name: "gatk4_leftalignandtrimvariants"
description: Left align and trim variants using GATK4 LeftAlignAndTrimVariants.
keywords:
  - normalize
  - norm
  - vcf
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 ]
  - vcf:
      type: file
      description: |
        The vcf file to be normalized
        e.g. 'file1.vcf.gz'
  - tbi:
      type: file
      description: |
        Index of the vcf file to be normalized
        e.g. 'file1.vcf.gz.tbi'
  - intervals:
      type: file
      description: Bed file with the genomic regions included in the library (optional)
  - fasta:
      type: file
      description: The reference fasta file
      pattern: "*.fasta"
  - fai:
      type: file
      description: Index of reference fasta file
      pattern: "*.fasta.fai"
  - dict:
      type: file
      description: GATK sequence dictionary
      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"
  - vcf:
      type: file
      description: VCF normalized output file
      pattern: "*.{vcf.gz}"
  - tbi:
      type: file
      description: Tbi index for VCF file
      pattern: "*.tbi"
authors:
  - "@adamrtalbot"