Re-enable bash strict mode on Linux (#1135)

snakemake/shell.py

@@ -85,6 +85,8 @@ def executable(cls, cmd):
                     )
                 cls._process_prefix = "set -euo pipefail; "
                 cls._win_command_prefix = "-c"
+        elif os.path.split(cmd)[-1].lower() == "bash":
+            cls._process_prefix = "set -euo pipefail; "
         cls._process_args["executable"] = cmd
 
     @classmethod

tests/test_strict_mode/Snakefile

@@ -0,0 +1,12 @@
+shell.executable("bash")
+
+rule a:
+    output:
+        "test.out"
+    shell:
+        """
+        echo 'prints 1'
+        $(exit 1)  # Should fail with set -e
+        echo 'prints 2'
+        echo 'hello' > {output}
+        """

tests/tests.py

@@ -1286,3 +1286,7 @@ def test_touch_pipeline_with_temp_dir():
 
 def test_all_temp():
     run(dpath("test_all_temp"), all_temp=True)
+
+
+def test_strict_mode():
+    run(dpath("test_strict_mode"), shouldfail=True)