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