name: "gatk4_shiftfasta"
description: Create a fasta with the bases shifted by offset
keywords:
  - mitochondria
  - shiftfasta
  - shiftchain
  - shiftintervals
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
      tool_dev_url: "https://github.com/broadinstitute/gatk"
      doi: 10.1158/1538-7445.AM2017-3590
      licence: ["Apache-2.0"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - fasta:
      type: file
      description: fasta file
      pattern: "*.{fa,fasta}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - fasta_fai:
      type: file
      description: index for fasta file
      pattern: "*.{fai}"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - dict:
      type: file
      description: sequence dictionary file
      pattern: "*.{dict}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing fasta information
        e.g. [ id:'test' ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - dict:
      type: file
      description: sequence dictionary file
      pattern: "*.{dict}"
  - intervals:
      type: file
      description: Intervals file for the fasta file
      pattern: "*.{intervals}"
  - shift_back_chain:
      type: file
      description: The shiftback chain file to use when lifting over
      pattern: "*.{back_chain}"
  - shift_fa:
      type: file
      description: Shifted fasta file
      pattern: "*.{fa,fasta}"
  - shift_intervals:
      type: file
      description: Intervals file for the shifted fasta file
      pattern: "*.{shifted.intervals}"

authors:
  - "@ramprasadn"
