nf-core/svtk/countsvtypes @ 0.0.0-3fc6d40
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 | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:33:51 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsvtk%2Fcountsvtypes/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/svtk/countsvtypes/blobs/sha256:04a6f291f7952ae0afa43241452797a379aabd84eff2ecfcfd5d237c77873f3f |
| Size | 2.3 KB |
| Checksum | sha256:04a6f291f7952ae0afa43241452797a379aabd84eff2ecfcfd5d237c77873f3f |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:48:52 (UTC) | 4 | 2.2 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:33:51 (UTC) | 3 | 2.3 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:41:36 (UTC) | 4 | 2.2 KB |