How is param "orientation" in `rename_star_rpm_for_alfa` used?
The rule rename_star_rpm_for_alfa contains a param section, with orientation specified. The pipeline documentation also states that the renaming depends on library orientation, which will be derived from the kallisto_directionality. However, I do not understand where in the Snakefile the parameter is called, orientation is never mentioned again. Is this expanded as a wildcard somewhere?
Thanks for double-checking. Main Snakefile line 1042.