From bffcbfdc9360881016339d2fa4a9ae7c817e3f0d Mon Sep 17 00:00:00 2001
From: Johannes Koester <johannes.koester@uni-due.de>
Date: Tue, 23 Jan 2024 10:37:29 +0100
Subject: [PATCH] fix: further adaptation to Snakemake 8

---
 workflow/Snakefile        |  4 ----
 workflow/rules/common.smk | 37 ++++++++++++++++++++++---------------
 2 files changed, 22 insertions(+), 19 deletions(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index 0321906..5bc14bc 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -10,10 +10,6 @@ report: "report/report.rst"
 configfile: "config/config.yaml"
 
 
-envvars:
-    "ZENODO_TOKEN",
-
-
 include: "rules/common.smk"
 
 
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 7137324..de8ddc9 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -1,24 +1,31 @@
+def get_zenodo_tag(entry):
+    if "restricted-access-token-envvar" in entry:
+        return f"zenodo_{entry['deposition']}"
+    else:
+        return "zenodo"
+
+
 # add path to callsets
 for key, callset in config["variant-calls"].items():
-    if "path" not in callset and "zenodo" in callset:
-        filename = callset["zenodo"]["filename"]
-        callset["path"] = f"resources/zenodo/variant-calls/{key}/{filename}"
+    if "zenodo" in callset:
+        if "path" not in callset:
+            filename = callset["zenodo"]["filename"]
+            callset["path"] = f"resources/zenodo/variant-calls/{key}/{filename}"
+        tag = get_zenodo_tag(callset["zenodo"])
+        if tag != "zenodo":
+            workflow.storage_registry.register_storage(
+                provider="zenodo",
+                tag=tag,
+                restricted_access_token=os.environ[
+                    callset["zenodo"]["restricted-access-token-envvar"]
+                ],
+            )
 
 
 def get_zenodo_input(wildcards):
     entry = config[wildcards.section][wildcards.entry]["zenodo"]
 
-    provider = "zenodo"
-    if "restricted-access-token-envvar" in entry:
-        tag = f"zenodo_{entry['deposition']}"
-        storage.register_storage(
-            provider="zenodo",
-            tag=tag,
-            restricted_access_token=os.environ[
-                entry["restricted-access-token-envvar"]
-            ],
-        )
-        provider = tag
-    return getattr(storage, provider)(
+    tag = get_zenodo_tag(entry)
+    return getattr(storage, tag)(
         f"zenodo://record/{entry['deposition']}/{entry['filename']}"
     )