Simulate an SV VCF file based on a reference genome
meta{:bash}
:map
Groovy Map containing fasta information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
fasta{:bash}
:file
The reference genome
*.{fasta,fna,fa}
meta2{:bash}
Groovy Map containing fasta index information e.g. [ id:'test', single_end:false ]
fai{:bash}
The index of the reference genome
*.fai
meta3{:bash}
Groovy Map containing parameters information e.g. [ id:'test', single_end:false ]
parameters{:bash}
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{:bash}
:float
The SNP mutation frequency in the output VCF (0-1)
sim_reads{:bash}
:integer
Whether or not to simulate reads (1==yes, else no)
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.txt{:bash}
The created parameters file
vcf{:bash}
*.vcf{:bash}
A VCF containing the simulated variants
*.vcf
bed{:bash}
*.bed{:bash}
A BED file of the simulated structural variants
*.bed
*.fasta{:bash}
A Fasta file file containing the variants from the output VCF
*.fasta
insertions{:bash}
*.insertions.fa{:bash}
A Fasta file file containing insertion sequences
*.insertions.fa
versions_survivor{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
survivor{:bash}
The name of the tool
SURVIVOR 2>&1 | grep 'Version' | sed 's/Version: //'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Toolset for SV simulation, comparison and filtering
