From 7b37910083317103d6683440295a53e07121422f Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 30 Apr 2025 12:26:39 +0000 Subject: [PATCH] Template update for nf-core/tools version 3.2.1 --- .github/workflows/awsfulltest.yml | 41 ++++++++----------------------- .github/workflows/ci.yml | 1 + .nf-core.yml | 5 +++- nextflow.config | 2 +- ro-crate-metadata.json | 12 ++++----- 5 files changed, 22 insertions(+), 39 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 462793b..d1250a5 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/deepmodeloptim' && 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/deepmodeloptim' && 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/deepmodeloptim/work-${{ github.sha }} + revision: ${{ steps.revision.outputs.revision }} + workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/deepmodeloptim/work-${{ steps.revision.outputs.revision }} parameters: | { "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/deepmodeloptim/results-${{ github.sha }}" + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/deepmodeloptim/results-${{ steps.revision.outputs.revision }}" } profiles: test_full diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9fa1b28..a9bdb6d 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 15a9c89..6bf90ea 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -6,6 +6,7 @@ lint: - conf/igenomes.config - conf/igenomes_ignored.config - assets/multiqc_config.yml + - conf/test_full.config files_unchanged: - .github/CONTRIBUTING.md - assets/sendmail_template.txt @@ -15,7 +16,9 @@ lint: - docs/images/nf-core-deepmodeloptim_logo_light.png - docs/images/nf-core-deepmodeloptim_logo_dark.png multiqc_config: false -nf_core_version: 3.2.0 + nextflow_config: + - params.input +nf_core_version: 3.2.1 repository_type: pipeline template: author: Mathys Grapotte diff --git a/nextflow.config b/nextflow.config index e40267b..0630a79 100644 --- a/nextflow.config +++ b/nextflow.config @@ -236,7 +236,7 @@ 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 1832fec..e18def2 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,7 +22,7 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-01-27T14:45:57+00:00", + "datePublished": "2025-04-30T12:26:10+00:00", "description": "

\n \n \n \"nf-core/deepmodeloptim\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/deepmodeloptim/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/deepmodeloptim/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/deepmodeloptim/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/deepmodeloptim/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/deepmodeloptim/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/deepmodeloptim)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23deepmodeloptim-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/deepmodeloptim)[![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/deepmodeloptim** is a bioinformatics pipeline that ...\n\n\n\n\n\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/deepmodeloptim \\\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/deepmodeloptim/usage) and the [parameter documentation](https://nf-co.re/deepmodeloptim/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/deepmodeloptim/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/deepmodeloptim/output).\n\n## Credits\n\nnf-core/deepmodeloptim was originally written by Mathys Grapotte.\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 `#deepmodeloptim` channel](https://nfcore.slack.com/channels/deepmodeloptim) (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": [ { @@ -93,7 +93,7 @@ }, "mentions": [ { - "@id": "#9409a0dc-6aae-4911-8324-cd8f483edf4a" + "@id": "#87a4bfa3-7a32-4d11-b67a-b9c2b8e3bbea" } ], "name": "nf-core/deepmodeloptim" @@ -117,7 +117,7 @@ "@id": "main.nf", "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "dateCreated": "", - "dateModified": "2025-01-27T14:45:57Z", + "dateModified": "2025-04-30T12:26:10Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -154,11 +154,11 @@ "version": "!>=24.04.2" }, { - "@id": "#9409a0dc-6aae-4911-8324-cd8f483edf4a", + "@id": "#87a4bfa3-7a32-4d11-b67a-b9c2b8e3bbea", "@type": "TestSuite", "instance": [ { - "@id": "#1a6db2be-77de-4bd1-a2e0-b38728d1b764" + "@id": "#5c05c4c3-ce37-4b82-ac3a-579cce863726" } ], "mainEntity": { @@ -167,7 +167,7 @@ "name": "Test suite for nf-core/deepmodeloptim" }, { - "@id": "#1a6db2be-77de-4bd1-a2e0-b38728d1b764", + "@id": "#5c05c4c3-ce37-4b82-ac3a-579cce863726", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/deepmodeloptim", "resource": "repos/nf-core/deepmodeloptim/actions/workflows/ci.yml",