nf-core/bbmap/align @ 0.0.0-0c7146d
Summary
Align short or PacBio reads to a reference genome using BBMap
Get started
Add the following snippet to your workflow script to include this module.
include { BBMAP_ALIGN } from 'nf-core/bbmap/align'
License
MIT License
Name
|
BBMAP_ALIGN |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
fastq
file
|
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. |
ref
file
|
Either "ref" a directory containing an index, the name of another directory with a "ref" subdirectory containing an index or the name of a fasta formatted nucleotide file containing the reference to map to. |
|---|
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bam
file
|
BAM file *.{bam}
|
log
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.log
file
|
Log file *.{log}
|
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 | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:24:36 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbbmap%2Falign/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bbmap/align/blobs/sha256:af603ba5122fd7dc509fd6ee67ea16a060d33e6e5545f91a7dcdbcd7a31c1c7c |
| Size | 3.1 KB |
| Checksum | sha256:af603ba5122fd7dc509fd6ee67ea16a060d33e6e5545f91a7dcdbcd7a31c1c7c |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:24:36 (UTC) | 1 | 3.1 KB | - |