name: "gatk4_printsvevidence"
description: Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.
keywords:
  - structural variants
  - gatk4
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 ]
  - evidence:
      type: file
      description: The evidence file created by CollectSVEvidence
      pattern: "*.{pe,sr,baf,rd}.txt(.gz)"
  - evidence_index:
      type: file
      description: The index of the evidence file created by CollectSVEvidence
      pattern: "*.{pe,sr,baf,rd}.txt(.gz).tbi"
  - bed:
      type: file
      description: An optional BED file
      pattern: "*.bed"
  - fasta:
      type: file
      description: An optional reference FASTA file
      pattern: "*.{fa,fasta}"
  - fasta_fai:
      type: file
      description: An optional reference FASTA file index
      pattern: "*.fai"
  - dict:
      type: file
      description: The mandatory sequence 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"
  - printed_evidence:
      type: file
      description: The output file containing the discordant read pairs or the soft clipped reads
      pattern: "*.{pe,sr,baf,rd}.txt.gz"
  - printed_evidence:
      type: file
      description: The index of the output file containing the discordant read pairs or the soft clipped reads
      pattern: "*.{pe,sr,baf,rd}.txt.gz.tbi"

authors:
  - "@nvnieuwk"