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
