nf-core/svtk/standardize @ 0.0.0-0c7146d
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 | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:17:40 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsvtk%2Fstandardize/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/svtk/standardize/blobs/sha256:22b6f8327ee777556e91707d1bd62c8c2594d6d4c4497955cffb0ad4d90a5f90 |
| Size | 2.5 KB |
| Checksum | sha256:22b6f8327ee777556e91707d1bd62c8c2594d6d4c4497955cffb0ad4d90a5f90 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:17:40 (UTC) | 1 | 2.5 KB | - |