custom_formatmergedbed

Reformat consensus peaks from bedtools merge. Used in the consensus_peaks subworkflow.

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

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

Input

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]	NA
merged_bed	file	Merged output file from calling

bedtools merge -c 1,5,6,7,8,9 -o count,collapse,collapse,collapse,collapse,collapse on a concatenated & sorted peak file |*.bed |

Output

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]	NA
bed	file	A narrow peak bed file with the best p-value for each consensus peak	NA
versions	file	File containing software versions	versions.yml

Tools

R

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