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

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

Locate and tag duplicate reads in a BAM file

markduplicates pcr duplicates bam sam cram

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @drpatelh @projectoriented @ramprasadn

Maintainers: @drpatelh @projectoriented @ramprasadn

Locate and tag duplicate reads in a BAM file

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

include { PICARD_MARKDUPLICATES } from 'nf-core/picard/markduplicates'

MIT License

Process

`Name`	`PICARD_MARKDUPLICATES`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	Sequence reads file, can be SAM/BAM/CRAM format `*.{bam,cram,sam}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	Reference genome fasta file, required for CRAM input `*.{fasta,fa}`
`fai` file	Reference genome fasta index `*.{fai}`

Output 5 channels

#1 bai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bai` file	An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag `*.{bai}`

#2 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bam` file	BAM file with duplicate reads marked/removed `*.{bam}`

#3 cram tuple

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

#4 metrics tuple

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

#5 versions_picard tuple

`${task.process}` string	The process the versions were collected from
`picard` string	The tool name
`picard MarkDuplicates --version 2>&1 \| sed -n 's/.*Version://p'` string	The command used to generate the version of the tool

Tool	Description	Homepage
picard	A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.	https://broadinstitute.github.io/picard/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:02:52 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fmarkduplicates/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/picard/markduplicates/blobs/sha256:2c3326314b55a89d397998a033db1526a728f6ba3c94346bdd824b9336f21daa
Size	4.1 KB
Checksum	sha256:2c3326314b55a89d397998a033db1526a728f6ba3c94346bdd824b9336f21daa
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0