diff --git a/requirements-cwl.txt b/requirements-cwl.txt index a12220702e..e506d444a7 100644 --- a/requirements-cwl.txt +++ b/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 diff --git a/src/toil/cwl/cwltoil.py b/src/toil/cwl/cwltoil.py index 3064641519..e13c97d116 100644 --- a/src/toil/cwl/cwltoil.py +++ b/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" diff --git a/src/toil/test/cwl/cwlTest.py b/src/toil/test/cwl/cwlTest.py index 5b8a13733e..4098976352 100644 --- a/src/toil/test/cwl/cwlTest.py +++ b/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)