nf-core/svtk/countsvtypes @ 0.0.0-0c7146d
Summary
Count the instances of each SVTYPE observed in each sample in a VCF.
Get started
Add the following snippet to your workflow script to include this module.
include { SVTK_COUNTSVTYPES } from 'nf-core/svtk/countsvtypes'
License
MIT License
Process
Name
|
SVTK_COUNTSVTYPES |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
vcf
file
|
The VCF file containing structural variants *.vcf.gz
|
Output
2 channels
#1
counts
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.tsv
file
|
A tab-delimited file containing the counts of the SV types *.tsv
|
#2
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 19:17:36 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsvtk%2Fcountsvtypes/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/svtk/countsvtypes/blobs/sha256:c36dd6c12070a56b2eefd575ebcf411ef2a4a3dd30f47d37b108e675893715d8 |
| Size | 2.2 KB |
| Checksum | sha256:c36dd6c12070a56b2eefd575ebcf411ef2a4a3dd30f47d37b108e675893715d8 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:17:36 (UTC) | 1 | 2.2 KB | - |