Nextflow Registry | nf-core/gatk4spark/markduplicates@0.0.0-0c7146d

nf-core/gatk4spark/markduplicates @ 0.0.0-0c7146d

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 gatk4spark markduplicates sort

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @ajodeh-juma @FriederikeHanssen @maxulysse @SusiJo

Maintainers: @ajodeh-juma @FriederikeHanssen @maxulysse @SusiJo

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 { GATK4SPARK_MARKDUPLICATES } from 'nf-core/gatk4spark/markduplicates'

MIT License

Process

`Name`	`GATK4SPARK_MARKDUPLICATES`

Input 4 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	The reference fasta file `*.fasta`

`fasta_fai` file	Index of reference fasta file `*.fai`

`dict` file	GATK sequence dictionary `*.dict`

Output 4 channels

#1 output tuple

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

#2 metrics tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.metrics` file	Metrics file `*.metrics`

#3 bam_index tuple

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

#4 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

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	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:05:11 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4spark%2Fmarkduplicates/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4spark/markduplicates/blobs/sha256:b9a82785ed402dce19a90beb5492f518287aa9ba0779f143d80b5bd2b348f6a0
Size	4.1 KB
Checksum	sha256:b9a82785ed402dce19a90beb5492f518287aa9ba0779f143d80b5bd2b348f6a0
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:20:48 (UTC)		3	4.1 KB
0.0.0-0c7146d	08 Apr 2026 19:05:11 (UTC)		3	4.1 KB