diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 298b2feb..0dca1c0e 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 39d0fbfc..ac1e4e2d 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,7 +1,7 @@ lint: files_unchanged: - .github/CONTRIBUTING.md -nf_core_version: 3.1.1 +nf_core_version: 3.1.2 repository_type: pipeline template: author: Jonas Scheid, Steffen Lemke, Leon Bichmann, Marissa Dubbelaar @@ -11,4 +11,4 @@ template: name: mhcquant org: nf-core outdir: . - version: 2.6.1dev + version: 2.7.0dev diff --git a/CHANGELOG.md b/CHANGELOG.md index bc59e734..159b2a89 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). -## v2.6.1dev - [date] +## v2.7.0dev - [date] Initial release of nf-core/mhcquant, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index 1ed36824..b0bd941b 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 63b9f359..0bfe5d61 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,9 @@ nf-core/mhcquant -[![GitHub Actions CI Status](https://github.com/nf-core/mhcquant/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mhcquant/actions/workflows/ci.yml) + + +[![GitHub Actions CI Status](https://github.com/nf-core/mhcquant/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mhcquant/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/mhcquant/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mhcquant/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/mhcquant/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/conf/test.config b/conf/test.config index 801bde69..0e60d4d6 100644 --- a/conf/test.config +++ b/conf/test.config @@ -25,8 +25,6 @@ params { // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' - - // Genome references + input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'// Genome references genome = 'R64-1-1' } diff --git a/nextflow.config b/nextflow.config index a1c2134a..8aeb0f8c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -267,13 +267,13 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.04.2' - version = '2.6.1dev' + version = '2.7.0dev' 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 { diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index a5842c85..c6864376 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2024-12-20T13:10:38+00:00", - "description": "

\n \n \n \"nf-core/mhcquant\"\n \n

[![GitHub Actions CI Status](https://github.com/nf-core/mhcquant/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mhcquant/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/mhcquant/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mhcquant/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/mhcquant/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/mhcquant)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23mhcquant-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/mhcquant)[![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/mhcquant** 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/mhcquant \\\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/mhcquant/usage) and the [parameter documentation](https://nf-co.re/mhcquant/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/mhcquant/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/mhcquant/output).\n\n## Credits\n\nnf-core/mhcquant was originally written by Jonas Scheid, Steffen Lemke, Leon Bichmann, Marissa Dubbelaar.\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 `#mhcquant` channel](https://nfcore.slack.com/channels/mhcquant) (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", + "datePublished": "2025-01-20T14:34:38+00:00", + "description": "

\n \n \n \"nf-core/mhcquant\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/mhcquant/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mhcquant/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/mhcquant/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mhcquant/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/mhcquant/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/mhcquant)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23mhcquant-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/mhcquant)[![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/mhcquant** 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/mhcquant \\\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/mhcquant/usage) and the [parameter documentation](https://nf-co.re/mhcquant/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/mhcquant/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/mhcquant/output).\n\n## Credits\n\nnf-core/mhcquant was originally written by Jonas Scheid, Steffen Lemke, Leon Bichmann, Marissa Dubbelaar.\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 `#mhcquant` channel](https://nfcore.slack.com/channels/mhcquant) (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": "#e383d394-18d6-4086-8233-3f861a7331e0" + "@id": "#1379486e-73e5-4aa7-8c2c-39c609f02e3a" } ], "name": "nf-core/mhcquant" @@ -121,24 +121,20 @@ }, { "@id": "main.nf", - "@type": [ - "File", - "SoftwareSourceCode", - "ComputationalWorkflow" - ], + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "creator": [ { "@id": "https://orcid.org/0000-0002-8937-3457" }, { - "@id": "https://orcid.org/0000-0002-6503-2180" + "@id": "https://orcid.org/0000-0001-7135-0073" }, { - "@id": "https://orcid.org/0000-0001-7135-0073" + "@id": "https://orcid.org/0000-0002-6503-2180" } ], "dateCreated": "", - "dateModified": "2024-12-20T13:10:38Z", + "dateModified": "2025-01-20T14:34:38Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -150,30 +146,21 @@ "openms", "peptides" ], - "license": [ - "MIT" - ], + "license": ["MIT"], "maintainer": [ { "@id": "https://orcid.org/0000-0001-7135-0073" } ], - "name": [ - "nf-core/mhcquant" - ], + "name": ["nf-core/mhcquant"], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": [ - "https://github.com/nf-core/mhcquant", - "https://nf-co.re/mhcquant/dev/" - ], - "version": [ - "2.6.1dev" - ] + "url": ["https://github.com/nf-core/mhcquant", "https://nf-co.re/mhcquant/dev/"], + "version": ["2.7.0dev"] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -188,11 +175,11 @@ "version": "!>=24.04.2" }, { - "@id": "#e383d394-18d6-4086-8233-3f861a7331e0", + "@id": "#1379486e-73e5-4aa7-8c2c-39c609f02e3a", "@type": "TestSuite", "instance": [ { - "@id": "#909351b3-952c-4cbb-9dd8-5645ee8a0e7d" + "@id": "#60b229d8-92e4-4c50-a90e-59aadb3ec356" } ], "mainEntity": { @@ -201,7 +188,7 @@ "name": "Test suite for nf-core/mhcquant" }, { - "@id": "#909351b3-952c-4cbb-9dd8-5645ee8a0e7d", + "@id": "#60b229d8-92e4-4c50-a90e-59aadb3ec356", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/mhcquant", "resource": "repos/nf-core/mhcquant/actions/workflows/ci.yml", @@ -335,17 +322,17 @@ "email": "lukas.heumos@gmail.com", "name": "Lukas Heumos" }, - { - "@id": "https://orcid.org/0000-0002-6503-2180", - "@type": "Person", - "email": "apeltzer@users.noreply.github.com", - "name": "Alexander Peltzer" - }, { "@id": "https://orcid.org/0000-0001-7135-0073", "@type": "Person", "email": "bichmann@informatik.uni-tuebingen.de", "name": "Leon Bichmann" + }, + { + "@id": "https://orcid.org/0000-0002-6503-2180", + "@type": "Person", + "email": "apeltzer@users.noreply.github.com", + "name": "Alexander Peltzer" } ] -} \ No newline at end of file +}