Nextflow Registry | nf-core/survivor/simsv@0.0.0-6c4ed3a

nf-core/survivor/simsv @ 0.0.0-6c4ed3a

Simulate an SV VCF file based on a reference genome

structural variants simulation sv vcf

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

Simulate an SV VCF file based on a reference genome

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

include { SURVIVOR_SIMSV } from 'nf-core/survivor/simsv'

MIT License

Process

`Name`	`SURVIVOR_SIMSV`

Input 5 channels

#1 tuple

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

#2 tuple

`meta2` map	Groovy Map containing fasta index information e.g. `[ id:'test', single_end:false ]`
`fai` file	The index of the reference genome `*.fai`

#3 tuple

`meta3` map	Groovy Map containing parameters information e.g. `[ id:'test', single_end:false ]`
`parameters` file	A text file containing the parameters to be used for the simulation. Gets automatically generated using defaults when this is not supplied `*.txt`

`snp_mutation_frequency` float	The SNP mutation frequency in the output VCF (0-1)

`sim_reads` integer	Whether or not to simulate reads (1==yes, else no)

Output 6 channels

#1 bed tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.bed` file	A BED file of the simulated structural variants `*.bed`

#2 vcf tuple

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

#3 fasta tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.fasta` file	A Fasta file file containing the variants from the output VCF `*.fasta`

#4 insertions tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.insertions.fa` file	A Fasta file file containing insertion sequences `*.insertions.fa`

#5 parameters tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.txt` file	The created parameters file `*.txt`

#6 versions_survivor tuple

`${task.process}` string	The process the versions were collected from
`survivor` string	The name of the tool
`SURVIVOR 2>&1 \| grep 'Version' \| sed 's/Version: //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
survivor	Toolset for SV simulation, comparison and filtering	https://github.com/fritzsedlazeck/SURVIVOR/wiki

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:47:54 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsurvivor%2Fsimsv/0.0.0-6c4ed3a/download