Merge pull request #133 from Daniel-VM/update_nf-core-tools-2.14.1

Template update nf-core tools v2.14.1
nf-core · May 17, 2024 · 548e298 · 548e298
2 parents 9e0399c + ba84cd4
commit 548e298
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/baca
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/bacass _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -8,12 +8,12 @@ on:
     types: [published]
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS full tests
     if: github.repository == 'nf-core/bacass'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch workflow via tower
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
@@ -32,7 +32,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -5,13 +5,13 @@ name: nf-core AWS test
 on:
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS tests
     if: github.repository == 'nf-core/bacass'
     runs-on: ubuntu-latest
     steps:
-      # Launch workflow using Tower CLI tool action
-      - name: Launch workflow via tower
+      # Launch workflow using Seqera Platform CLI tool action
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -27,7 +27,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -28,10 +28,10 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
@@ -32,9 +32,12 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:

diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -14,13 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |

diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
@@ -31,7 +31,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.10"
       - name: Install dependencies

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -8,3 +8,4 @@ lint:
   nextflow_config:
     - config_defaults:
         - params.dfast_config
+nf_core_version: "2.14.1"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,6 +3,9 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - [email protected]
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#133](https://github.com/nf-core/bacass/pull/133) Update nf-core/bacass to the new nf-core 2.14.1 `TEMPLATE`.
+
 ### `Fixed`
 
 - [#125](https://github.com/nf-core/bacass/pull/125) - Fixed conflicting settings in save_trimmed_fail parameter.

diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@
 [![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/)
-[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/bacass)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/bacass)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23bacass-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/bacass)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 

diff --git a/conf/base.config b/conf/base.config
@@ -57,7 +57,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 3
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }
diff --git a/conf/test.config b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_short.tsv'
+    input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv'
 
     // some extra args to speed tests up
     unicycler_args  = "--no_correct --no_pilon"

diff --git a/conf/test_dfast.config b/conf/test_dfast.config
@@ -20,7 +20,7 @@ params {
     max_time   = 6.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_short.tsv'
+    input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv'
 
     // some extra args to speed tests up
     unicycler_args  = "--no_correct --no_pilon"

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -15,6 +15,6 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input       = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_full.tsv'
+    input       = params.pipelines_testdata_base_path + 'bacass/bacass_full.tsv'
     kraken2db   = 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz'
 }
diff --git a/conf/test_hybrid.config b/conf/test_hybrid.config
@@ -20,7 +20,7 @@ params {
     max_time   = 6.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_hybrid.tsv'
+    input = params.pipelines_testdata_base_path + 'bacass/bacass_hybrid.tsv'
 
     // some extra args to speed tests up
     assembly_type   = 'hybrid'

diff --git a/conf/test_hybrid_dragonflye.config b/conf/test_hybrid_dragonflye.config
@@ -20,7 +20,7 @@ params {
     max_time   = 6.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_hybrid_dragonflye.tsv'
+    input = params.pipelines_testdata_base_path + 'bacass/bacass_hybrid_dragonflye.tsv'
 
     // some extra args to speed tests up
     assembly_type   = 'hybrid'

diff --git a/conf/test_long.config b/conf/test_long.config
@@ -20,7 +20,7 @@ params {
     max_time   = 6.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_long_miniasm.tsv'
+    input = params.pipelines_testdata_base_path + 'bacass/bacass_long_miniasm.tsv'
 
     // some extra args to speed tests up
     prokka_args     = " --fast"

diff --git a/conf/test_long_dragonflye.config b/conf/test_long_dragonflye.config
@@ -15,7 +15,7 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_long_miniasm.tsv'
+    input = params.pipelines_testdata_base_path + 'bacass/bacass_long_miniasm.tsv'
 
     // some extra args to speed tests up
     prokka_args     = " --fast"

diff --git a/conf/test_long_miniasm.config b/conf/test_long_miniasm.config
@@ -20,7 +20,7 @@ params {
     max_time   = 6.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_long_miniasm.tsv'
+    input = params.pipelines_testdata_base_path + 'bacass/bacass_long_miniasm.tsv'
 
     // some extra args to speed tests up
     prokka_args     = " --fast"

diff --git a/docs/usage.md b/docs/usage.md
@@ -141,6 +141,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
+- `wave`
+  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 

diff --git a/modules.json b/modules.json
@@ -33,7 +33,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
+                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["fastq_trim_fastp_fastqc"]
                     },
                     "gunzip": {
@@ -118,7 +118,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {

diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf