fix: fix function call when creating report and hashes for between wo…

…rkflow caching (#1198)

* Fix report

* black fmt

* fix: hashing of scripts, notebooks and wrappers

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

snakemake/caching/hash.py

@@ -50,7 +50,7 @@ def _get_provenance_hash(self, job: Job):
             # resources, and filenames (which shall be irrelevant for the hash).
             h.update(job.rule.shellcmd.encode())
         elif job.is_script:
-            _, source, _ = script.get_source(
+            _, source, _, _ = script.get_source(
                 job.rule.script,
                 job.rule.workflow.sourcecache,
                 basedir=job.rule.basedir,
@@ -59,7 +59,7 @@ def _get_provenance_hash(self, job: Job):
             )
             h.update(source)
         elif job.is_notebook:
-            _, source, _ = script.get_source(
+            _, source, _, _ = script.get_source(
                 job.rule.notebook,
                 job.rule.workflow.sourcecache,
                 basedir=job.rule.basedir,
@@ -68,7 +68,7 @@ def _get_provenance_hash(self, job: Job):
             )
             h.update(source)
         elif job.is_wrapper:
-            _, source, _ = script.get_source(
+            _, source, _, _ = script.get_source(
                 wrapper.get_script(job.rule.wrapper, prefix=workflow.wrapper_prefix),
                 job.rule.workflow.sourcecache,
                 basedir=job.rule.basedir,

snakemake/report/__init__.py

@@ -260,26 +260,27 @@ def code(self):
             language = "bash"
         elif self._rule.script is not None and not contains_wildcard(self._rule.script):
             logger.info("Loading script code for rule {}".format(self.name))
-            _, source, language = script.get_source(
+            _, source, language, _ = script.get_source(
                 self._rule.script, self._rule.workflow.sourcecache, self._rule.basedir
             )
             sources = [source.decode()]
         elif self._rule.wrapper is not None and not contains_wildcard(
             self._rule.wrapper
         ):
             logger.info("Loading wrapper code for rule {}".format(self.name))
-            _, source, language = script.get_source(
+            _, source, language, _ = script.get_source(
                 wrapper.get_script(
                     self._rule.wrapper,
                     self._rule.workflow.sourcecache,
                     prefix=self._rule.workflow.wrapper_prefix,
-                )
+                ),
+                self._rule.workflow.sourcecache,
             )
             sources = [source.decode()]
         elif self._rule.notebook is not None and not contains_wildcard(
             self._rule.notebook
         ):
-            _, source, language = script.get_source(
+            _, source, language, _ = script.get_source(
                 self._rule.notebook, self._rule.workflow.sourcecache, self._rule.basedir
             )
             language = language.split("_")[1]