Merge pull request #449 from JoseEspinosa/merging-template-3.2.0

JoseEspinosa · web-flow · commit 16a7d15e299b · 2025-02-26T11:59:23.000+01:00
Merging-template-3.2.0
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -46,6 +46,8 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
@@ -34,6 +34,17 @@ jobs:
       REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
       REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
       REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
+    steps:
+      - name: Get the repository name and current branch
+        id: get_repo_properties
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
+
+  download:
+    runs-on: ubuntu-latest
+    needs: configure
     steps:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -56,21 +67,10 @@ jobs:
           python -m pip install --upgrade pip
           pip install git+https://github.com/nf-core/tools.git@dev
 
-      - name: Get the repository name and current branch set as environment variable
-        id: get_repo_properties
-        run: |
-          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
-          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
-
       - name: Make a cache directory for the container images
         run: |
           mkdir -p ./singularity_container_images
 
-  download:
-    runs-on: ubuntu-latest
-    needs: configure
-    steps:
       - name: Download the pipeline
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
@@ -87,6 +87,9 @@ jobs:
       - name: Inspect download
         run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
 
+      - name: Inspect container images
+        run: tree ./singularity_container_images | tee ./container_initial
+
       - name: Count the downloaded number of container images
         id: count_initial
         run: |
@@ -123,7 +126,8 @@ jobs:
             final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
             difference=$((final_count - initial_count))
             echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
-            tree ./singularity_container_images
+            tree ./singularity_container_images > ./container_afterwards
+            diff ./container_initial ./container_afterwards
             exit 1
           else
             echo "The pipeline can be downloaded successfully!"
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@80620a5d27ce0ae443b965134db88467fc607b43 # v7
+        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
@@ -27,39 +27,6 @@ jobs:
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
-  send-tweet:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.10"
-      - name: Install dependencies
-        run: pip install tweepy==4.14.0
-      - name: Send tweet
-        shell: python
-        run: |
-          import os
-          import tweepy
-
-          client = tweepy.Client(
-              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
-              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
-              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
-              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
-          )
-          tweet = os.getenv("TWEET")
-          client.create_tweet(text=tweet)
-        env:
-          TWEET: |
-            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            Please see the changelog: ${{ github.event.release.html_url }}
-          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
-          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
-          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
-          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
-
   bsky-post:
     runs-on: ubuntu-latest
     steps:
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -3,7 +3,7 @@ lint:
     - config_defaults:
         - params.bamtools_filter_se_config
         - params.bamtools_filter_pe_config
-nf_core_version: 3.1.1
+nf_core_version: 3.2.0
 repository_type: pipeline
 template:
   author: Espinosa-Carrasco J, Patel H, Wang C, Ewels P
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
           - prettier@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.0.3"
+    rev: "3.1.2"
     hooks:
       - id: editorconfig-checker
         alias: ec
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #434](https://github.com/nf-core/chipseq/pull/434)] - Prevent pipeline fails from erroneous param validation when igenomes is used.
 - [[#432](https://github.com/nf-core/chipseq/issues/432)] - Fix `GFFREAD` call to have the two expected input channels.
 - [[PR #444](https://github.com/nf-core/chipseq/pull/444)] - Add empty map to ch_gff so that when provided by the user `GFFREAD` works.
+- Updated pipeline template to [nf-core/tools 3.2.0](https://github.com/nf-core/tools/releases/tag/3.2.0)
 
 ### Parameters
 
diff --git a/README.md b/README.md
@@ -3,7 +3,9 @@
     <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-chipseq_logo_dark.png">
     <img alt="nf-core/chipseq" src="docs/images/nf-core-chipseq_logo_light.png">
   </picture>
-</h1>[![GitHub Actions CI Status](https://github.com/nf-core/chipseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/chipseq/actions/workflows/ci.yml)
+</h1>
+
+[![GitHub Actions CI Status](https://github.com/nf-core/chipseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/chipseq/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/chipseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/chipseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/chipseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3240506-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3240506)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
@@ -70,7 +72,7 @@ You can find numerous talks on the [nf-core events page](https://nf-co.re/events
 ## 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. 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.
 
 To run on your data, prepare a tab-separated samplesheet with your input data. Please follow the [documentation on samplesheets](https://nf-co.re/chipseq/usage#samplesheet-input) for more details. An example samplesheet for running the pipeline looks as follows:
 
diff --git a/modules.json b/modules.json
@@ -63,7 +63,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
                         "installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
                     },
                     "gffread": {
@@ -93,7 +93,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
+                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
                         "installed_by": ["modules"]
                     },
                     "phantompeakqualtools": {
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
@@ -1,5 +1,5 @@
 process FASTQC {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
@@ -19,30 +19,30 @@ process FASTQC {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args          = task.ext.args ?: ''
+    def prefix        = task.ext.prefix ?: "${meta.id}"
     // Make list of old name and new name pairs to use for renaming in the bash while loop
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
-    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def rename_to     = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ')
 
     // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
     // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
     // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
-    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
+    def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
     """
-    printf "%s %s\\n" $rename_to | while read old_name new_name; do
+    printf "%s %s\\n" ${rename_to} | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
     done
 
     fastqc \\
-        $args \\
-        --threads $task.cpus \\
-        --memory $fastqc_memory \\
-        $renamed_files
+        ${args} \\
+        --threads ${task.cpus} \\
+        --memory ${fastqc_memory} \\
+        ${renamed_files}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.25.1
+  - bioconda::multiqc=1.27
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.27--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,40 +2,40 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-02T17:51:46.317523"
+        "timestamp": "2025-01-27T09:29:57.631982377"
     },
     "multiqc_stub": {
         "content": [
             [
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-02T17:52:20.680978"
+        "timestamp": "2025-01-27T09:30:34.743726958"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-02T17:52:09.185842"
+        "timestamp": "2025-01-27T09:30:21.44383553"
     }
 }
diff --git a/nextflow.config b/nextflow.config
@@ -219,7 +219,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa
 
 // Load nf-core/chipseq custom profiles from different institutions.
 // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/chipseq.config" : "/dev/null"
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/chipseq.config" : "/dev/null"
 
 // 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
@@ -245,14 +245,14 @@ env {
 }
 
 // Set bash options
-process.shell = """\
-bash
-
-set -e # Exit if a tool returns a non-zero status/exit code
-set -u # Treat unset variables and parameters as an error
-set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
-set -C # No clobber - prevent output redirection from overwriting files.
-"""
+process.shell = [
+    "bash",
+    "-C",         // No clobber - prevent output redirection from overwriting files.
+    "-e",         // Exit if a tool returns a non-zero status/exit code
+    "-u",         // Treat unset variables and parameters as an error
+    "-o",         // Returns the status of the last command to exit..
+    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
+]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
@@ -323,7 +323,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
