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

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

Re-pairs reads that became disordered or had some mates eliminated.

paired reads re-pairing fastq preprocessing

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @mazzalab

Maintainers: @mazzalab @tm4zza

Re-pairs reads that became disordered or had some mates eliminated.

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

include { BBMAP_REPAIR } from 'nf-core/bbmap/repair'

MIT License

Process

`Name`	`BBMAP_REPAIR`

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 4 channels

#1 log

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

#2 repaired tuple

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

#3 singleton tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}_singleton.fastq.gz` file	singleton reads `*singleton.fastq.gz`

#4 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
repair	Repair.sh is a tool that re-pairs reads that became disordered or had some mates eliminated tools.	https://jgi.doe.gov/data-and-tools/software-tools/bbtools/

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 18:45:37 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbbmap%2Frepair/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bbmap/repair/blobs/sha256:5247ac876eaed268c32e061ad29fd7ff697e23d7d71a3b549b03ef973a6902bf
Size	3.1 KB
Checksum	sha256:5247ac876eaed268c32e061ad29fd7ff697e23d7d71a3b549b03ef973a6902bf
Downloads	2

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:04:44 (UTC)		3	3.2 KB
0.0.0-0c7146d	08 Apr 2026 18:45:37 (UTC)		2	3.1 KB