Nextflow Registry | nf-core/bbmap/bbmerge@0.0.0-0c7146d

nf-core/bbmap/bbmerge @ 0.0.0-0c7146d

Merging overlapping paired reads into a single read.

paired reads merging fastq overlap-based merging

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @guille0387

Maintainers: @guille0387

Merging overlapping paired reads into a single read.

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

include { BBMAP_BBMERGE } from 'nf-core/bbmap/bbmerge'

MIT License

Process

`Name`	`BBMAP_BBMERGE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`reads` file	List of input paired end fastq files `*.{fastq,fq}.gz`

`interleave` boolean	Indicates whether the input paired reads are interleaved or not

Output 5 channels

#1 log

`*.log` file	log file containing stdout and stderr from bbmerge.sh `*.log`

#2 ihist tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*_ihist.txt` file	insert size histogram `*_ihist.txt`

#3 merged tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*_merged.fastq.gz` file	merged reads `*_merged.fastq`

#4 unmerged tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*_unmerged.fastq.gz` file	unmerged reads `*_unmerged.fastq`

#5 versions_bbmap tuple

`${task.process}` string	The name of the process
`bbmap` string	The name of the tool
`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	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 18:45:23 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbbmap%2Fbbmerge/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bbmap/bbmerge/blobs/sha256:0253107af6fda930db6aab771042992f01af52d3d18282e9349d0b76c74da37e
Size	3.2 KB
Checksum	sha256:0253107af6fda930db6aab771042992f01af52d3d18282e9349d0b76c74da37e
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:04:35 (UTC)		4	3.2 KB
0.0.0-0c7146d	08 Apr 2026 18:45:23 (UTC)		3	3.2 KB