Nextflow Registry | nf-core/bbmap/bbsplit@0.0.0-6c4ed3a

nf-core/bbmap/bbsplit @ 0.0.0-6c4ed3a

Split sequencing reads by mapping them to multiple references simultaneously

align map fastq genome reference

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @joseespinosa @drpatelh @pinin4fjords

Maintainers: @joseespinosa @drpatelh @pinin4fjords

Split sequencing reads by mapping them to multiple references simultaneously

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

include { BBMAP_BBSPLIT } from 'nf-core/bbmap/bbsplit'

MIT License

Process

`Name`	`BBMAP_BBSPLIT`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

`index` directory	Directory to place generated index `*`

`primary_ref` file	Path to the primary reference `*`

#4 tuple

`other_ref_names` list	List of other reference ids apart from the primary
`other_ref_paths` list	Path to other references paths corresponding to "other_ref_names"

`only_build_index` string	true = only build index; false = mapping

Output 6 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.log` file	Log file `*.log`

#2 index

`bbsplit_index` directory	Directory with index files `bbsplit_index`

#3 stats tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*txt` file	Tab-delimited text file containing mapping statistics `*.txt`

#4 all_fastq tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*fastq.gz` file	All reads mapping to any of the references `*fastq.gz`

#5 primary_fastq tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`primaryfastq.gz` file	Output reads that map to the primary reference `primaryfastq.gz`

#6 versions_bbmap tuple

`${task.process}` string	The process the versions were collected from
`bbmap` string	The tool name
`bbversion.sh \| grep -v "Duplicate cpuset"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
bbmap	BBMap is a short read aligner, as well as various other bioinformatic tools.	https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:04:37 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbbmap%2Fbbsplit/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bbmap/bbsplit/blobs/sha256:3dbaf5dd183407c3b5e3d2b160aeee75e7cbaea56f98039d82f40a8f2f655bf3