Convert a BED file to a VCF file according to a YAML config
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
bed{:bash}
:file
The BED file to convert to VCF
*.bed
config{:bash}
The config file to use for the conversion
*.{yml,yaml}
meta2{:bash}
Groovy Map containing fasta index information e.g. [ id:'test', single_end:false ]
fai{:bash}
The fasta index file
*.fai
vcf{:bash}
*.vcf.gz{:bash}
The converted VCF file
*.vcf.gz
versions_bedgovcf{:bash}
${task.process}{:bash}
:string
The process name
bedgovcf{:bash}
The tool name
bedgovcf --version 2>&1 | sed 's/^bedgovcf version //'{:bash}
:eval
The tool version
versions_bgzip{:bash}
bgzip{:bash}
bgzip --version | head -1 | sed "s/bgzip (htslib) //"{:bash}
The expression to obtain the version of the tool
versions{:bash}
A simple tool to convert BED files to VCF files
