Description

Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

ipbam (file)

The ChIP-seq treatment file

controlbam (file)

The control file

macs2_gsize (string)

Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:‘hs’ for human (2.7e9), ‘mm’ for mouse (1.87e9), ‘ce’ for C. elegans (9e7) and ‘dm’ for fruitfly (1.2e8)

Output

Name (Type)
Description
Pattern

versions (file)

File containing software version

versions.yml

peak (file)

BED file containing annotated peaks

*.gappedPeak,*.narrowPeak}

xls (file)

xls file containing annotated peaks

*.xls

gapped (file)

Optional BED file containing gapped peak

*.gappedPeak

bed (file)

Optional BED file containing peak summits locations for every peak

*.bed

bdg (file)

Optional bedGraph files for input and treatment input samples

*.bdg

Tools