QC options in biobakery workflow

Infrastructure and utilities bioBakery workflows
1

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
–qc-options=“–bypass-trf”
–qc-options=“–run-fastqc-start”
–bypass-taxonomic-profiling
–bypass-functional-profiling
–bypass-strain-profiling

2

I think I figured it out and it works if I stack the qc options together like so

biobakery_workflows wmgx --input Trial_Run --output Kneaddata_Output
–qc-options=“–bypass-trf –run-fastqc-start”
–bypass-taxonomic-profiling
–bypass-functional-profiling
–bypass-strain-profiling

3

Yes, you are right! Thank you for posting the solution and sorry for the slow response on our end.

Thanks!
Lauren