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