BugFix: paths for snakedeploy (fix: #147)

- "function.sh" script path:
  when running directly from github, caching path logic is different
  and causes a 404 when run from main Snakefile
- cache input that could be fetched from resources/ gene GFF

workflow/Snakefile

@@ -12,13 +12,6 @@ LOGGER.info("VPIPE_BASEDIR = %s", VPIPE_BASEDIR)
 include: "rules/common.smk"
 
 
-functions = cachepath(
-    "scripts/functions.sh",
-    executable=True,
-    localsource=True,
-)
-
-
 # DUMMY RULES
 rule all:
     input:

workflow/rules/common.smk

@@ -948,3 +948,14 @@ def temp_prefix(p):
 
 def temp_with_prefix(p):
     return temp(temp_prefix(p))
+
+
+###############
+#   Globals   #
+###############
+
+functions = cachepath(
+    "../scripts/functions.sh",
+    executable=True,
+    localsource=True,
+)

workflow/rules/consensus.smk

@@ -186,7 +186,7 @@ rule frameshift_deletions_checks:
         BAM=alignment_wildcard,
         #REF_majority_dels="{dataset}/references/ref_majority_dels.fasta",
         REF_majority_dels="{dataset}/references/consensus.bcftools.fasta",
-        GENES_GFF=(config.input["genes_gff"] if config.input["genes_gff"] else []),
+        GENES_GFF=(cachepath(config.input["genes_gff"]) if config.input["genes_gff"] else []),
     output:
         FRAMESHIFT_DEL_CHECK_TSV="{dataset}/references/frameshift_deletions_check.tsv",
     params: