fix: do not wait for named or containerized conda envs

snakemake/jobs.py

@@ -1015,7 +1015,10 @@ def get_wait_for_files(self):
             self.dag.workflow.use_conda
             and self.conda_env
             and not self.conda_env.is_named
+            and not self.conda_env.is_containerized
         ):
+            # Named or containerized envs are not present on the host FS,
+            # hence we don't need to wait for them.
             wait_for_files.append(self.conda_env.address)
         return wait_for_files
 

tests/test_github_issue1469/Snakefile

@@ -0,0 +1,22 @@
+ruleorder: single_file > both_files
+
+
+rule all:
+    input:
+        "foo.txt",
+        "bar.txt",
+
+
+rule both_files:
+    output:
+        "foo.txt",
+        "bar.txt",
+    shell:
+        "if [[ -e foo.txt ]]; then exit 1; fi; touch {output}"
+
+
+rule single_file:
+    output:
+        "foo.txt",
+    shell:
+        "if [[ -e foo.txt ]]; then exit 1; fi; touch {output}"