name: cnvkit_batch description: Copy number variant detection from high-throughput sequencing data keywords: - bam - fasta - copy number tools: - cnvkit: description: | CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. homepage: https://cnvkit.readthedocs.io/en/stable/index.html documentation: https://cnvkit.readthedocs.io/en/stable/index.html licence: ['Apache-2.0'] params: - outdir: type: string description: | The pipeline's output directory. By default, the module will output files into `$params.outdir/` - publish_dir_mode: type: string description: | Value for the Nextflow `publishDir` mode parameter. Available: symlink, rellink, link, copy, copyNoFollow, move. - enable_conda: type: boolean description: | Run the module with Conda using the software specified via the `conda` directive - singularity_pull_docker_container: type: boolean description: | Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead. input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - tumour: type: file description: | Input tumour sample bam file (or cram) - normal: type: file description: | Input normal sample bam file (or cram) - fasta: type: file description: | Input reference genome fasta file - targetfile: type: file description: | Input target bed file - reference: type: file description: | Input reference cnn-file (only for germline and tumor-only running) output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bed: type: file description: File containing genomic regions pattern: "*.{bed}" - cnn: type: file description: File containing coverage information pattern: "*.{cnn}" - cnr: type: file description: File containing copy number ratio information pattern: "*.{cnr}" - cns: type: file description: File containing copy number segment information pattern: "*.{cns}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@kaurravneet4123" - "@KevinMenden" - "@MaxUlysse" - "@drpatelh" - "@fbdtemme" - "@lassefolkersen"