params_clearlabs.yaml

# The parameters "input", "bams", "assemblies" and "output" are the absolute paths of the folders. Do not include the "/" at the end of the paths.
input     : "/blue/bphl-florida/dongyibo/Dev_module_DaytonaCombine/fastqs"
bams      : "/blue/bphl-florida/dongyibo/Dev_module_DaytonaCombine/bams"
assemblies : "/blue/bphl-florida/dongyibo/Dev_module_DaytonaCombine/assemblies"
output    : "/blue/bphl-florida/dongyibo/Dev_module_DaytonaCombine/output"

# comma separated list of SOTCs to screen, default as "S:L452R,S:E484K"
sotc : "S:L452R,S:E484K"

#Do not change the parameter settings below:
pangolin_docker  : "docker://staphb/pangolin:4.1.2-pdata-1.13"
pangolin_version : "v4.1.2"
pangolin_data_version : "v1.13"