Minor refinements

workflow/rules/pileup.smk

@@ -118,6 +118,7 @@ rule all_pileups:
             if "all-merged-samples" in config["settings"]["pileups"]
             else []
         ),
+        "mapping/final.done"
     output:
         touch("mpileup/all-pileups.done"),
 

workflow/rules/prepare-reference.smk

@@ -101,6 +101,10 @@ elif config["data"]["reference-genome-download"]["full-url"]:
         shell:
             "(curl -L {params.url} >> {output[0]}) > {log} 2>&1"
 
+    localrules:
+        download_reference_genome,
+
+
 else:
 
     rule download_reference_genome:
@@ -129,9 +133,8 @@ else:
         wrapper:
             "v3.13.6/bio/reference/ensembl-sequence"
 
-
-localrules:
-    download_reference_genome,
+    localrules:
+        download_reference_genome,
 
 
 # =================================================================================================
@@ -390,6 +393,11 @@ elif config["data"]["known-variants-download"]["full-url"]:
         script:
             "../scripts/ensembl-variation.py"
 
+
+    localrules:
+        download_known_variants,
+
+
 else:
 
     rule download_known_variants:
@@ -418,6 +426,10 @@ else:
             "v3.13.6/bio/reference/ensembl-variation"
 
 
+    localrules:
+        download_known_variants,
+
+
 # =================================================================================================
 #     Known Variants Processing
 # =================================================================================================