nf-core/jvarkit/vcf2table @ 0.0.0-0c7146d
Summary
Convert VCF to a user friendly table
Get started
Add the following snippet to your workflow script to include this module.
include { JVARKIT_VCF2TABLE } from 'nf-core/jvarkit/vcf2table'
License
MIT License
Process
Name
|
JVARKIT_VCF2TABLE |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing VCF information e.g. [ id:'genome' ] |
|---|---|
vcf
file
|
Input vcf/bcf file *.{vcf,bcf,vcf.gz,bcf.gz}
|
tbi
file
|
Optional index file for the VCF *.{tbi,csi}
|
regions_file
file
|
Optional. Restrict to regions listed in a file *.{bed,bed.gz,txt,tsv}
|
#2
tuple
meta2
map
|
Groovy Map containing pedigree information |
|---|---|
pedigree
file
|
Optional pedigree for jvarkit *.{ped,pedigree}
|
Output
2 channels
#1
output
tuple
meta
map
|
Groovy Map containing VCF information e.g. [ id:'test', single_end:false ] |
|---|---|
*.${extension}
file
|
Output file *.{txt,html}
|
#2
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| jvarkit | Java utilities for Bioinformatics. | https://github.com/lindenb/jvarkit |
| bcftools | View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF | http://samtools.github.io/bcftools/bcftools.html |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:50:24 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fjvarkit%2Fvcf2table/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/jvarkit/vcf2table/blobs/sha256:ed9a64da188a039f5975dfaed25dcd7a9312e8ab13dccb1ae9798e544a44297c |
| Size | 2.9 KB |
| Checksum | sha256:ed9a64da188a039f5975dfaed25dcd7a9312e8ab13dccb1ae9798e544a44297c |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:50:24 (UTC) | 1 | 2.9 KB | - |