nf-core_modules/modules/gatk4/mergebamalignment/meta.yml

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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
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"
- version:
type: file
description: File containing software version
pattern: "*.version.txt"
authors:
- "@kevinmenden"