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

Assigns all the reads in a file to a single new read-group

add replace read-group picard
Latest version: 0.0.0-0c7146d
Total downloads: 1
Source: nf-core/modules
Authors: @sateeshperi @mjcipriano @hseabolt @cmatKhan @muffato
Maintainers: @sateeshperi @mjcipriano @hseabolt @cmatKhan @muffato

Summary

Assigns all the reads in a file to a single new read-group

Get started

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

include { PICARD_ADDORREPLACEREADGROUPS } from 'nf-core/picard/addorreplacereadgroups'

License

MIT License

Process
Name PICARD_ADDORREPLACEREADGROUPS
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 sample information e.g. [ id:'test', single_end:false ]
fasta file

Reference genome file

 *.{fasta,fa,fasta.gz,fa.gz}
fai file

Reference genome index file

 *.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}
Output 4 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

 *.{bai}
#2 bam tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.bam file

Output BAM file

 *.{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 versions_picard tuple
${task.process} string

The process the versions were collected from
picard string

The tool name
picard AddOrReplaceReadGroups --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 19:02:20 (UTC)
Download URL https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Faddorreplacereadgroups/0.0.0-0c7146d/download
OCI Store URL https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/picard/addorreplacereadgroups/blobs/sha256:d11e2d7574d31aab945ba6637b7889ef000a411deb055bf738962b69849f94b7
Size 3.3 KB
Checksum sha256:d11e2d7574d31aab945ba6637b7889ef000a411deb055bf738962b69849f94b7
Downloads 1
Version Date Status Downloads Size Diff
0.0.0-0c7146d 08 Apr 2026 19:02:20 (UTC) 1 3.3 KB -