name: picard_collectwgsmetrics
description: Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.
keywords:
  - alignment
  - metrics
  - statistics
  - quality
  - bam
tools:
  - picard:
      description: |
        A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
        data and formats such as SAM/BAM/CRAM and VCF.
      homepage: https://broadinstitute.github.io/picard/
      documentation: https://broadinstitute.github.io/picard/
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: Aligned reads file
      pattern: "*.{bam, cram}"
  - bai:
      type: file
      description: (Optional) Aligned reads file index
      pattern: "*.{bai,crai}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fasta:
      type: file
      description: Genome fasta file
      pattern: "*.{fa,fasta,fna}"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fai:
      type: file
      description: Genome fasta file index
      pattern: "*.{fai}"
  - intervallist:
      type: file
      description: Picard Interval List. Defines which contigs to include. Can be generated from a BED file with GATK BedToIntervalList.
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - metrics:
      type: file
      description: Alignment metrics files generated by picard
      pattern: "*_{metrics}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@drpatelh"
  - "@flowuenne"
  - "@lassefolkersen"
  - "@ramprasadn"
