nf-core/svtk/rdtest2vcf @ 0.0.0-0c7146d
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 | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:17:38 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsvtk%2Frdtest2vcf/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/svtk/rdtest2vcf/blobs/sha256:725de065c102a63ded341d5d88dca24a5b1792672ec46cb3a48ad0095a4bc682 |
| Size | 2.8 KB |
| Checksum | sha256:725de065c102a63ded341d5d88dca24a5b1792672ec46cb3a48ad0095a4bc682 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:17:38 (UTC) | 1 | 2.8 KB | - |