Merge branch 'TEMPLATE' of https://github.com/nf-core/chipseq into merging-template-3.2.1

JoseEspinosa · JoseEspinosa · commit 5e48b5e8773f · 2025-05-09T11:51:53.000+02:00
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -4,61 +4,39 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  pull_request:
-    branches:
-      - main
-      - master
   workflow_dispatch:
   pull_request_review:
     types: [submitted]
+  release:
+    types: [published]
 
 jobs:
   run-platform:
     name: Run AWS full tests
-    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
-    if: github.repository == 'nf-core/chipseq' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
+    if: github.repository == 'nf-core/chipseq' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     strategy:
       matrix:
         aligner: ["bwa", "bowtie2", "chromap", "star"]
     steps:
-      - name: Get PR reviews
-        uses: octokit/request-action@v2.x
-        if: github.event_name != 'workflow_dispatch'
-        id: check_approvals
-        continue-on-error: true
-        with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Check for approvals
-        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
-        run: |
-          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
-          exit 1
-
-      - name: Check for enough approvals (>=2)
-        id: test_variables
-        if: github.event_name != 'workflow_dispatch'
+      - name: Set revision variable
+        id: revision
         run: |
-          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
-          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
-          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+          echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/chipseq/work-${{ github.sha }}
+          revision: ${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/chipseq/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/chipseq/results-${{ github.sha }}",
-              "aligner": "${{ matrix.aligner }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/chipseq/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -33,8 +33,22 @@ jobs:
           - "conda"
           - "docker"
           - "singularity"
+        test_profile:
+          - "test"
         test_name:
           - "test"
+          - "skip_trimming"
+          - "skip_consensus_peaks"
+          - "bowtie2"
+          - "chromap"
+          - "star"
+        parameters:
+          - ""
+          - "--skip_trimming"
+          - "--skip_consensus_peaks"
+          - "--aligner bowtie2"
+          - "--aligner chromap"
+          - "--aligner star"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev
@@ -58,7 +72,8 @@ jobs:
         if: matrix.profile == 'singularity'
         uses: eWaterCycle/setup-apptainer@main
 
-      - name: Run pipeline with test data (docker)
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
         run: |
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
@@ -72,56 +87,17 @@ jobs:
           conda-solver: libmamba
           channels: conda-forge,bioconda
 
-      - name: Run pipeline with test data (singularity)
+      - name: Set up Conda
+        if: matrix.profile == 'conda'
         run: |
           echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
           echo $(realpath python) >> $GITHUB_PATH
 
       - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data (conda)
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results
-        if: "${{ github.base_ref == 'master' }}"
-
-  parameters:
-    name: Test workflow parameters
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/chipseq') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "24.04.2"
-          - "latest-everything"
-        parameters:
-          - "--skip_trimming"
-          - "--skip_consensus_peaks"
-          - "--aligner bowtie2"
-          - "--aligner chromap"
-          - "--aligner star"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
-      - name: Run pipeline with various parameters (docker)
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
-
-      - name: Run pipeline with various parameters (singularity)
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results ${{ matrix.parameters }}
-        if: "${{ github.base_ref == 'master' }}"
-
-      - name: Run pipeline with various parameters (conda)
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_profile }},${{ matrix.profile }} --outdir ./results ${{ matrix.parameters }}
         if: "${{ github.base_ref == 'master' }}"
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: 3.2.0
+nf_core_version: 3.2.1
 repository_type: pipeline
 template:
   author: Espinosa-Carrasco J, Patel H, Wang C, Ewels P
diff --git a/nextflow.config b/nextflow.config
@@ -323,7 +323,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.2.0' // 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
@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-01-27T14:44:38+00:00",
+            "datePublished": "2025-04-30T12:25:55+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-chipseq_logo_dark.png\">\n    <img alt=\"nf-core/chipseq\" src=\"docs/images/nf-core-chipseq_logo_light.png\">\n  </picture>\n</h1>\n\n[![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)\n[![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.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![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/chipseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23chipseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/chipseq)[![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)\n\n## Introduction\n\n**nf-core/chipseq** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- 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/))\n\n## Usage\n\n> [!NOTE]\n> 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.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/chipseq \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/chipseq/usage) and the [parameter documentation](https://nf-co.re/chipseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/chipseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/chipseq/output).\n\n## Credits\n\nnf-core/chipseq was originally written by Espinosa-Carrasco J, Patel H, Wang C, Ewels P.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#chipseq` channel](https://nfcore.slack.com/channels/chipseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- 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. -->\n<!-- If you use nf-core/chipseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#a198f2b1-ce70-44ed-a64f-2c5e386fee8f"
+                    "@id": "#be26b39c-8ae7-447d-a6dd-8b423bd521ec"
                 }
             ],
             "name": "nf-core/chipseq"
@@ -123,7 +123,7 @@
             "@id": "main.nf",
             "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
             "dateCreated": "",
-            "dateModified": "2025-01-27T14:44:38Z",
+            "dateModified": "2025-04-30T12:25:55Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -158,11 +158,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#a198f2b1-ce70-44ed-a64f-2c5e386fee8f",
+            "@id": "#be26b39c-8ae7-447d-a6dd-8b423bd521ec",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#23cae47c-f2c2-409a-8db5-e4b53e248092"
+                    "@id": "#ab6a8ea3-81bb-44bf-a564-11b2997ed6d3"
                 }
             ],
             "mainEntity": {
@@ -171,7 +171,7 @@
             "name": "Test suite for nf-core/chipseq"
         },
         {
-            "@id": "#23cae47c-f2c2-409a-8db5-e4b53e248092",
+            "@id": "#ab6a8ea3-81bb-44bf-a564-11b2997ed6d3",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/chipseq",
             "resource": "repos/nf-core/chipseq/actions/workflows/ci.yml",

Original file line number	Diff line number	Diff line change
`@@ -323,7 +323,7 @@ manifest {`
`323`	`323`
`324`	`324`	`// Nextflow plugins`
`325`	`325`	`plugins {`
`326`		`- id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet`
	`326`	`+ id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet`
`327`	`327`	`}`
`328`	`328`
`329`	`329`	`validation {`