nf-core/jvarkit/vcf2table @ 0.0.0-6c4ed3a
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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:26:27 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fjvarkit%2Fvcf2table/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/jvarkit/vcf2table/blobs/sha256:da14d1716e40d09d2cd5029248b2e741c3964317ef9c095c9220e880dbf2598d |
| Size | 2.9 KB |
| Checksum | sha256:da14d1716e40d09d2cd5029248b2e741c3964317ef9c095c9220e880dbf2598d |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:26:27 (UTC) | 3 | 2.9 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:18:26 (UTC) | 3 | 3.0 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:12:16 (UTC) | 3 | 2.9 KB |