custom_consensuspeaks

Find consensus peaks from two or more peak files. The consensus_peaks subworkflow is a re-implementation of this module; new pipelines should use the subworkflow instead.

nf-core modules \
  --git-remote https://github.com/CCBR/nf-modules \
  install custom/consensuspeaks

https://github.com/CCBR/nf-modules/…/modules/CCBR/custom/consensuspeaks/

Input

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]	NA
peaks	file	Peak files	*.{broadPeak,narrowPeak,bed}

Output

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]	NA
peaks	file	A single consensus peak file	*.{broadPeak,narrowPeak,bed}
versions	file	File containing software versions	versions.yml

Tools

Python

Home       Python License 2.0

The Python Programming Language

bedtools

  Docs     MIT

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

bedops

  Docs   Code   GPLv2

fast, highly scalable and easily-parallelizable genome analysis toolkit

bedSort

  Docs    

UCSC Genome Browser tool for sorting .bed files by chrom,chromStart.