nf-core/gatk4/fastqtosam @ 0.0.0-0c7146d
Summary
Converts FastQ file to SAM/BAM format
Get started
Add the following snippet to your workflow script to include this module.
include { GATK4_FASTQTOSAM } from 'nf-core/gatk4/fastqtosam'
License
MIT License
Process
Name
|
GATK4_FASTQTOSAM |
|---|
Input
1 channel
#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. *.fastq.gz
|
Output
2 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bam
file
|
Converted BAM file *.bam
|
#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 | Genome Analysis Toolkit (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 | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:41:39 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Ffastqtosam/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/fastqtosam/blobs/sha256:d62a26f6dabf06945bcb7fdc494488ed520534f03f7ab5ef9fa76fe8615330e6 |
| Size | 2.9 KB |
| Checksum | sha256:d62a26f6dabf06945bcb7fdc494488ed520534f03f7ab5ef9fa76fe8615330e6 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:41:39 (UTC) | 1 | 2.9 KB | - |