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"