CWL: Fix --no-container & prepull (#5188)

* CWL container prepull: no reason to if extensions are enabled, they are now supported by cwl-utils 0.36+

* CWL container prepull: skip if --no-containers is specified

* Use checksumming revsort test

---------

Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>

requirements-cwl.txt

@@ -6,4 +6,4 @@ ruamel.yaml>=0.15,<=0.19
 ruamel.yaml.clib>=0.2.6
 networkx!=2.8.1,<4
 CacheControl[filecache]
-cwl-utils>=0.32
+cwl-utils>=0.36

src/toil/cwl/cwltoil.py

@@ -4336,15 +4336,8 @@ def main(args: Optional[list[str]] = None, stdout: TextIO = sys.stdout) -> int:
                 raise
 
             # Attempt to prepull the containers
-            if not options.no_prepull:
-                if not options.enable_ext:
-                    # The CWL utils parser does not support cwltool extensions and will crash if encountered, so don't prepull if extensions are enabled
-                    # See https://github.com/common-workflow-language/cwl-utils/issues/309
-                    try_prepull(uri, runtime_context, expected_config.batchSystem)
-                else:
-                    logger.debug(
-                        "Not prepulling containers as cwltool extensions are not supported."
-                    )
+            if not options.no_prepull and not options.no_container:
+                try_prepull(uri, runtime_context, expected_config.batchSystem)
 
             options.tool_help = None
             options.debug = options.logLevel == "DEBUG"

src/toil/test/cwl/cwlTest.py

@@ -421,6 +421,11 @@ def test_run_revsort_nochecksum(self) -> None:
             "revsort.cwl", partial(self._tester, main_args=["--no-compute-checksum"])
         )
 
+    def test_run_revsort_no_container(self) -> None:
+        self.revsort(
+            "revsort.cwl", partial(self._tester, main_args=["--no-container"])
+        )
+
     def test_run_revsort2(self) -> None:
         self.revsort("revsort2.cwl", self._tester)