name: "gatk_indelrealigner"
description: Performs local realignment around indels to correct for mapping errors
keywords:
  - bam
  - vcf
  - variant calling
  - indel
  - realignment
tools:
  - "gatk":
      description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
      homepage: "https://gatk.broadinstitute.org/hc/en-us"
      documentation: "https://github.com/broadinstitute/gatk-docs"
      licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input:
      type: file
      description: Sorted and indexed BAM/CRAM/SAM file
      pattern: "*.bam"
  - index:
      type: file
      description: BAM index file
      pattern: "*.bai"
  - intervals:
      type: file
      description: Intervals file created by gatk3 RealignerTargetCreator
      pattern: "*.{intervals,list}"
  - fasta:
      type: file
      description: Reference file used to generate BAM file
      pattern: ".{fasta,fa,fna}"
  - fai:
      type: file
      description: Index of reference file used to generate BAM file
      pattern: ".fai"
  - dict:
      type: file
      description: GATK dict file for reference
      pattern: ".dict"
  - known_vcf:
      type: file
      description: Optional input VCF file(s) with known indels
      pattern: ".vcf"

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 and indexed BAM/CRAM/SAM file with local realignment around variants
      pattern: "*.bam"
  - bai:
      type: file
      description: Output BAM Index file
      pattern: "*.bai"

authors:
  - "@jfy133"