nf-core/svtyper/svtypersso @ 0.0.0-3fc6d40
Summary
SVTyper-sso computes structural variant (SV) genotypes based on breakpoint depth on a SINGLE sample
Get started
Add the following snippet to your workflow script to include this module.
include { SVTYPER_SVTYPERSSO } from 'nf-core/svtyper/svtypersso'
License
MIT License
Process
Name
|
SVTYPER_SVTYPERSSO |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test'] |
|---|---|
bam
file
|
BAM or CRAM file with alignments *.{bam,cram}
|
bam_index
file
|
BAI file matching the BAM file *.{bai}
|
vcf
file
|
Matching VCF of alignments *.vcf
|
#2
tuple
meta2
map
|
Groovy Map containing sample information for reference FASTA file e.g. [ id:'fasta'] |
|---|---|
fasta
file
|
indexed reference FASTA file (recommended for reading CRAM files) *.{fa,fasta}
|
Output
3 channels
#1
json
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
*.json
file
|
JSON file including library information *.json
|
#2
gt_vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
*.vcf
file
|
Genotyped SVs *.vcf
|
#3
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| svtyper | Bayesian genotyper for structural variants | https://github.com/hall-lab/svtyper |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:33:58 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsvtyper%2Fsvtypersso/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/svtyper/svtypersso/blobs/sha256:b8fe877e85759ac1098bb40c7814d51dd8d633b36cae5a604a0423f1036752b7 |
| Size | 2.9 KB |
| Checksum | sha256:b8fe877e85759ac1098bb40c7814d51dd8d633b36cae5a604a0423f1036752b7 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:48:59 (UTC) | 3 | 2.9 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:33:58 (UTC) | 3 | 2.9 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:41:47 (UTC) | 3 | 2.9 KB |