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

Locate and tag duplicate reads in a BAM file

markduplicates pcr duplicates bam sam cram
Latest version: 0.0.0-6c4ed3a
Total downloads: 6
Source: nf-core/modules
Authors: @drpatelh @projectoriented @ramprasadn
Maintainers: @drpatelh @projectoriented @ramprasadn

Summary

Locate and tag duplicate reads in a BAM file

Get started

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

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

License

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 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:36:10 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fmarkduplicates/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/picard/markduplicates/blobs/sha256:eee0d0be6db6587030da0a87bc384dafdfcb663bd104d898138a64b9a9baae5a
Size 4.1 KB
Checksum sha256:eee0d0be6db6587030da0a87bc384dafdfcb663bd104d898138a64b9a9baae5a
Downloads 3
Version Date Status Downloads Size
0.0.0-6c4ed3a