nf-core/gatk4/combinegvcfs @ 0.0.0-0c7146d
Summary
Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file
Get started
Add the following snippet to your workflow script to include this module.
include { GATK4_COMBINEGVCFS } from 'nf-core/gatk4/combinegvcfs'
License
MIT License
Process
Name
|
GATK4_COMBINEGVCFS |
|---|
Input
4 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
vcf
file
|
Compressed VCF files *.vcf.gz
|
vcf_idx
file
|
VCF Index file *.vcf.gz.idx
|
fasta
file
|
The reference fasta file *.fasta
|
|---|
fai
file
|
FASTA index file *.fasta.fai
|
|---|
dict
file
|
FASTA dictionary file *.dict
|
|---|
Output
2 channels
#1
combined_gvcf
tuple
meta
file
|
Compressed Combined GVCF file *.combined.g.vcf.gz
|
|---|---|
*.combined.g.vcf.gz
file
|
Compressed Combined GVCF file *.combined.g.vcf.gz
|
#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 | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:02:49 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fcombinegvcfs/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/combinegvcfs/blobs/sha256:3b7c73b53c5d989c766a10d2c8f991da765fc119a86f7509935094e7fdaf8104 |
| Size | 5.2 KB |
| Checksum | sha256:3b7c73b53c5d989c766a10d2c8f991da765fc119a86f7509935094e7fdaf8104 |
| Downloads | 2 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:18:32 (UTC) | 3 | 5.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:02:49 (UTC) | 2 | 5.2 KB |