name: picard_collecthsmetrics
description: Collects hybrid-selection (HS) metrics for a SAM or BAM file.
keywords:
  - alignment
  - metrics
  - statistics
  - insert
  - hybrid-selection
  - 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/
      tool_dev_url: https://github.com/broadinstitute/picard/
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: An aligned BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - bai:
      type: file
      description: Optional aligned BAM/CRAM/SAM file index
      pattern: "*.{bai,crai,sai}"
  - bait_intervals:
      type: file
      description: An interval file that contains the locations of the baits used.
      pattern: "*.{interval_list,bed,bed.gz}"
  - target_intervals:
      type: file
      description: An interval file that contains the locations of the targets.
      pattern: "*.{interval_list,bed,bed.gz}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fasta:
      type: file
      description: |
        A reference file to calculate dropout metrics measuring reduced representation of reads.
        Optional input.
      pattern: "*.{fa,fasta,fna}"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fai:
      type: file
      description: Index of FASTA file. Only needed when fasta is supplied.
      pattern: "*.fai"
  - meta4:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fai:
      type: file
      description: Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied.
      pattern: "*.dict"
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"
  - metrics:
      type: file
      description: Alignment metrics files generated by picard
      pattern: "*_{metrics}"

authors:
  - "@projectoriented"
  - "@matthdsm"
