bedtools_map

Allows one to screen for overlaps between two sets of genomic 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/map

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

Input

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]	NA
intervals1	file	BAM/BED/GFF/VCF	*.{bed|gff|vcf}
intervals2	file	BAM/BED/GFF/VCF	*.{bed|gff|vcf}
meta2	map	Groovy Map containing reference chromosome sizes
e.g. [ id:‘test’ ]	NA
chrom_sizes	file	Chromosome sizes file	*{.sizes,.txt}

Output

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]	NA
map	file	File containing the description of overlaps found between the features in A and the features in B, with statistics	*.${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.