name: "picard_crosscheckfingerprints"
description: Checks that all data in the set of input files appear to come from the same individual
keywords:
  - alignment
  - metrics
  - statistics
  - fingerprint
  - 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 ]
  - input1:
      type: file
      description: List containing 1 or more bam/vcf files or a file containing filepaths
      pattern: "*.{bam,vcf,vcf.gz,txt,fofn}"
  - input2:
      type: file
      description: Optional list containing 1 or more bam/vcf files or a file containing filepaths
      pattern: "*.{bam,vcf,vcf.gz,txt,fofn}"
  - haplotype_map:
      type: file
      description: Haplotype map file
      pattern: "*.{txt,vcf,vcf.gz}"
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"
  - crosscheck_metrics:
      type: file
      description: Metrics created by crosscheckfingerprints
      pattern: "*.{crosscheck_metrics.txt}"

authors:
  - "@matthdsm"