Nextflow Registry | nf-core/sniffles@0.0.0-0c7146d

nf-core/sniffles @ 0.0.0-0c7146d

structural-variant calling with sniffles

sniffles structural-variant calling long-read

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @christopher-hakkaart @yuukiiwa

Maintainers: @christopher-hakkaart @yuukiiwa @fellen31

structural-variant calling with sniffles

Add the following snippet to your workflow script to include this module.

include { SNIFFLES } from 'nf-core/sniffles'

MIT License

Process

`Name`	`SNIFFLES`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`input` file	A single .bam/.cram file - OR - one or more .snf files - OR - a single .tsv file containing a list of .snf files and optional sample ids as input `*.{bam,cram,snf,tsv}`
`index` file	Index of BAM/CAM file `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'fasta' ]
`fasta` file	Reference database in FASTA format

#3 tuple

`meta3` map	Groovy Map containing tandem repeat information e.g. [ id:'hg38' ]
`tandem_file` file	Tandem repeat file `*.bed`

`vcf_output` file	VCF output file `*.vcf.gz`

`snf_output` file	SNF output file

Output 4 channels

#1 snf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.snf` file	SNF file `*.snf`

#2 tbi tuple

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

#3 vcf tuple

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

#4 versions_sniffles tuple

`${task.process}` string	The name of the process
`sniffles` string	The name of the tool
`sniffles --version \| sed 's/.* //g'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
sniffles	a fast structural variant caller for long-read sequencing	https://github.com/fritzsedlazeck/Sniffles

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:15:15 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsniffles/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sniffles/blobs/sha256:8725eaf7cd59dcd048a20460131dfac1913cfebc0785a79175199c66ad506a04
Size	4.8 KB
Checksum	sha256:8725eaf7cd59dcd048a20460131dfac1913cfebc0785a79175199c66ad506a04
Downloads	1

Version	Date	Status