nf-core/gridss/somaticfilter @ 0.0.0-56a9b6d
Summary
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
Get started
Add the following snippet to your workflow script to include this module.
include { GRIDSS_SOMATICFILTER } from 'nf-core/gridss/somaticfilter'
License
MIT License
Process
Name
|
GRIDSS_SOMATICFILTER |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test'] |
|---|---|
vcf
file
|
Input VCF file, must be generated with GRIDSS *.{vcf,vcf.gz}
|
#2
tuple
meta2
map
|
Groovy Map containing information for PONDIR e.g. [ id:'test'] |
|---|---|
pondir
directory
|
Directory containing Panel Of Normal bed/bedpe used to filter FP somatic events. Use gridss.GeneratePonBedpe to generate the PON. |
Output
3 channels
#1
all_sv
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test'] |
|---|---|
*.all_somatic.vcf.bgz
file
|
VCF file including all somatic SVs *.vcf.bgz
|
#2
high_conf_sv
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test'] |
|---|---|
*.high_confidence_somatic.vcf.bgz
file
|
VCF file including high confidence somatic SVs *.vcf.bgz
|
#3
versions_gridss
tuple
${task.process}
string
|
The process |
|---|---|
gridss
string
|
The tool name |
GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| gridss | GRIDSS: the Genomic Rearrangement IDentification Software Suite | n/a |
| Version | 0.0.0-56a9b6d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 10 Apr 2026 15:00:43 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgridss%2Fsomaticfilter/0.0.0-56a9b6d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gridss/somaticfilter/blobs/sha256:174c8819c6027ec703e4d70cb9e9e619d0a0b805c71d527c8f1f9aa718420271 |
| Size | 3.0 KB |
| Checksum | sha256:174c8819c6027ec703e4d70cb9e9e619d0a0b805c71d527c8f1f9aa718420271 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:22:04 (UTC) | 3 | 3.0 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:14:32 (UTC) | 3 | 3.0 KB | |
| 0.0.0-c24122a | 11 Apr 2026 15:00:19 (UTC) | 3 | 3.0 KB | |
| 0.0.0-56a9b6d | 10 Apr 2026 15:00:43 (UTC) | 3 | 3.0 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:07:00 (UTC) | 3 | 3.0 KB |