Nextflow Registry | nf-core/biobambam/bamsormadup@0.0.0-0c7146d

nf-core/biobambam/bamsormadup @ 0.0.0-0c7146d

Parallel sorting and duplicate marking

markduplicates sort bam cram

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @matthdsm

Maintainers: @matthdsm

Parallel sorting and duplicate marking

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

include { BIOBAMBAM_BAMSORMADUP } from 'nf-core/biobambam/bamsormadup'

MIT License

Process

`Name`	`BIOBAMBAM_BAMSORMADUP`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bams` file	List containing 1 or more bam files

#2 tuple

`meta2` map	Groovy Map containing genome information e.g. [ id:'genome' ]
`fasta` file	Reference genome in FASTA format (optional) `*.{fa,fasta,fna}`
`fai` file	Reference genome in FASTA index format (optional) `*.{fai}`

Output 5 channels

#1 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`

#2 cram tuple

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

#3 metrics tuple

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

#4 bam_index tuple

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

#5 versions_biobambam tuple

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

Tool	Description	Homepage
biobambam	biobambam is a set of tools for early stage alignment file processing.	https://gitlab.com/german.tischler/biobambam2

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:26:54 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbiobambam%2Fbamsormadup/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/biobambam/bamsormadup/blobs/sha256:e07b0ac9d00e77640228075f713c33a727811b813c236944de7656a7c76506c1
Size	3.0 KB
Checksum	sha256:e07b0ac9d00e77640228075f713c33a727811b813c236944de7656a7c76506c1
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:26:54 (UTC)		1	3.0 KB	-