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     : "/path/to/fastqs"
bams      : "/path/to/bams"
assemblies : "/path/to/assemblies"
output    : "/path/to/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:4.3.1-pdata-1.25.1"
pangolin_version : "v4.3.1"
pangolin_data_version : "v1.25.1"

vadr_docker : "docker://staphb/vadr:1.3"
samtools_docker : "docker://staphb/samtools:1.12"
nextclade_docker : "docker://nextstrain/nextclade:0.14.1"