fix: proper error message when defining cache eligibility for rules with multiple output files and no multiext declaration.

snakemake/caching/__init__.py

@@ -47,6 +47,9 @@ def get_outputfiles(self, job: Job):
             )
             yield from ((f, f[prefix_len:]) for f in job.output)
         else:
+            assert (
+                len(job.output) == 1
+            ), "bug: multiple output files in cacheable job but multiext not used for declaring them"
             yield (job.output[0], "")
 
     def raise_write_error(self, entry, exception=None):

snakemake/caching/local.py

@@ -95,6 +95,12 @@ def fetch(self, job: Job):
             if not cachefile.exists():
                 self.raise_cache_miss_exception(job)
 
+            logger.debug(
+                "Output file {} exists as {} in the cache.".format(
+                    outputfile, cachefile
+                )
+            )
+
             self.check_readable(cachefile)
             if cachefile.is_dir():
                 # For directories, create a new one and symlink each entry.

snakemake/workflow.py

@@ -1541,6 +1541,14 @@ def decorate(ruleinfo):
                 rule.is_handover = True
 
             if ruleinfo.cache is True:
+                if len(rule.output) > 1:
+                    if not rule.output[0].is_multiext:
+                        raise WorkflowError(
+                            "Rule is marked for between workflow caching but has multiple output files. "
+                            "This is only allowed if multiext() is used to declare them (see docs on between "
+                            "workflow caching).",
+                            rule=rule,
+                        )
                 if not self.enable_cache:
                     logger.warning(
                         "Workflow defines that rule {} is eligible for caching between workflows "

tests/test_cache_multioutput/Snakefile

@@ -0,0 +1,7 @@
+rule a:
+    output:
+        "1.txt",
+        "2.txt",
+    cache: True
+    shell:
+        "touch {output}"

tests/tests.py

@@ -1397,3 +1397,7 @@ def test_modules_ruledeps_inheritance():
 @skip_on_windows
 def test_conda_named():
     run(dpath("test_conda_named"), use_conda=True)
+
+
+def test_cache_multioutput():
+    run(dpath("test_cache_multioutput"), shouldfail=True)