nf-core/bbmap/repair @ 0.0.0-0c7146d
Summary
Re-pairs reads that became disordered or had some mates eliminated.
Get started
Add the following snippet to your workflow script to include this module.
include { BBMAP_REPAIR } from 'nf-core/bbmap/repair'
License
MIT License
Process
Name
|
BBMAP_REPAIR |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
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. |
|---|---|
*_repaired.fastq.gz
file
|
re-paired reads *_repaired.fastq.gz
|
#3
singleton
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${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 | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:24:53 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbbmap%2Frepair/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bbmap/repair/blobs/sha256:b4b8e1d23afd3dfbbdcd520b52c5738177f2aa47fc77abb25d3cd7d195ac324d |
| Size | 3.1 KB |
| Checksum | sha256:b4b8e1d23afd3dfbbdcd520b52c5738177f2aa47fc77abb25d3cd7d195ac324d |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:24:53 (UTC) | 1 | 3.1 KB | - |