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

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name: gatk4_markduplicates
description: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
keywords:
- markduplicates
- bam
- sort
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/articles/360037052812-MarkDuplicates-Picard-
tool_dev_url: https://github.com/broadinstitute/gatk
doi: 10.1158/1538-7445.AM2017-3590
licence: ['BSD-3-clause']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Sorted BAM file
pattern: "*.{bam}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: Marked duplicates BAM file
pattern: "*.{bam}"
- metrics:
type: file
description: Duplicate metrics file generated by GATK
pattern: "*.{metrics.txt}"
authors:
- "@ajodeh-juma"