name: picard_collectmultiplemetrics
description: Collect multiple metrics from a BAM file
keywords:
  - alignment
  - metrics
  - statistics
  - insert
  - 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: BAM file
      pattern: "*.{bam}"
  - fasta:
      type: file
      description: Genome fasta file
  - fai:
      type: file
      description: Index of FASTA file. Only needed when fasta is supplied.
      pattern: "*.fai"
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}"
  - pdf:
      type: file
      description: PDF plots of metrics
      pattern: "*.{pdf}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@drpatelh"
