Hi I am trying to use just Kneaddata on multiple samples using the biobakery workflow. I would like to edit some qc options. However, when I do this, only the last QC option runs. For example, here only the FASTQC start runs and bypass trf does not. If I switch them, only the bypass trf runs, not the fastqc. This is also the case if I run 3 or more qc options. What am I doing wrong? How do I get more than one qc option to run?
biobakery_workflows wmgx --input Trial_Run --output Kneaddata_Output