nf-core/svdb/query @ 0.0.0-6c4ed3a
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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:48:49 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsvdb%2Fquery/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/svdb/query/blobs/sha256:975dc58b9e1c6619309d7db8d67b315e2eb7f22e60e6f0e4d04d5b3d07b10096 |
| Size | 2.6 KB |
| Checksum | sha256:975dc58b9e1c6619309d7db8d67b315e2eb7f22e60e6f0e4d04d5b3d07b10096 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:48:49 (UTC) | 3 | 2.6 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:41:31 (UTC) | 3 | 2.6 KB |