Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
ipbam{:bash}
:file
The ChIP-seq treatment file
controlbam{:bash}
:file
The control file
macs2_gsize{:bash}
: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
peak{:bash}
meta{:bash}
:file
BED file containing annotated peaks
*.gappedPeak,*.narrowPeak}
*.{narrowPeak,broadPeak}{:bash}
:file
BED file containing annotated peaks
*.gappedPeak,*.narrowPeak}
xls{:bash}
meta{:bash}
:file
BED file containing annotated peaks
*.gappedPeak,*.narrowPeak}
*.xls{:bash}
:file
xls file containing annotated peaks
*.xls
versions{:bash}
versions.yml{:bash}
:file
File containing software version
versions.yml
gapped{:bash}
meta{:bash}
:file
BED file containing annotated peaks
*.gappedPeak,*.narrowPeak}
*.gappedPeak{:bash}
:file
Optional BED file containing gapped peak
*.gappedPeak
bed{:bash}
meta{:bash}
:file
BED file containing annotated peaks
*.gappedPeak,*.narrowPeak}
*.bed{:bash}
:file
Optional BED file containing peak summits locations for every peak
*.bed
bdg{:bash}
meta{:bash}
:file
BED file containing annotated peaks
*.gappedPeak,*.narrowPeak}
*.bdg{:bash}
:file
Optional bedGraph files for input and treatment input samples
