Nextflow Registry | nf-core/smoove/call@0.0.0-0c7146d

nf-core/smoove/call @ 0.0.0-0c7146d

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.

structural variants SV vcf wgs

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @scorreard @nvnieuwk

Maintainers: @scorreard @nvnieuwk

Summary

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

Process

`Name`	`SMOOVE_CALL`

Input 3 channels

#1 tuple

`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`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	The reference fasta file `*.{fasta,fna,fa}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fai` file	Index of reference fasta file `*.fai`

Output 2 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz` file	Compressed VCF file `*.vcf.gz`

#2 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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:15:08 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsmoove%2Fcall/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/smoove/call/blobs/sha256:b7f197f0d804316ebacdad26857e68a2b4d32fd9b7c78fee5c1a055dfbbc9c59
Size	2.7 KB
Checksum	sha256:b7f197f0d804316ebacdad26857e68a2b4d32fd9b7c78fee5c1a055dfbbc9c59
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:15:08 (UTC)		1	2.7 KB	-