config.yaml

## General pipeline parameters:
# Name of the pipeline:
pipeline: "Pausing Site Detection Pipeline"
# Repository URL:
repo: ""

## Pipeline-specific parameters
#bedGraph files should be in "Data" folder
sample:
  neg: "samplename.neg.bedGraph"
  pos: "samplename.pos.bedGraph"

prefix: "samplename"

#bed6 file with regions to mask eg. chrY for female cell line
#full path necessary
mask_bed: "masked.bed"

#bed6 files used to assign peaks to regions
#full path necessary
region_bed: "Regions.bed"

#size of the window used to calculate the local read density
window_size: 200

#minimal number of reads to call a peak
minimum_intensity: 5

#should reads with no supporting density in the window be included
include_spikes: FALSE

#number of redistributions of reads done to obtain the distribution of
#the expected maximum
bootstrap_N: 10000

#adjusted pvalue required to report as significant
padj: 0.05