diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 1ffcdcaf..e44a93d1 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. -Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mag/tree/main/.github/CONTRIBUTING.md) +Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mag/tree/main/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/mag _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e388119e..e2213e03 100644 --- 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 index 13b51e2c..ab06316e 100644 --- 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/.nf-core.yml b/.nf-core.yml index ebf94c11..5ae8e4aa 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,11 +1,11 @@ lint: files_unchanged: - - lib/NfcoreTemplate.groovy + - lib/NfcoreTemplate.groovy nextflow_config: - - config_defaults: - - params.phix_reference - - params.lambda_reference -nf_core_version: 3.1.1 + - config_defaults: + - params.phix_reference + - params.lambda_reference +nf_core_version: 3.1.2 repository_type: pipeline template: author: "Hadrien Gourl\xE9, Daniel Straub, Sabrina Krakau, James A. Fellows Yates,\ @@ -16,4 +16,4 @@ template: name: mag org: nf-core outdir: . - version: 3.3.0 + version: 3.3.1dev diff --git a/CHANGELOG.md b/CHANGELOG.md index 42737ad9..71be1fcf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v3.3.0 - [date] +## v3.3.1dev - [date] Initial release of nf-core/mag, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index 06da5147..0b6c25b1 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,9 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. + +- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. diff --git a/README.md b/README.md index 8f0506ce..9a23fd99 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,9 @@ nf-core/mag -[![GitHub Actions CI Status](https://github.com/nf-core/mag/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/ci.yml) + + +[![GitHub Actions CI Status](https://github.com/nf-core/mag/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/mag/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mag/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/mag/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) @@ -32,7 +34,7 @@ ## 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. - + + + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 79420f89..a4c656e2 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/mag + This report has been generated by the nf-core/mag analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-mag-methods-description": order: -1000 diff --git a/assets/schema_input.json b/assets/schema_input.json index 9beebbc6..9485ea88 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/mag/main/assets/schema_input.json", + "$id": "https://raw.githubusercontent.com/nf-core/mag/master/assets/schema_input.json", "title": "nf-core/mag pipeline - params.input schema", "description": "Schema for the file provided with params.input", "type": "array", diff --git a/nextflow.config b/nextflow.config index a61c5b4d..ee8d7289 100644 --- a/nextflow.config +++ b/nextflow.config @@ -273,15 +273,15 @@ manifest { homePage = 'https://github.com/nf-core/mag' description = """Assembly, binning and annotation of metagenomes""" mainScript = 'main.nf' - defaultBranch = 'main' + defaultBranch = 'master' nextflowVersion = '!>=24.04.2' - version = '3.3.0' + version = '3.3.1dev' doi = '' } // Nextflow plugins plugins { - id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { @@ -307,7 +307,7 @@ validation { https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/nf-core/mag/blob/main/CITATIONS.md + https://github.com/nf-core/mag/blob/master/CITATIONS.md """ } summary { diff --git a/nextflow_schema.json b/nextflow_schema.json index 9fd246c9..5f022229 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/mag/main/nextflow_schema.json", + "$id": "https://raw.githubusercontent.com/nf-core/mag/master/nextflow_schema.json", "title": "nf-core/mag pipeline parameters", "description": "Assembly, binning and annotation of metagenomes", "type": "object", diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index e28de57a..241911b9 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,9 +21,9 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "Stable", - "datePublished": "2024-12-20T15:59:00+00:00", - "description": "

\n \n \n \"nf-core/mag\"\n \n

[![GitHub Actions CI Status](https://github.com/nf-core/mag/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/mag/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mag/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/mag/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/mag)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23mag-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/mag)[![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/mag** 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/mag \\\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/mag/usage) and the [parameter documentation](https://nf-co.re/mag/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/mag/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/mag/output).\n\n## Credits\n\nnf-core/mag was originally written by Hadrien Gourl\u00e9, Daniel Straub, Sabrina Krakau, James A. Fellows Yates, Maxime Borry.\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 `#mag` channel](https://nfcore.slack.com/channels/mag) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\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", + "creativeWorkStatus": "InProgress", + "datePublished": "2025-01-20T14:35:56+00:00", + "description": "

\n \n \n \"nf-core/mag\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/mag/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/mag/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mag/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/mag/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/mag)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23mag-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/mag)[![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/mag** 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/mag \\\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/mag/usage) and the [parameter documentation](https://nf-co.re/mag/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/mag/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/mag/output).\n\n## Credits\n\nnf-core/mag was originally written by Hadrien Gourl\u00e9, Daniel Straub, Sabrina Krakau, James A. Fellows Yates, Maxime Borry.\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 `#mag` channel](https://nfcore.slack.com/channels/mag) (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": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#21020cd0-8c47-4a1a-84a3-6e758cb60d64" + "@id": "#7529fbd9-35e2-468b-8f87-4e11f77f53b2" } ], "name": "nf-core/mag" @@ -121,18 +121,14 @@ }, { "@id": "main.nf", - "@type": [ - "File", - "SoftwareSourceCode", - "ComputationalWorkflow" - ], + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "creator": [ { "@id": "https://orcid.org/0000-0001-9807-1082" } ], "dateCreated": "", - "dateModified": "2024-12-20T16:59:00Z", + "dateModified": "2025-01-20T14:35:56Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -146,30 +142,21 @@ "nanopore", "nanopore-sequencing" ], - "license": [ - "MIT" - ], + "license": ["MIT"], "maintainer": [ { "@id": "https://orcid.org/0000-0001-9807-1082" } ], - "name": [ - "nf-core/mag" - ], + "name": ["nf-core/mag"], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": [ - "https://github.com/nf-core/mag", - "https://nf-co.re/mag/3.3.0/" - ], - "version": [ - "3.3.0" - ] + "url": ["https://github.com/nf-core/mag", "https://nf-co.re/mag/dev/"], + "version": ["3.3.1dev"] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -184,11 +171,11 @@ "version": "!>=24.04.2" }, { - "@id": "#21020cd0-8c47-4a1a-84a3-6e758cb60d64", + "@id": "#7529fbd9-35e2-468b-8f87-4e11f77f53b2", "@type": "TestSuite", "instance": [ { - "@id": "#acf0ce89-1a77-4ced-8205-a251112f5a94" + "@id": "#befa69d0-369e-4215-9af0-e21f944de36e" } ], "mainEntity": { @@ -197,7 +184,7 @@ "name": "Test suite for nf-core/mag" }, { - "@id": "#acf0ce89-1a77-4ced-8205-a251112f5a94", + "@id": "#befa69d0-369e-4215-9af0-e21f944de36e", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/mag", "resource": "repos/nf-core/mag/actions/workflows/ci.yml", @@ -332,4 +319,4 @@ "name": "Hadrien Gourl\u00e9" } ] -} \ No newline at end of file +}