From a901a807fac816db4ccbf8e85bfeba4e8201ea1a Mon Sep 17 00:00:00 2001
From: Ivan Blagoev Topolsky <ivan.topolsky@bsse.ethz.ch>
Date: Wed, 26 Jul 2023 23:58:25 +0200
Subject: [PATCH] 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           |  7 -------
 workflow/rules/common.smk    | 11 +++++++++++
 workflow/rules/consensus.smk |  2 +-
 3 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index 94344d05..435db60e 100644
--- a/workflow/Snakefile
+++ b/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:
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 67e2240a..f673c269 100644
--- a/workflow/rules/common.smk
+++ b/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,
+)
diff --git a/workflow/rules/consensus.smk b/workflow/rules/consensus.smk
index df4f5c64..66d5b4eb 100644
--- a/workflow/rules/consensus.smk
+++ b/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: