nf-core/gatk4/samtofastq @ 0.0.0-6c4ed3a
Summary
Converts BAM/SAM file to FastQ format
Get started
Add the following snippet to your workflow script to include this module.
include { GATK4_SAMTOFASTQ } from 'nf-core/gatk4/samtofastq'
License
MIT License
Process
Name
|
GATK4_SAMTOFASTQ |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test'] |
|---|---|
bam
file
|
Input SAM/BAM file *.{bam,sam}
|
Output
2 channels
#1
fastq
tuple
meta
map
|
A Groovy map containing sample information |
|---|---|
*.fastq.gz
file
|
converted fastq file *.fastq
|
#2
versions_gatk4
tuple
${task.process}
string
|
The name of the process |
|---|---|
gatk4
string
|
The name of the tool |
gatk --version | sed -n '/GATK.*v/s/.*v//p'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| gatk4 | Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. | https://gatk.broadinstitute.org/hc/en-us |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:20:29 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fsamtofastq/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/samtofastq/blobs/sha256:b82639346e3ec52a0a592c7db04d648b9b789da470d5ceb375231d98d6af382f |
| Size | 3.0 KB |
| Checksum | sha256:b82639346e3ec52a0a592c7db04d648b9b789da470d5ceb375231d98d6af382f |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:20:29 (UTC) | 3 | 3.0 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:04:41 (UTC) | 3 | 3.0 KB |