Update QC thresholds
The strains are assigned a green/orange/red status at the end of script 10. The thresholds for assigning status are not well defined for SARS-CoV-2, because they are too strict (Tim to provide new thresholds) => we need to update the thresholds, which are hard-coded in this file: https://gitlab.sib.swiss/SPSP/spsp-tools/-/blob/master/pipeline/generate_trimming-cleaning_report.pl
Could you please make a virus-specific script based on "generate_trimming-cleaning_report.pl" that will be called from script 10 (i.e. script 00 with
$CLADE = 'virus'). I could then update the thresholds in that new file as soon as I get them from Tim, thanks a lot.