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

meta (map)

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

]

sorted (file)

Sorted output file

*.${extension}

versions (file)

File containing software versions

versions.yml
included in
hicar nascent radseq ssds
authors
Github user Emiller88 Github user sruthipsuresh Github user drpatelh Github user chris-cheshire Github user adamrtalbot
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

bedtools
MIT

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

bedtools.readthedocs.io/en/latest/content/tools/sort