I realized that --illumination manual may be semi-redundant with including the ffp and/or dfp columns in the sample sheet. We should either add a check in PIPELINE_INITIALISATION that these two things are aligned, or rethink the interface to this feature (perhaps the presence of user-provided illumination profiles would imply illumination="manual" and the illumination param would only serve to invoke basicpy or another future tool).
Description of feature
I realized that
--illumination manualmay be semi-redundant with including theffpand/ordfpcolumns in the sample sheet. We should either add a check in PIPELINE_INITIALISATION that these two things are aligned, or rethink the interface to this feature (perhaps the presence of user-provided illumination profiles would imply illumination="manual" and theilluminationparam would only serve to invoke basicpy or another future tool).