From 4bc328316772a1cf70de65cb7b7f35b0c82ddaf7 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 30 Apr 2025 12:26:04 +0000 Subject: [PATCH 1/8] Template update for nf-core/tools version 3.2.1 --- .github/workflows/awsfulltest.yml | 41 ++++++++----------------------- .github/workflows/ci.yml | 1 + .nf-core.yml | 2 +- nextflow.config | 2 +- ro-crate-metadata.json | 12 ++++----- 5 files changed, 19 insertions(+), 39 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 5bcb7bfa2..fb0e2f5f7 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -4,44 +4,23 @@ 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 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 @@ -52,12 +31,12 @@ jobs: 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 }}" + "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 index 0c0dcf543..0cda01aa8 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -83,5 +83,6 @@ jobs: uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - 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 ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results diff --git a/.nf-core.yml b/.nf-core.yml index de03068fa..29d8676e8 100644 --- 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 index 82febd2cb..7855e57ca 100644 --- a/nextflow.config +++ b/nextflow.config @@ -273,7 +273,7 @@ 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 index dd1e8136b..18efc9297 100644 --- 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": "

\n \n \n \"nf-core/chipseq\"\n \n

\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\n\n\n1. 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\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/chipseq \\\n -profile \\\n --input samplesheet.csv \\\n --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\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\n\n\n\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", From 390b9d25ad87ee1d65c427640d8718d7bbae1222 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 9 May 2025 12:41:26 +0200 Subject: [PATCH 2/8] Update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a94b28f26..0fe5fccbc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,8 +11,8 @@ 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). - [[#451](https://github.com/nf-core/chipseq/issues/451)] - Pass `map.single_read` to `SUBREAD_FEATURECOUNTS` as to correctly set parameter `-p`. +- [[PR #462](https://github.com/nf-core/chipseq/pull/462)] - Updated pipeline template to [nf-core/tools 3.2.1](https://github.com/nf-core/tools/releases/tag/3.2.1) ### Parameters From cb1e5ce65b24915452e360dffe8297f5b4f11824 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 9 May 2025 12:41:47 +0200 Subject: [PATCH 3/8] Fix ci --- .github/workflows/ci.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1f6d33036..ac4fe8ce1 100755 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,8 +33,6 @@ jobs: - "conda" - "docker" - "singularity" - test_profile: - - "test" test_name: - "test" - "skip_trimming" @@ -99,5 +97,5 @@ jobs: - 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 ${{ matrix.test_profile }},${{ matrix.profile }} --outdir ./results ${{ matrix.parameters }} + nextflow run ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} --outdir ./results ${{ matrix.parameters }} if: "${{ github.base_ref == 'master' }}" From c2f4f557cb3d7e6edc0e1f9a455c0ceaf2b14023 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 9 May 2025 12:43:24 +0200 Subject: [PATCH 4/8] Fix ci --- .github/workflows/ci.yml | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ac4fe8ce1..9bdd84f27 100755 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,13 +33,6 @@ jobs: - "conda" - "docker" - "singularity" - test_name: - - "test" - - "skip_trimming" - - "skip_consensus_peaks" - - "bowtie2" - - "chromap" - - "star" parameters: - "" - "--skip_trimming" @@ -94,7 +87,7 @@ jobs: - name: Clean up Disk space uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" + - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }}" continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} run: | nextflow run ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} --outdir ./results ${{ matrix.parameters }} From 517a377f94394d5ec4e8e3a7d55ef1cc8806f644 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 9 May 2025 13:02:12 +0200 Subject: [PATCH 5/8] Update ci --- .github/workflows/ci.yml | 63 ++++++++++++++++++++++++++++++++++------ 1 file changed, 54 insertions(+), 9 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9bdd84f27..56492a863 100755 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,13 +33,8 @@ jobs: - "conda" - "docker" - "singularity" - parameters: - - "" - - "--skip_trimming" - - "--skip_consensus_peaks" - - "--aligner bowtie2" - - "--aligner chromap" - - "--aligner star" + test_name: + - "test" isMaster: - ${{ github.base_ref == 'master' }} # Exclude conda and singularity on dev @@ -87,8 +82,58 @@ jobs: - name: Clean up Disk space uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }}" + - 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 ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} --outdir ./results ${{ matrix.parameters }} + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + + - name: Run pipeline with test data (singularity) + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results + if: "${{ github.base_ref == 'master' }}" + + - 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) + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results ${{ matrix.parameters }} if: "${{ github.base_ref == 'master' }}" From 4186fc4f9043011fc0b77dabf990fe072f6e661a Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 9 May 2025 17:03:08 +0200 Subject: [PATCH 6/8] apply suggestion from review --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index f005f52f8..66b3da706 100644 --- a/nextflow.config +++ b/nextflow.config @@ -323,7 +323,7 @@ manifest { // Nextflow plugins plugins { - id 'nf-schema@2.2.0' // 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 { From a4cb332e2229dabbb43400a83760c6ebcfc1087b Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 9 May 2025 17:07:25 +0200 Subject: [PATCH 7/8] Apply review suggestion --- .github/workflows/ci.yml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 56492a863..2a1dc7391 100755 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -85,12 +85,7 @@ jobs: - 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,docker --outdir ./results - - - name: Run pipeline with test data (singularity) - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results - if: "${{ github.base_ref == 'master' }}" + nextflow run ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} --outdir ./results - name: Run pipeline with test data (conda) run: | From 1a9e92390abbd82a6ca1f8bea0f6c542f6dd0688 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 9 May 2025 17:13:20 +0200 Subject: [PATCH 8/8] Fix tyop --- .github/workflows/ci.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2a1dc7391..0e3a5cc09 100755 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -87,11 +87,6 @@ jobs: run: | nextflow run ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} --outdir ./results - - 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') }}"