nf-core/samtools/bam2fq @ 0.0.0-0c7146d
Summary
The module uses bam2fq method from samtools to convert a SAM, BAM or CRAM file to FASTQ format
Get started
Add the following snippet to your workflow script to include this module.
include { SAMTOOLS_BAM2FQ } from 'nf-core/samtools/bam2fq'
License
MIT License
Name
|
SAMTOOLS_BAM2FQ |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
inputbam
file
|
BAM/CRAM/SAM file *.{bam,cram,sam}
|
split
boolean
|
TRUE/FALSE value to indicate if reads should be separated into /1, /2 and if present other, or singleton. Note: choosing TRUE will generate 4 different files. Choosing FALSE will produce a single file, which will be interleaved in case the input contains paired reads. |
|---|
reads
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.fq.gz
file
|
FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton) or a single interleaved .fq.gz file if the user chooses not to split the reads. *.fq.gz
|
versions_samtools
tuple
${task.process}
string
|
The name of the process |
|---|---|
samtools
string
|
The name of the tool |
samtools version | sed '1!d;s/.* //'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| samtools | Tools for dealing with SAM, BAM and CRAM files | n/a |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:09:39 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fbam2fq/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samtools/bam2fq/blobs/sha256:fa6ed6b3b57b3ab372eac58b0a58fbbdc93add77bf66f028b7bad88fd52367a2 |
| Size | 3.0 KB |
| Checksum | sha256:fa6ed6b3b57b3ab372eac58b0a58fbbdc93add77bf66f028b7bad88fd52367a2 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:09:39 (UTC) | 1 | 3.0 KB | - |