nf-core/svtk/rdtest2vcf @ 0.0.0-3fc6d40
Summary
Convert an RdTest-formatted bed to the standard VCF format.
Get started
Add the following snippet to your workflow script to include this module.
include { SVTK_RDTEST2VCF } from 'nf-core/svtk/rdtest2vcf'
License
MIT License
Process
Name
|
SVTK_RDTEST2VCF |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bed
file
|
An RdTest-formatted bed *.bed
|
samples
file
|
A text file containing the names of all samples that need to be added to the VCF *.txt
|
fasta_fai
file
|
The reference file of a FASTA file containing the contigs *.fai
|
|---|
Output
3 channels
#1
tbi
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.vcf.gz.tbi
file
|
The index of the converted VCF *.vcf.gz.tbi
|
#2
vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.vcf.gz
file
|
The converted VCF *.vcf.gz
|
#3
versions_svtk
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
svtk
string
|
The tool name |
0.0.20190615
string
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| svtk | Utilities for consolidating, filtering, resolving, and annotating structural variants. | https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:33:52 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsvtk%2Frdtest2vcf/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/svtk/rdtest2vcf/blobs/sha256:bc49186895bdfbd541a84bef6c493e73622173749117c904f770b875047c2d67 |
| Size | 2.8 KB |
| Checksum | sha256:bc49186895bdfbd541a84bef6c493e73622173749117c904f770b875047c2d67 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:48:53 (UTC) | 3 | 2.8 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:33:52 (UTC) | 3 | 2.8 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:41:38 (UTC) | 3 | 2.8 KB |