name: gatk4_mergebamalignment
description: Merge unmapped with mapped BAM files
keywords:
  - bam
  - 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']
  - aligned:
      type: file
      description: The aligned bam file
      pattern: "*.{bam}"
  - unaligned:
      type: file
      description: The unmaped bam file
      pattern: "*.{bam}"
  - fasta:
      type: file
      description: The reference fasta file
  - dict:
      type: file
      description: GATK sequence dictionary
output:
  - bam:
      type: file
      description: The merged bam file
      pattern: "*.bam"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@kevinmenden"