nf-core/smoove/call @ 0.0.0-3fc6d40
Summary
smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls. Developed by Brent Pedersen.
Get started
Add the following snippet to your workflow script to include this module.
include { SMOOVE_CALL } from 'nf-core/smoove/call'
License
MIT License
Name
|
SMOOVE_CALL |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
input
file
|
BAM/CRAM file *.{bam,cram}
|
index
file
|
Index of BAM/CRAM file *.{bai,crai}
|
exclude_beds
file
|
A BED file containing the regions to exclude from the SV calling *.bed
|
meta2
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
fasta
file
|
The reference fasta file *.{fasta,fna,fa}
|
meta3
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
fai
file
|
Index of reference fasta file *.fai
|
vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.vcf.gz
file
|
Compressed VCF file *.vcf.gz
|
versions_smoove
tuple
${task.process}
string
|
The name of the process |
|---|---|
smoove
string
|
The name of the tool |
smoove -v |& sed -n 's/smoove version: *//p'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| smoove | structural variant calling and genotyping with existing tools, but, smoothly | https://github.com/brentp/smoove |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:32:11 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsmoove%2Fcall/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/smoove/call/blobs/sha256:672b00ab73c56438780142050952141c263f17f30454e13c02ed872f96ca9a98 |
| Size | 2.7 KB |
| Checksum | sha256:672b00ab73c56438780142050952141c263f17f30454e13c02ed872f96ca9a98 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:46:30 (UTC) | 4 | 2.7 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:32:11 (UTC) | 3 | 2.7 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:39:11 (UTC) | 3 | 2.7 KB |