Convert VCF with structural variations to CytoSure format
meta
:map
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
sv_vcf
:file
VCF file with structural variants
*.{vcf,vcf.gz}
meta2
coverage_bed
Bed file with coverage data
*.bed
meta3
cns
CN file from CNVkit, not compatible with coverage_bed file
meta4
snv_vcf
VCF file with SNVs to calculate probe coverage, not compatible with coverage_bed pattern: ”*.{vcf,vcf.gz}”
blacklist_bed
Bed file with regions to exclude
cgh
*.cgh
SV:s in CytoSure format
versions_vcf2cytosure
${task.process}
:string
The name of the process
vcf2cytosure
The name of the tool
vcf2cytosure --version 2>&1 | sed -n 's/.*cytosure //p'
:eval
The expression to obtain the version of the tool
versions
