Prodigal training files are moved in Makefile but not in config files

[samuell]

Just noted (after a Makefile update and trying to run an MRSA analysis) that the prodigal training files are moved into assets/prodigal_training_files, which makes sense and looks good.

But in the config files, the paths still point to cgmlst/<species>/alleles_rereffed/<Species>.trn (and cgmlst/<species>/ecoli_INNUENDO_wgMLST/<Species>.trn for E.coli).

I'm a little confused about how the CI pipeline is still working though 🤔

[samuell]

Well, turns out both the old and the new paths are used in the Makefile:

$ grep Staphylococcus_aureus.trn Makefile 
staphylococcus_aureus_download_prodigal_training_file: $(PRODIGAL_TRAINING_DIR)/Staphylococcus_aureus.trn
$(PRODIGAL_TRAINING_DIR)/Staphylococcus_aureus.trn:
        && wget https://raw.githubusercontent.com/B-UMMI/chewBBACA/master/CHEWBBACA/prodigal_training_files/Staphylococcus_aureus.trn \
staphylococcus_aureus_prep_cgmlst_schema: | $(SAUR_CGMLST_DIR)/alleles_rereffed/Staphylococcus_aureus.trn
$(SAUR_CGMLST_DIR)/alleles_rereffed/Staphylococcus_aureus.trn: $(SAUR_CGMLST_DIR)/alleles_rereffed
                --ptf $(PRODIGAL_TRAINING_DIR)/Staphylococcus_aureus.trn |& tee -a $(INSTALL_LOG)

So, both $(PRODIGAL_TRAINING_DIR) and $(SAUR_CGMLST_DIR)/alleles_rereffed is used, for S. Aureus, for example.

Maybe it is fine? It just looked a little off at a quick glance ... ?