Nextflow Registry | nf-core/biobambam/bamsormadup@0.0.0-6c4ed3a

nf-core/biobambam/bamsormadup @ 0.0.0-6c4ed3a

Parallel sorting and duplicate marking

markduplicates sort bam cram

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:06:08 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbiobambam%2Fbamsormadup/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/biobambam/bamsormadup/blobs/sha256:eb52274f740a36e02806d5255082cb9b36c9a5fd47361977a593b1cdaab35187
Size	3.0 KB
Checksum	sha256:eb52274f740a36e02806d5255082cb9b36c9a5fd47361977a593b1cdaab35187
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:06:08 (UTC)		3	3.0 KB
0.0.0-3fc6d40	22 Apr 2026 15:04:11 (UTC)		3	3.1 KB