name: "gatk4_printreads"
description: Print reads in the SAM/BAM/CRAM file
keywords:
  - gatk4
  - bam
  - cram
  - sam
  - printreads
tools:
  - gatk4:
      description: |
        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
        with a primary focus on variant discovery and genotyping. Its powerful processing engine
        and high-performance computing features make it capable of taking on projects of any size.
      homepage: https://gatk.broadinstitute.org/hc/en-us
      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
      doi: 10.1158/1538-7445.AM2017-3590
      licence: ["Apache-2.0"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - index:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bai,crai,sai}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fasta:
      type: file
      description: reference fasta file
      pattern: "*.{fa,fasta}"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fai:
      type: file
      description: reference fasta index file
      pattern: "*.{fai}"
  - meta4:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - dict:
      type: file
      description: reference fasta dictionary file
      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"
  - bam:
      type: file
      description: Sorted BAM file
      pattern: "*.{bam}"
  - cram:
      type: file
      description: Sorted CRAM file
      pattern: "*.{cram}"
  - sam:
      type: file
      description: Sorted SAM file
      pattern: "*.{sam}"

authors:
  - "@ramprasadn"
