nf-core/svim/alignment @ 0.0.0-6c4ed3a
Summary
Structural variant detection from long-read sequencing alignments using SVIM.
Get started
Add the following snippet to your workflow script to include this module.
include { SVIM_ALIGNMENT } from 'nf-core/svim/alignment'
License
MIT License
Process
Name
|
SVIM_ALIGNMENT |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
bam
file
|
Coordinate-sorted BAM/CRAM/SAM alignment file generated from long-read mapping *.{bam,cram,sam}
|
bai
file
|
BAM index file *.bai
|
#2
tuple
meta2
map
|
Groovy Map containing reference information e.g. [ id:'genome' ] |
|---|---|
fasta
file
|
Reference genome in FASTA format *.{fa,fasta,fna}
|
Output
2 channels
#1
vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
*.vcf
file
|
Structural variant calls in VCF format generated by SVIM *.vcf
|
#2
versions_svim
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
svim
string
|
The tool name |
svim --version | sed "s/^.*svim //; s/ .*//"
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| svim | SVIM is a structural variant caller for long-read sequencing data that detects deletions, insertions, duplications, inversions and translocations from read alignments. | https://github.com/eldariont/svim |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:48:50 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsvim%2Falignment/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/svim/alignment/blobs/sha256:3a89aeeca6629d29e6f8954a901b330ac48c9b064fe10226e688eee88a13dfde |
| Size | 3.1 KB |
| Checksum | sha256:3a89aeeca6629d29e6f8954a901b330ac48c9b064fe10226e688eee88a13dfde |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:48:50 (UTC) | 3 | 3.1 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:33:49 (UTC) | 3 | 3.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:41:33 (UTC) | 4 | 3.1 KB |