nf-core/svdb/query @ 0.0.0-0c7146d
Summary
Query a structural variant database, using a vcf file as query
Get started
Add the following snippet to your workflow script to include this module.
include { SVDB_QUERY } from 'nf-core/svdb/query'
License
MIT License
Process
Name
|
SVDB_QUERY |
|---|
Input
7 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
vcf
file
|
query vcf file *.{vcf,vcf.gz}
|
in_occs
list
|
A list of allele count tags |
|---|
in_frqs
list
|
A list of allele frequency tags |
|---|
out_occs
list
|
A list of allele count tags |
|---|
out_frqs
list
|
A list of allele frequency tags |
|---|
vcf_dbs
file
|
path to a database vcf, or a comma separated list of vcfs *.{vcf,vcf.gz}
|
|---|
bedpe_dbs
file
|
path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, or a comma separated list of files *.{bedpe}
|
|---|
Output
2 channels
#1
vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
*_query.vcf
file
|
Annotated output VCF file *_query.vcf
|
#2
versions_svdb
tuple
${task.process}
string
|
The name of the process |
|---|---|
svdb
string
|
The name of the tool |
svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\1/p'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| svdb | structural variant database software | https://github.com/J35P312/SVDB |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:17:30 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsvdb%2Fquery/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/svdb/query/blobs/sha256:6142f65560ccd8f3974d27af4c0e2ad02c0e719dc776f49171bfd99b54644726 |
| Size | 2.6 KB |
| Checksum | sha256:6142f65560ccd8f3974d27af4c0e2ad02c0e719dc776f49171bfd99b54644726 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:17:30 (UTC) | 1 | 2.6 KB | - |