bedtools_merge

combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features. 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/merge

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

Input

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]	NA
bed	file	Input BED file	*.{bed}
args	string	optional arguments for bedtools merge	NA

Output

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]	NA
bed	file	Overlapped bed file with combined features	*.{bed}
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.