Description

Sorts a feature file by chromosome and other criteria.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

intervals:file

BED/BEDGRAPH

*.{bed|bedGraph}

genome_file:file

Optional reference genome 2 column file that defines the expected chromosome order.

*.{fai,txt,chromsizes}

Output

name:type
description
pattern

sorted

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.${extension}:file

Sorted output file

*.${extension}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

bedtools
MIT

A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.