name: "cnvnator_cnvnator"
description: CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads.
keywords:
  - cnvnator
  - cnv
  - cna
tools:
  - "cnvnator":
      description: "Tool for calling copy number variations."
      homepage: "https://github.com/abyzovlab/CNVnator"
      documentation: "https://github.com/abyzovlab/CNVnator/blob/master/README.md"
      tool_dev_url: "https://github.com/abyzovlab/CNVnator"
      licence: "['MIT']"
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'test', single_end:false ]`
  - meta2:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'test', single_end:false ]`
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. `[ id:'test' ]`
  - meta4:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. `[ id:'test' ]`
  - bam:
      type: file
      description: Sorted BAM/CRAM/SAM file
      pattern: "*.bam"
  - bai:
      type: file
      description: Sorted BAM/CRAM/SAM file
      pattern: "*.bam"
  - root:
      type: file
      description: ROOT file
      pattern: "*.root"
  - fasta:
      type: file
      description: Path to a directory containing fasta files or a fasta file
      pattern: "*.fa"
  - fai:
      type: file
      description: Path to a fasta file index
      pattern: "*.fai"
output:
  - output_meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'test', single_end:false ]`
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - root:
      type: file
      description: A ROOT file
      pattern: "*.root"
  - tab:
      type: file
      description: A tab file containing cnvnator calls
      pattern: "*.tab"
authors:
  - "@ramprasadn"
maintainers:
  - "@ramprasadn"
