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ro-crate-metadata.json
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"datePublished": "2025-02-06T02:10:10+00:00",
"description": "# qbic-pipelines/vcftocounts\n\n[](https://github.com/qbic-pipelines/vcftocounts/actions/workflows/ci.yml)\n[](https://github.com/qbic-pipelines/vcftocounts/actions/workflows/linting.yml)[](https://doi.org/10.5281/zenodo.14616650)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/qbic-pipelines/vcftocounts)\n\n## Introduction\n\n**qbic-pipelines/vcftocounts** is a bioinformatics pipeline that processes g.vcf files to a matrix suitable for downstream analysis. The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:\n\n1. Indexes (g.)vcf files ([`tabix`](http://www.htslib.org/doc/tabix.html))\n2. Converts g.vcf files to vcf with `genotypegvcf` ([`GATK`](https://gatk.broadinstitute.org/hc/en-us))\n3. Concatenates all vcfs that have the same id and the same label with `bcftools/concat` ([`bcftools`](https://samtools.github.io/bcftools/bcftools.html))\n4. Changes the sample name in the vcf file to the filename with `bcftools/reheader` ([`bcftools`](https://samtools.github.io/bcftools/bcftools.html)) - This can be turned off by adding `--rename false` to the `nextflow run` command.\n5. Merges all vcfs from the same sample with `bcftools/merge` ([`bcftools`](https://samtools.github.io/bcftools/bcftools.html))\n6. Removes entries in the ID column with `bcftools/annotate` ([`bcftools`](https://samtools.github.io/bcftools/bcftools.html)) - his can be turned off by adding `--removeIDs false` to the `nextflow run` command.\n7. Converts the (merged) vcfs to a matrix using a custom R script written by @ellisdoro ([`R`](https://www.r-project.org/))\n8. Collects all reports into a MultiQC report ([`MultiQC`](http://multiqc.info/))\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\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,label,gvcf,vcf_path,vcf_index_path\nSAMPLE-1,pipelineA-callerA,false,path/to/vcf.gz,path/to/.vcf.gz.tbi\nSAMPLE-1,pipelineB-callerA,false,path/to/vcf.gz,path/to/.vcf.gz.tbi\nSAMPLE-2,pipelineB-callerB,true,path/to/g.vcf.gz,path/to/g.vcf.gz.tbi\nSAMPLE-2,pipelineB-callerB,true,path/to/g.vcf.gz,path/to/g.vcf.gz.tbi\n```\n\nEach row represents a VCF file coming from a sample. The `label` column enables concatenation of vcfs (for example when the pipeline produces different vcfs for chrM and chrY). The `gvcf` column indicates whether the file is a g.vcf file or not. The `vcf_path` and `vcf_index_path` columns contain the path to the VCF file and its index, respectively.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run qbic-pipelines/vcftocounts \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --genome GATK.GRCh38 \\\n --outdir <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\n## Credits\n\nqbic-pipelines/vcftocounts was originally written by Famke B\u00e4uerle, Dorothy Ellis.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\nIf you use qbic-pipelines/vcftocounts for your analysis, please cite it using the following doi: [10.5281/zenodo.14616650](https://doi.org/10.5281/zenodo.14616650)\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\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 uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\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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"description": "JSON schema for pipeline parameter specification"
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"@type": "File",
"description": "Information on changes made to the pipeline"
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{
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"description": "The license - should be MIT"
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