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/<SOFTWARE>`
  - 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"