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            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-rnadnavar_logo_dark.png\">\n    <img alt=\"nf-core/rnadnavar\" src=\"docs/images/nf-core-rnadnavar_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/rnadnavar)\n[![GitHub Actions CI Status](https://github.com/nf-core/rnadnavar/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/rnadnavar/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnadnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnadnavar/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/rnadnavar/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%A525.10.4-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-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\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/rnadnavar)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnadnavar-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnadnavar)[![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\nThe **nf-core/rnadnavar** is a bioinformatics best-practice\nanalysis pipeline for RNA somatic mutation detection\nable to perform in parallel.\n\nInitially designed for cancer research, the pipeline\nuses different variant calling algorithms and applies a\nconsensus approach. A final filtering stage, should\nprovide a set of annotated somatic variants.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across\nmultiple compute infrastructures in a very portable\nmanner. It uses Docker/Singularity containers making\ninstallation trivial and results highly reproducible.\nThe [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this\npipeline uses one container per process which makes it\nmuch easier to maintain and update software\ndependencies. Where possible, these processes have been\nsubmitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\n## Pipeline summary\n\nDepending on the options and samples provided, the\npipeline will run different tasks. This is controlled\nmainly through `--step` and `--tools` parameters. This\nis a summary of the possible tasks to run with the pipeline:\n\n- Quality control and trimming (enabled by\n  `--trim_fastq` and runs [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and\n  [`fastp`](https://github.com/OpenGene/fastp))\n- Map Reads to Reference (BWA-mem, BWA-mem2, dragmap\n  and/or STAR)\n- GATK preprocessing for DNA and RNA bulk sequencing\n  samples (`GATK MarkDuplicates`, `GATK SplitNCigarReads`,`GATK\nBaseRecalibrator` and `GATK ApplyBQSR`)\n- Summarise alignment statistics (`samtools stats`, `mosdepth`)\n- Variant calling (enabled with `--tools`)\n  - `Mutect2`\n  - `Strelka2`\n  - `SAGE`\n- Annotation with `VEP` (enabled with `--tools` adding\n  `vep`)\n- Normalisation of VCFs with VT (enabled with `--tools`\n  adding `normalisation`)\n- Transformation of VCF to MAF and consensus of variant\n  calling results (enabled with `--tools` adding\n  `consensus`)\n- Filtering of MAF files applying optional gnomad,\n  whitelisting and blacklisting (enabled with `--tools`\n  adding `filtering`)\n- Realignment step where reads from regions where a variant\n  was found will be extracted and re-processed, only for\n  RNA due to higher levels of background noise (enabled\n  with `--tools` adding `realignment`).\n- Filtering of MAF files specific for RNA (enabled with\n  `--tools` adding `rna_filtering`)\n\n<p align=\"center\">\n    <img title=\"RNADNAVAR Workflow\"\nsrc=\"docs/images/rnadnavar_schemav3.png\">\n</p>\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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n### Key requirements for the analysis\n\n- RNA tumor samples must be associated with a DNA normal sample using the same patient ID. DNA tumour sample is optional.\n- Sample types are specified with status: 0 (normal DNA), 1 (tumor DNA), 2 (tumor RNA)\n- Reference files are required for the analysis.\n\n### Quick Start\n\nThe typical command for running the pipeline is:\n\n```bash\nnextflow run nf-core/rnadnavar \\\n   -r <VERSION> \\\n   -profile <PROFILE> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --genome <GENOME> \\\n   --tools <TOOLS>\n```\n\n### Pipeline Steps\n\nThe pipeline can start from different entry points but `tools` need to be specified to run. If you are planning to run the pipeline by stages please read [usage](docs/usage.md#starting-from-different-steps).\n\n### Input requirements\n\nYou will need to create a samplesheet with information about the samples you want to analyze. The samplesheet must be a comma-separated file with a header row.\n\nEssential columns are:\n\n- `patient` - Unique patient identifier\n- `status` - Sample type (0/1/2)\n- `sample` - Unique sample identifier\n- And one of these options:\n  - if variant calling is going to be performed of these three options should be an input (_note that this is included in the `realignment` step by default_):\n    - `fastq_1`, `fastq_2` - Paths to paired-end FASTQ files (for raw data) (this also needs `lane` column)\n    - `bam`,`bai` - Paths to BAM files and indices (for pre-aligned data)\n    - `cram`,`crai` - Paths to CRAM files and indices (for pre-aligned data)\n  - if the starting step is from `consensus` and no `realignment` will be performed (add `--skip_tools 'realignment'` to your command or params file) then the input are VCF/MAF:\n    - `caller` - Caller used to generate that MAF (to annotate it during the consensus approach)\n    - `maf` - Paths to MAF file\n  - if `realignment` is desired then please add `normal_id` and take a look to [usage](docs/usage.md#starting-from-different-steps).\n\nExamples CSVs:\n\nStarting from `mapping`:\n\n```csv\npatient,sample,status,lane,fastq_1,fastq_2\nPT1,DNA_NORMAL_SAMPLE,0,LX,DNA_NORMAL_SAMPLE_L002_R1_001.fastq.gz,DNA_NORMAL_SAMPLE1_L002_R2_001.fastq.gz\nPT1,DNA_TUMOUR_SAMPLE,1,LX,DNA_TUMOUR_SAMPLE_L002_R1_001.fastq.gz,DNA_TUMOUR_SAMPLE_L002_R2_001.fastq.gz\nPT1,RNA_TUMOUR_SAMPLE,2,LX,RNA_TUMOUR_SAMPLE_L002_R1_001.fastq.gz,RNA_TUMOUR_SAMPLE_L002_R2_001.fastq.gz\n```\n\nStarting from `consensus` no realignment:\n\n```csv\npatient,sample,status,caller,maf\nPT1,RNA_TUMOUR_SAMPLE_1,2,mutect,DNA_TUMOUR_SAMPLE_1.mutect.maf\nPT1,RNA_TUMOUR_SAMPLE_1,2,strelka,RNA_TUMOUR_SAMPLE_1.strelka.maf\nPT1,RNA_TUMOUR_SAMPLE_2,2,mutect,DNA_TUMOUR_SAMPLE_2.mutect.maf\nPT1,RNA_TUMOUR_SAMPLE_2,2,strelka,RNA_TUMOUR_SAMPLE_2.strelka.maf\n```\n\n### Parameters\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/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnadnavar/usage) and the [parameter documentation](https://nf-co.re/rnadnavar/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/rnadnavar/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/rnadnavar/output).\n\n## Credits\n\nThe nf-core/rnadnavar was originally written by Raquel\nManzano Garcia at Cancer Research UK Cambridge Institute\nwith the continuous support of [Maxime U Garcia](https://github.com/maxulysse). The\nworkflow is based on\n[RNA-MuTect](https://github.com/broadinstitute/RNA_MUTECT_1.0-1) which was\noriginally published by [Yizhak, _et al_ 2019 (Science)](https://www.science.org/doi/10.1126/science.aaw0726)\n\nWe thank the following people for their assistance in the development of this pipeline:\nTBC\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnadnavar` channel](https://nfcore.slack.com/channels/rnadnavar) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/rnadnavar for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\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",
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