bedtools_sort

Sorts a feature file by chromosome and other criteria. Adapted from https://github.com/nf-core/modules/tree/fff2c3fc7cdcb81a2a37c3263b8ace9b353af407/modules/nf-core/bedtools

nf-core modules \
  --git-remote https://github.com/CCBR/nf-modules \
  install bedtools/sort

https://github.com/CCBR/nf-modules/…/modules/CCBR/bedtools/sort/

Input

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]	NA
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:false ]	NA
sorted	file	Sorted output file	*.${extension}
versions	file	File containing software versions	versions.yml

Tools

bedtools

  Docs     MIT

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