nf-core/svtk/standardize @ 0.0.0-6c4ed3a
Summary
Convert SV calls to a standardized format.
Get started
Add the following snippet to your workflow script to include this module.
include { SVTK_STANDARDIZE } from 'nf-core/svtk/standardize'
License
MIT License
Process
Name
|
SVTK_STANDARDIZE |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information. Caller can be one of the tools: delly, manta, melt, wham e.g. [ id:'test', caller:"delly" ] |
|---|---|
input
file
|
A gzipped VCF file to be standardized *.vcf.gz
|
#2
tuple
meta2
map
|
Groovy Map containing reference information e.g. [ id:'test2' ] |
|---|---|
fai
file
|
Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37) *.fai
|
Output
2 channels
#1
vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', caller:"delly" ] |
|---|---|
*.vcf.gz
file
|
A gzipped version of the standardized VCF file *.vcf.gz
|
#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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:48:54 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsvtk%2Fstandardize/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/svtk/standardize/blobs/sha256:ba74e53822a01e7ba11c4efe1b9468c86f93d05d3ed78777426d245b65e1d89a |
| Size | 2.6 KB |
| Checksum | sha256:ba74e53822a01e7ba11c4efe1b9468c86f93d05d3ed78777426d245b65e1d89a |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:48:54 (UTC) | 3 | 2.6 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:33:53 (UTC) | 4 | 2.6 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:41:39 (UTC) | 3 | 2.5 KB |