,6 +68,81 @@ def test_nextflow_config_missing_test_profile_failed(self):
         assert len(result["failed"]) > 0
         assert len(result["warned"]) == 0
 
+    def test_default_values_fail(self):
+        """Test linting fails if the default values in nextflow.config do not match the ones defined in the nextflow_schema.json."""
+        # Change the default value of max_multiqc_email_size in nextflow.config
+        nf_conf_file = Path(self.new_pipeline) / "nextflow.config"
+        with open(nf_conf_file) as f:
+            content = f.read()
+            fail_content = re.sub(r"\bmax_multiqc_email_size\s*=\s*'25.MB'", "max_multiqc_email_size = '0'", content)
+        with open(nf_conf_file, "w") as f:
+            f.write(fail_content)
+        # Change the default value of custom_config_version in nextflow_schema.json
+        nf_schema_file = Path(self.new_pipeline) / "nextflow_schema.json"
+        with open(nf_schema_file) as f:
+            content = f.read()
+            fail_content = re.sub(r'"default": "master"', '"default": "main"', content)
+        with open(nf_schema_file, "w") as f:
+            f.write(fail_content)
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+        result = lint_obj.nextflow_config()
+        assert len(result["failed"]) == 2
+        assert (
+            "Config default value incorrect: `params.max_multiqc_email_size` is set as `25.MB` in `nextflow_schema.json` but is `0` in `nextflow.config`."
+            in result["failed"]
+        )
+        assert (
+            "Config default value incorrect: `params.custom_config_version` is set as `main` in `nextflow_schema.json` but is `master` in `nextflow.config`."
+            in result["failed"]
+        )
+
+    def test_catch_params_assignment_in_main_nf(self):
+        """Test linting fails if main.nf contains an assignment to a parameter from nextflow_schema.json."""
+        # Add parameter assignment in main.nf
+        main_nf_file = Path(self.new_pipeline) / "main.nf"
+        with open(main_nf_file, "a") as f:
+            f.write("params.custom_config_base = 'test'")
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+        result = lint_obj.nextflow_config()
+        assert len(result["failed"]) == 1
+        assert (
+            result["failed"][0]
+            == "Config default value incorrect: `params.custom_config_base` is set as `https://raw.githubusercontent.com/nf-core/configs/master` in `nextflow_schema.json` but is `null` in `nextflow.config`."
+        )
+
+    def test_allow_params_reference_in_main_nf(self):
+        """Test linting allows for references like `params.aligner == 'bwa'` in main.nf. The test will detect if the bug mentioned in GitHub-issue #2833 reemerges."""
+        # Add parameter reference in main.nf
+        main_nf_file = Path(self.new_pipeline) / "main.nf"
+        with open(main_nf_file, "a") as f:
+            f.write("params.custom_config_version == 'main'")
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+        result = lint_obj.nextflow_config()
+        assert len(result["failed"]) == 0
+
+    def test_default_values_ignored(self):
+        """Test ignoring linting of default values."""
+        # Add custom_config_version to the ignore list
+        nf_core_yml_path = Path(self.new_pipeline) / ".nf-core.yml"
+        nf_core_yml = NFCoreYamlConfig(
+            repository_type="pipeline",
+            lint={"nextflow_config": [{"config_defaults": ["params.custom_config_version"]}]},
+        )
+        with open(nf_core_yml_path, "w") as f:
+            yaml.dump(nf_core_yml.model_dump(), f)
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+        lint_obj._load_lint_config()
+        result = lint_obj.nextflow_config()
+        assert len(result["failed"]) == 0
+        assert len(result["ignored"]) == 1
+        assert "Config default value correct: params.custom_config_version" not in str(result["passed"])
+        assert "Config default ignored: params.custom_config_version" in str(result["ignored"])
+
     def test_default_values_float(self):
         """Test comparing two float values."""
         # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params`

From c568ce9e207d6c2bd9b43954912754661004147f Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 16 Sep 2024 17:06:04 +0200
Subject: [PATCH 405/414] more pytest fixing

---
 tests/pipelines/lint/test_nextflow_config.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/pipelines/lint/test_nextflow_config.py b/tests/pipelines/lint/test_nextflow_config.py
index d2296618b0..a655fb8ace 100644
--- a/tests/pipelines/lint/test_nextflow_config.py
+++ b/tests/pipelines/lint/test_nextflow_config.py
@@ -106,9 +106,9 @@ def test_catch_params_assignment_in_main_nf(self):
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
         lint_obj.load_pipeline_config()
         result = lint_obj.nextflow_config()
-        assert len(result["failed"]) == 1
+        assert len(result["failed"]) == 2
         assert (
-            result["failed"][0]
+            result["failed"][1]
             == "Config default value incorrect: `params.custom_config_base` is set as `https://raw.githubusercontent.com/nf-core/configs/master` in `nextflow_schema.json` but is `null` in `nextflow.config`."
         )
 

From c2488b5218975975cc6ad4a17f5e76ef84c7c8dd Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 18 Sep 2024 10:33:42 +0200
Subject: [PATCH 406/414] Strip hyphens from hashtags for mastodon
 compatibiluty

---
 .../.github/workflows/release-announcements.yml                 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/.github/workflows/release-announcements.yml b/nf_core/pipeline-template/.github/workflows/release-announcements.yml
index 8fee061fdd..035ed63bba 100644
--- a/nf_core/pipeline-template/.github/workflows/release-announcements.yml
+++ b/nf_core/pipeline-template/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:

From 53448ce341b6280f0a4967f100c1bd0d9f649965 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 18 Sep 2024 10:38:16 +0200
Subject: [PATCH 407/414] fixes for linting modules without an input

---
 nf_core/components/nfcore_component.py | 1 +
 nf_core/modules/lint/__init__.py       | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index b6e3520ee5..84c9a651ed 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -184,6 +184,7 @@ def get_inputs_from_main_nf(self) -> None:
         # don't match anything inside comments or after "output:"
         if "input:" not in data:
             log.debug(f"Could not find any inputs in {self.main_nf}")
+            return
         input_data = data.split("input:")[1].split("output:")[0]
         for line in input_data.split("\n"):
             channel_elements: list[dict[str, dict[str, str]]] = []
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index 43a5fe71e9..49012cff40 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -288,7 +288,7 @@ def update_meta_yml_file(self, mod):
         if "output" in meta_yml:
             correct_outputs, meta_outputs = self.obtain_correct_and_specified_outputs(mod, meta_yml)
 
-        if correct_inputs != meta_inputs:
+        if "input" in meta_yml and correct_inputs != meta_inputs:
             log.debug(
                 f"Correct inputs: '{correct_inputs}' differ from current inputs: '{meta_inputs}' in '{mod.meta_yml}'"
             )
@@ -319,7 +319,7 @@ def update_meta_yml_file(self, mod):
                                             ][feature]
                                     break
 
-        if correct_outputs != meta_outputs:
+        if "output" in meta_yml and correct_outputs != meta_outputs:
             log.debug(
                 f"Correct outputs: '{correct_outputs}' differ from current outputs: '{meta_outputs}' in '{mod.meta_yml}'"
             )

From bebc6bc1cdb065654a0d33e25c42e7f6e9a2ccca Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 18 Sep 2024 13:45:44 +0200
Subject: [PATCH 408/414] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1bcc937852..f2d494ab13 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -38,6 +38,7 @@
 - add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
 - run nf-core lint `--release` on PRs to master ([#3148](https://github.com/nf-core/tools/pull/3148))
 - Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))
+- Fixed release announcement hashtags for Mastodon ([#3099](https://github.com/nf-core/tools/pull/3176))
 
 ### Linting
 

From 494a03ff12a45d235d2a8c62ca86d52e5de064dc Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 19 Sep 2024 12:15:19 +0200
Subject: [PATCH 409/414] fix broken lint test by adding module dependency
 version

---
 tests/modules/test_lint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py
index 51c814b88c..07e12924c6 100644
--- a/tests/modules/test_lint.py
+++ b/tests/modules/test_lint.py
@@ -432,7 +432,7 @@ def test_modules_environment_yml_file_sorted_incorrectly(self):
         ) as fh:
             yaml_content = yaml.safe_load(fh)
         # Add a new dependency to the environment.yml file and reverse the order
-        yaml_content["dependencies"].append("z")
+        yaml_content["dependencies"].append("z=0.0.0")
         yaml_content["dependencies"].reverse()
         yaml_content = yaml.dump(yaml_content)
         with open(

From 17dc0bc34cfd22782221532508a883d65a2c6590 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 19 Sep 2024 12:39:02 +0200
Subject: [PATCH 410/414] change order of profiles used for CI

---
 .github/workflows/create-test-wf.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 56c6c822a9..e3918bffdf 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -75,7 +75,7 @@ jobs:
           pwd
           # echo content of current directory
           ls -la
-          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
+          nextflow run nf-core-testpipeline -profile self_hosted_runner,test --outdir ./results
 
       - name: Upload log file artifact
         if: ${{ always() }}

From c494c268e0873f82e340a47aabcf24e36d59a29a Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 19 Sep 2024 12:55:36 +0200
Subject: [PATCH 411/414] update nextflow version on CI

---
 .github/workflows/create-lint-wf.yml               | 2 +-
 .github/workflows/create-test-wf.yml               | 2 +-
 nf_core/pipeline-template/.github/workflows/ci.yml | 2 +-
 nf_core/pipeline-template/README.md                | 2 +-
 nf_core/pipelines/lint/readme.py                   | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index f07b31e9de..1a3e283d00 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -38,7 +38,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.10.0"
+          - "24.04.2"
           - "latest-everything"
     steps:
       - name: go to subdirectory and change nextflow workdir
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index e3918bffdf..09c5b01c37 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -39,7 +39,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.10.0"
+          - "24.04.2"
           - "latest-everything"
     steps:
       - name: go to working directory
diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index 63fa99cec8..06371cc974 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.10.0"
+          - "24.04.2"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index beb45ed511..4331454288 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -20,7 +20,7 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.10.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/nf_core/pipelines/lint/readme.py b/nf_core/pipelines/lint/readme.py
index 1c09104258..bdfad5200f 100644
--- a/nf_core/pipelines/lint/readme.py
+++ b/nf_core/pipelines/lint/readme.py
@@ -36,7 +36,7 @@ def readme(self):
 
     if "nextflow_badge" not in ignore_configs:
         # Check that there is a readme badge showing the minimum required version of Nextflow
-        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.10.0-23aa62.svg)](https://www.nextflow.io/)
+        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
         # and that it has the correct version
         nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-23aa62\.svg\)\]\(https://www\.nextflow\.io/\)"
         match = re.search(nf_badge_re, content)

From 2c0d2f6a325892a407500df8022c534167b4a7e0 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 19 Sep 2024 13:31:14 +0200
Subject: [PATCH 412/414] configs are included after profiles

---
 nf_core/pipeline-template/nextflow.config | 31 ++++++++++++-----------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 8c1d33244f..d129d1a492 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -76,21 +76,6 @@ process {
     maxErrors     = '-1'
 }
 {% endif %}
-{% if nf_core_configs -%}
-// Load nf-core custom profiles from different Institutions
-try {
-    includeConfig "${params.custom_config_base}/nfcore_custom.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
-}
-
-// Load {{ name }} custom profiles from different institutions.
-try {
-    includeConfig "${params.custom_config_base}/pipeline/{{ short_name }}.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config/{{ short_name }} profiles: ${params.custom_config_base}/pipeline/{{ short_name }}.config")
-}
-{% endif -%}
 
 profiles {
     debug {
@@ -199,6 +184,22 @@ profiles {
     {%- endif %}
 }
 
+{% if nf_core_configs -%}
+// Load nf-core custom profiles from different Institutions
+try {
+    includeConfig "${params.custom_config_base}/nfcore_custom.config"
+} catch (Exception e) {
+    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
+}
+
+// Load {{ name }} custom profiles from different institutions.
+try {
+    includeConfig "${params.custom_config_base}/pipeline/{{ short_name }}.config"
+} catch (Exception e) {
+    System.err.println("WARNING: Could not load nf-core/config/{{ short_name }} profiles: ${params.custom_config_base}/pipeline/{{ short_name }}.config")
+}
+{% endif -%}
+
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
 // Set to your registry if you have a mirror of containers

From d2959edebb53efb1479785d3258d2577546cf67d Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 19 Sep 2024 13:44:58 +0200
Subject: [PATCH 413/414] reduce memory in test profile

---
 nf_core/pipeline-template/conf/test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/conf/test.config b/nf_core/pipeline-template/conf/test.config
index 0f1d974101..bea6f670d0 100644
--- a/nf_core/pipeline-template/conf/test.config
+++ b/nf_core/pipeline-template/conf/test.config
@@ -13,7 +13,7 @@
 process {
     resourceLimits = [
         cpus: 4,
-        memory: '16.GB',
+        memory: '15.GB',
         time: '1.h'
     ]
 }

From 535477086cd8f90fc06ef6d98cfff3f0e0dbf4bc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Thu, 19 Sep 2024 14:00:02 +0200
Subject: [PATCH 414/414] Apply suggestions from code review

Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
---
 nf_core/modules/lint/meta_yml.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 80b40b0221..4f7ffd0739 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -130,7 +130,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
                 module.failed.append(
                     (
                         "correct_meta_inputs",
-                        f"Incorrect inputs specified in module `meta.yml`. Inputs should contain: {correct_inputs}\nRun `nf-core modules lint --fix` to update the `meta.yml` file.",
+                        f"Module `meta.yml` does not match `main.nf`. Inputs should contain: {correct_inputs}\nRun `nf-core modules lint --fix` to update the `meta.yml` file.",
                         module.meta_yml,
                     )
                 )
@@ -168,7 +168,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
                 module.failed.append(
                     (
                         "correct_meta_outputs",
-                        f"Incorrect outputs specified in module `meta.yml`. Outputs should contain: {correct_outputs}\nRun `nf-core modules lint --fix` to update the `meta.yml` file.",
+                        f"Module `meta.yml` does not match `main.nf`. Outputs should contain: {correct_outputs}\nRun `nf-core modules lint --fix` to update the `meta.yml` file.",
                         module.meta_yml,
                     )
                 )