config.yaml

#this is the main csv which contains the important information for all the following steps, it should be formated as samples.csv example
sampleCSVpath: /home/annbrown/data/nitin/data/CL0162/CL0162/sample.csv
#this is the full path to this pwgs_folder
pipeline_folder: /home/annbrown/data/nitin/pwgs_snakemake/


##every folder path should end in a trailing backslash, errors might crop up otherwise
##FACETS parameters
#path of output
cnv_files_folder : /home/annbrown/data/nitin/pwgs_inputs/


##PWGS pre-parsing
#this is where the parsed data is going to go
outputdirPhyloInput:  /home/annbrown/data/nitin/pwgs_inputs/
#if you don't want subsampling leave as " ". if you want a sample leave as " -s ### " with the spaces
subsampling: " "

##PWGS
#this is where pwgs is going to write the results of the multievolve.py script
outputdirPhyloOutput: /home/annbrown/data/nitin/pwgs_output/
#this is where all the PWGS python scripts are located
pwgsPythonDir: /home/annbrown/data/nitin/phylowgs/
#this is the data directory of the Witness viewer, the bottom folder should always be /data/
#a folder for each 'patient' or 'run', will be written here
outputdirWitness: /home/annbrown/data/nitin/pwgs_output/witness/data/
#number of chains that it should be run with
n_chains: 20
##multisample or single sample
multisample: True

##PWGS output parsing
#final output folder for the parsed tree data of PWGS
parsedOutputPWGS: /home/annbrown/data/nitin/pwgs_output/
#how many of the top trees do you want to look at?
k_trees: 30