Use wildcards conditionals to further combine rules

Use wildcard conditionals to further combine rules that take a different
set of input files for the genome and E gene builds.

Case 1: The E gene build excludes the "augur clades" command, resulting in the
absence of a clades_{serotype}_E.json file in the E gene export rule.

Case 2: The reference Genbank files for E genes are dynamically generated
in the results folder.

phylogenetic/Snakefile

@@ -15,9 +15,7 @@ include: "rules/prepare_sequences.smk"
 include: "rules/prepare_sequences_E.smk"
 include: "rules/construct_phylogeny.smk"
 include: "rules/annotate_phylogeny.smk"
-include: "rules/annotate_phylogeny_E.smk"
 include: "rules/export.smk"
-include: "rules/export_E.smk"
 
 # Include custom rules defined in the config.
 if "custom_rules" in config:

phylogenetic/rules/annotate_phylogeny.smk

@@ -42,11 +42,12 @@ rule ancestral:
 rule translate:
     """Translating amino acid sequences"""
     input:
-        tree = "results/tree_{serotype}_genome.nwk",
-        node_data = "results/nt-muts_{serotype}_genome.json",
-        reference = "config/reference_dengue_{serotype}.gb"
+        tree = "results/tree_{serotype}_{gene}.nwk",
+        node_data = "results/nt-muts_{serotype}_{gene}.json",
+        # The genbank references for the E gene are dynamically generated files located within the results folder.
+        reference = lambda wildcard: "config/reference_dengue_{serotype}.gb" if wildcard.gene in ["genome"] else "results/config/reference_dengue_{serotype}_{gene}.gb"
     output:
-        node_data = "results/aa-muts_{serotype}_genome.json"
+        node_data = "results/aa-muts_{serotype}_{gene}.json"
     shell:
         """
         augur translate \

phylogenetic/rules/export.smk

@@ -40,7 +40,7 @@ rule colors:
 rule prepare_auspice_config:
     """Prepare the auspice config file for each serotypes"""
     output:
-        auspice_config="results/config/auspice_config_{serotype}.json",
+        auspice_config="results/config/auspice_config_{serotype}_{gene}.json",
     params:
         replace_clade_key="clade_membership",
         replace_clade_title=lambda wildcard: r"Serotype" if wildcard.serotype in ['all'] else r"DENV genotype",
@@ -109,17 +109,17 @@ rule prepare_auspice_config:
 rule export:
     """Exporting data files for auspice"""
     input:
-        tree = "results/tree_{serotype}_genome.nwk",
+        tree = "results/tree_{serotype}_{gene}.nwk",
         metadata = "data/metadata_{serotype}.tsv",
-        branch_lengths = "results/branch-lengths_{serotype}_genome.json",
-        traits = "results/traits_{serotype}_genome.json",
-        clades = "results/clades_{serotype}_genome.json",
-        nt_muts = "results/nt-muts_{serotype}_genome.json",
-        aa_muts = "results/aa-muts_{serotype}_genome.json",
-        auspice_config = "results/config/auspice_config_{serotype}.json",
+        branch_lengths = "results/branch-lengths_{serotype}_{gene}.json",
+        traits = "results/traits_{serotype}_{gene}.json",
+        clades = lambda wildcard: "results/clades_{serotype}_{gene}.json" if wildcard.gene in ['genome'] else [],
+        nt_muts = "results/nt-muts_{serotype}_{gene}.json",
+        aa_muts = "results/aa-muts_{serotype}_{gene}.json",
+        auspice_config = "results/config/auspice_config_{serotype}_{gene}.json",
         colors = "results/colors_{serotype}.tsv",
     output:
-        auspice_json = "results/raw_dengue_{serotype}_genome.json",
+        auspice_json = "results/raw_dengue_{serotype}_{gene}.json",
     params:
         strain_id = config.get("strain_id_field", "strain"),
     shell: