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            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-variantprioritization_logo_dark.png\">\n    <img alt=\"nf-core/variantprioritization\" src=\"docs/images/nf-core-variantprioritization_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/variantprioritization)\n[![GitHub Actions CI Status](https://github.com/nf-core/variantprioritization/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/variantprioritization/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/variantprioritization/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/variantprioritization/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/variantprioritization/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/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.2)\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/variantprioritization)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23variantprioritization-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/variantprioritization)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![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/variantprioritization** is a bioinformatics analysis pipeline for the functional annotation and translation of somatic SNVs/InDels and copy number abberations for precision cancer medicine using [Personal Cancer Genome Reporter (PCGR)](https://github.com/sigven/pcgr/).\n**nf-core/variantprioritization** offers germline SNVs/INDELS intepretation and annotation using [Cancer Predisposition Sequencing Reporter (CPSR)](https://github.com/sigven/cpsr/).\n\n<picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/pipeline_dark.svg\">\n    <img alt=\"nf-core/variantprioritization metromap\" src=\"docs/images/pipeline_light.svg\">\n</picture>\n\nThe workflow has been designed to accept outputs generated by [nf-core/sarek](https://github.com/nf-core/sarek):\n\n| Tool                   |      Germline      | Somatic tumor-normal | Somatic tumor-only |\n| ---------------------- | :----------------: | :------------------: | :----------------: |\n| ASCAT                  |                    |  :heavy_check_mark:  |                    |\n| DeepVariant            | :heavy_check_mark: |                      |                    |\n| HaplotypeCaller        | :heavy_check_mark: |                      |                    |\n| Mutect2                |                    |  :heavy_check_mark:  | :heavy_check_mark: |\n| Strelka somatic indels |                    |  :heavy_check_mark:  |                    |\n| Strelka somatic snvs   |                    |  :heavy_check_mark:  |                    |\n\n## Usage\n\nThe workflow accepts as input a `samplesheet.csv` file containing the paths to SNV/InDel VCF files and `ASCAT` copy number abberation files. We have efforted to mimick the [samplesheet specifications of nf-core/sarek](https://github.com/nf-core/sarek/blob/master/docs/usage.md#input-sample-sheet-configurations) for ease of use:\n\n| Column  | Description                                                                                                          |\n| ------- | :------------------------------------------------------------------------------------------------------------------- |\n| patient | Designates the patient/subject; must be unique for each patient, but one patient can have multiple samples           |\n| status  | Normal/tumor (0/1) status of sample                                                                                  |\n| sample  | Designates the sample ID; must be unique. A patient may have multiple samples e.g a paired tumor-normal, tumor-only. |\n| vcf     | Full path to VCF file(s)                                                                                             |\n| cna     | Full path to segment file                                                                                            |\n\nAn example of a valid samplesheet is given below:\n\n```bash\npatient,status,sample,vcf,cna\nHCC1395,1,HCC1395T,HCC1395T_vs_HCC1395N.mutect2.vcf.gz,HCC1395T.segments.txt\nHCC1395,1,HCC1395T,HCC1395T_vs_HCC1395N.freebayes.vcf.gz,HCC1395T.segments.txt\nHCC1395,1,HCC1395T,HCC1395T_vs_HCC1395N.strelka.somatic_snvs.vcf.gz,HCC1395T.segments.txt\nHCC1395,1,HCC1395T,HCC1395T_vs_HCC1395N.strelka.somatic_indels.vcf.gz,HCC1395T.segments.txt\nHCC1395,0,HCC1395N,HCC1395N.deepvariant.vcf.gz,\nHCC1395,0,HCC1395N,HCC1395N.haplotypecaller.vcf.gz,\nHCC1396,1,HCC1396T,HCC1396T_vs_HCC1396N.mutect2.vcf.gz,\nHCC1396,1,HCC1396T,HCC1396T_vs_HCC1396N.strelka.somatic_snvs.vcf.gz,\nHCC1396,1,HCC1396T,HCC1396T_vs_HCC1396N.strelka.somatic_indels.vcf.gz,\n```\n\n> copy number abberation files must be present for every sample entry when `--cna_analysis true`.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/variantprioritization \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> `-profile conda` is not working with the CPSR and PCGR modules at the moment. We are working on a fix and hope to enable it in a future release.\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/variantprioritization/usage) and the [parameter documentation](https://nf-co.re/variantprioritization/parameters).\n\n## Credits\n\nnf-core/variantprioritization was originally written by @barrydigby, @yussab and @matbonfanti. @famosab joined to adapt the pipeline to nf-core standards towards a first release.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Peter Diakumis](https://github.com/pdiakumis)\n- [Sigve Nakken](https://github.com/sigven)\n\n## Contributions and Support\n\nPlease open an issue or reach out to me (Youssef Abili) on the nf-core slack channel.\n\nI am interested in adding compatability for additional variant calling tools and optimising the intake of large VCF files.\n\n## Citations\n\nYou can cite the variantprioritization zenodo record for a specific version using the following doi:\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline mainly uses CPSR and PCGR to prioritize variants:\n\n> **Cancer Predisposition Sequencing Reporter (CPSR): A flexible variant report engine for high-throughput germline screening in cancer**\n> Nakken S, Saveliev V, Hofmann O, M\u00f8ller P, Myklebost O, Hovig E.\n>\n> _Int J Cancer._ 2021 Dec 1;149(11):1955-1960. doi:[10.1002/ijc.33749](https://doi.org/10.1002/ijc.33749)\n\n> **Personal Cancer Genome Reporter: variant interpretation report for precision oncology**\n> Nakken S, Fournous G, Vod\u00e1k D, Aasheim LB, Myklebost O, Hovig E.\n>\n> _Bioinformatics._ 2018 May 15;34(10):1778-1780. doi: [10.1093/bioinformatics/btx817](https://doi.org/10.1093%2Fbioinformatics%2Fbtx817)\n\nThis pipeline builds ontop of [nf-core/sarek](https://github.com/nf-core/sarek) output:\n\n> **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants**\n> Garcia M, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, D\u00edaz De St\u00e5hl T, Ewels P, Wirta V, Nist\u00e9r M, K\u00e4ller M, Nystedt B.\n>\n> _F1000Res._ 2020 Jan 29;9:63. doi: [10.12688/f1000research.16665.2](https://doi.org/10.12688%2Ff1000research.16665.2)\n\nYou can cite the nf-core publication as follows:\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",
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