nf-core/bbmap/bbduk @ 0.0.0-0c7146d
Summary
Adapter and quality trimming of sequencing reads
Get started
Add the following snippet to your workflow script to include this module.
include { BBMAP_BBDUK } from 'nf-core/bbmap/bbduk'
License
MIT License
Process
Name
|
BBMAP_BBDUK |
|---|
Input
2 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. |
contaminants
file
|
Reference files containing adapter and/or contaminant sequences for sequence kmer matching |
|---|
Output
3 channels
#1
log
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.log
file
|
Bbduk log file *bbduk.log
|
#2
reads
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.fastq.gz
file
|
The trimmed/modified fastq reads *fastq.gz
|
#3
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 18:45:21 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fbbmap%2Fbbduk/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bbmap/bbduk/blobs/sha256:ee2a21de730d4e7e1609ccf7288d71ffb452e9d5ec8f2b1d94a1588f539a1d99 |
| Size | 3.2 KB |
| Checksum | sha256:ee2a21de730d4e7e1609ccf7288d71ffb452e9d5ec8f2b1d94a1588f539a1d99 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:04:34 (UTC) | 3 | 3.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:45:21 (UTC) | 3 | 3.2 KB |