Convert gtf format to bed format
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
gtf{:bash}
:file
A reference file in GTF format
*.{gtf,gtf.gz}
bed{:bash}
A reference file in BED format
*.{bed}
*.bed{:bash}
versions_bedops{:bash}
${task.process}{:bash}
:string
The name of the process
bedops{:bash}
The name of the tool
bedops --version | sed -n "s/.*version: *\([^ ]*\).*/\1/p"{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
The gtf2bed script converts 1-based, closed [start, end] Gene Transfer Format v2.2 (GTF2.2) to sorted, 0-based, half-open [start-1, end) extended BED-formatted data.
