Description

Simulate an SV VCF file based on a reference genome

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing fasta information
e.g. [ id:'test', single_end:false ]

fasta (file)

The reference genome

*.{fasta,fna,fa}

meta2 (map)

Groovy Map containing fasta index information
e.g. [ id:'test', single_end:false ]

fai (file)

The index of the reference genome

*.fai

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

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

versions (file)

File containing software versions

versions.yml

parameters (file)

The created parameters file

*.txt

vcf (file)

A VCF containing the simulated variants

*.vcf

bed (file)

A BED file of the simulated structural variants

*.bed

fasta (file)

A Fasta file file containing the variants from the output VCF

*.fasta

insertions (file)

A Fasta file file containing insertion sequences

*.insertions.fa