Sorts a feature file by chromosome and other criteria.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
intervals
:file
BED/BEDGRAPH
*.{bed|bedGraph}
genome_file
Optional reference genome 2 column file that defines the expected chromosome order.
*.{fai,txt,chromsizes}
suffix
:string
Extension of the output file (e.g. “bed”, “bam”, “txt”), which depends on the arguments used. If empty, the extension of intervals1 is used.
sorted
*.${extension}
Sorted output file
versions_bedtools
${task.process}
The name of the process
bedtools
The name of the tool
bedtools --version | sed -e 's/bedtools v//g'
:eval
The expression to obtain the version of the tool
versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
