name: gatk4_splitncigarreads
description: Splits reads that contain Ns in their cigar string
keywords:
  - vcf
  - merge
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']
  - bam:
      type: list
      description: BAM/SAM/CRAM file containing reads
      pattern: "*.{bam,sam,cram}"
  - bai:
      type: list
      description: BAI/SAI/CRAI index file (optional)
      pattern: "*.{bai,sai,crai}"
  - 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:
  - bam:
      type: file
      description: Output file with split reads (BAM/SAM/CRAM)
      pattern: "*.{bam,sam,cram}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@kevinmenden"