Nextflow Registry | nf-core/gatk4/markduplicates@0.0.0-6c4ed3a

nf-core/gatk4/markduplicates @ 0.0.0-6c4ed3a

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.

bam gatk4 markduplicates sort

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @ajodeh-juma @FriederikeHanssen @maxulysse

Maintainers: @ajodeh-juma @FriederikeHanssen @maxulysse

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.

Add the following snippet to your workflow script to include this module.

include { GATK4_MARKDUPLICATES } from 'nf-core/gatk4/markduplicates'

MIT License

Process

`Name`	`GATK4_MARKDUPLICATES`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	Sorted BAM file `*.{bam}`

`fasta` file	Fasta file `*.{fasta}`

`fasta_fai` file	Fasta index file `*.{fai}`

Output 7 channels

#1 bai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bai` file	BAM index file `*.{bam.bai}`

#2 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*bam` file	Marked duplicates BAM file `*.{bam}`

#3 crai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.crai` file	CRAM index file `*.{cram.crai}`

#4 cram tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*cram` file	Marked duplicates CRAM file `*.{cram}`

#5 metrics tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.metrics` file	Duplicate metrics file generated by GATK `*.{metrics.txt}`

#6 versions_gatk4 tuple

`${task.process}` string	The name of the process
`gatk4` string	The name of the tool
`gatk --version \| sed -n '/GATK.v/s/.v//p'` eval	The expression to obtain the version of the tool

#7 versions_samtools tuple

`${task.process}` string	The name of the process
`samtools` string	The name of the tool
`samtools version \| sed '1!d;s/.* //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
gatk4	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.	https://gatk.broadinstitute.org/hc/en-us

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:20:14 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fmarkduplicates/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seq