Tired of clicking through Galaxy? Here are some ad hoc scripts to run ARTIC COVID19 Galaxy workflow.
Runs ARTICv3 COVID-19 variation workflow. Takes shared data library name as argument. Parses automatically data library subfolders and runs workflow separately on each subfolder.
ARTICv3 primer bed file and NC_045512 reference genome fasta are imported from separate history (update their ids respectively).
python scripts/run_articv3_pe.py covid210407 > covid210407.log