Running partial workflow

[AroneyS]

Is there a way to only run the marker identification and MSA? I do not need the downstream products.

[fasnicar]

Hi there, not specifically as an option. You could though either (1) kill the job as soon as the MSA step is done, (2) edit the code to introduce a step right after the call of the msas() function, (3) in a separate script import PhyloPhlAn as a library and only call the gene_markers_identification(), gene_markers_selection(), gene_markers_extraction(), and msas() functions for your specific analysis.

I hope this helps.

Thanks, Francesco