FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_wf_wc_nomultiple_merge_nested - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘adb5f5c93f827949’, ‘create_time’: ‘2026-03-09T02:52:28.079144’, ‘update_time’: ‘2026-03-09T02:52:28.242819’, ‘workflow_id’: ‘adb5f5c93f827949’, ‘history_id’: ‘adb5f5c93f827949’, ‘uuid’: ‘025f8610-1b63-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘adb5f5c93f827949’, ‘update_time’: ‘2026-03-09T02:52:28.249174’, ‘job_id’: None, ‘workflow_step_id’: ‘529fd61ab1c6cc36’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘file1’, ‘workflow_step_uuid’: ‘7d18e72d-2880-4256-9677-94822bfda148’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘529fd61ab1c6cc36’, ‘update_time’: ‘2026-03-09T02:52:28.249177’, ‘job_id’: None, ‘workflow_step_id’: ‘adb5f5c93f827949’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘step1’, ‘workflow_step_uuid’: ‘0c1c7af1-5f26-4d18-ae93-4a78b4d5470d’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘0’: {‘id’: ‘adb5f5c93f827949’, ‘workflow_step_id’: ‘529fd61ab1c6cc36’, ‘label’: ‘file1’, ‘src’: ‘hda’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: “2 validation errors for :184edf70-ac16-4e52-b76a-a3cebb891baf (workflow step)\nfile1.list[union[DataRequestInternalHda,DataRequestInternalLdda]]\n Input should be a valid list [type=list_type, input_value={‘src’: ‘hda’, ‘id’: 1}, input_type=dict]\n For ”, ‘workflow_step_id’: 1}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_wf_scatter_two_nested_crossproduct - cwltest.compare.CompareFail: expected: [
[
“foo one three”,
“foo one four”
],
[
“foo two three”,
“foo two four”
]
]
got: [
“foo one three”,
“foo two four”
]
caused by: expected: [
“foo one three”,
“foo one four”
]
got: “foo one three”
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_wf_scatter_two_flat_crossproduct - cwltest.compare.CompareFail: expected: [
“foo one three”,
“foo one four”,
“foo two three”,
“foo two four”
]
got: [
“foo one three”,
“foo two four”
]
caused by: lengths don’t match
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_wf_scatter_nested_crossproduct_secondempty - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘f3f73e481f432006’, ‘create_time’: ‘2026-03-09T02:53:15.024077’, ‘update_time’: ‘2026-03-09T02:53:15.183093’, ‘workflow_id’: ‘f3f73e481f432006’, ‘history_id’: ‘f3f73e481f432006’, ‘uuid’: ‘1e5aeff8-1b63-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘da92407cb46a61f3’, ‘update_time’: ‘2026-03-09T02:53:15.185372’, ‘job_id’: None, ‘workflow_step_id’: ‘f06d708dacad69d8’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘inp1’, ‘workflow_step_uuid’: ‘8c648b06-00eb-4328-a5c4-a9118336ecbd’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘f06d708dacad69d8’, ‘update_time’: ‘2026-03-09T02:53:15.185374’, ‘job_id’: None, ‘workflow_step_id’: ‘f356c15ec7800da0’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘inp2’, ‘workflow_step_uuid’: ‘b92b0d21-e2c6-40eb-ae4a-139ae2ad279d’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘f356c15ec7800da0’, ‘update_time’: ‘2026-03-09T02:53:15.185376’, ‘job_id’: None, ‘workflow_step_id’: ‘da92407cb46a61f3’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘step1’, ‘workflow_step_uuid’: ‘cfffded7-b5cb-428e-a2e1-0b27829fcfc2’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘0’: {‘id’: ‘cb6e11b662890a90’, ‘workflow_step_id’: ‘f06d708dacad69d8’, ‘label’: ‘inp1’, ‘src’: ‘hdca’}, ‘1’: {‘id’: ‘9d37e53072ff9fa4’, ‘workflow_step_id’: ‘f356c15ec7800da0’, ‘label’: ‘inp2’, ‘src’: ‘hdca’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: ‘Cannot match collection types.’, ‘workflow_step_id’: 2}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_wf_scatter_nested_crossproduct_firstempty - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘2234cb1fd1df4331’, ‘create_time’: ‘2026-03-09T02:53:21.085601’, ‘update_time’: ‘2026-03-09T02:53:21.328683’, ‘workflow_id’: ‘2234cb1fd1df4331’, ‘history_id’: ‘2234cb1fd1df4331’, ‘uuid’: ‘21f7c672-1b63-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘22d3c31104d9102b’, ‘update_time’: ‘2026-03-09T02:53:21.330683’, ‘job_id’: None, ‘workflow_step_id’: ‘92c548528a9a67cb’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘inp1’, ‘workflow_step_uuid’: ‘9964f41f-9670-48a1-aee5-f5adcdbaf4ea’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘92c548528a9a67cb’, ‘update_time’: ‘2026-03-09T02:53:21.330685’, ‘job_id’: None, ‘workflow_step_id’: ‘5a77dbba84d2acbb’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘inp2’, ‘workflow_step_uuid’: ‘6878e79c-aef8-4b5f-9f35-c7df4b6b990d’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘5a77dbba84d2acbb’, ‘update_time’: ‘2026-03-09T02:53:21.330687’, ‘job_id’: None, ‘workflow_step_id’: ‘22d3c31104d9102b’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘step1’, ‘workflow_step_uuid’: ‘72ea7c80-fb66-459f-9c41-854838da8055’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘0’: {‘id’: ‘da92407cb46a61f3’, ‘workflow_step_id’: ‘92c548528a9a67cb’, ‘label’: ‘inp1’, ‘src’: ‘hdca’}, ‘1’: {‘id’: ‘f06d708dacad69d8’, ‘workflow_step_id’: ‘5a77dbba84d2acbb’, ‘label’: ‘inp2’, ‘src’: ‘hdca’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: None, ‘workflow_step_id’: None}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_wf_scatter_flat_crossproduct_oneempty - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘cb227cec8ca83994’, ‘create_time’: ‘2026-03-09T02:53:26.844014’, ‘update_time’: ‘2026-03-09T02:53:27.020419’, ‘workflow_id’: ‘cb227cec8ca83994’, ‘history_id’: ‘cb227cec8ca83994’, ‘uuid’: ‘256685c8-1b63-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘2c41b8145f7ed85e’, ‘update_time’: ‘2026-03-09T02:53:27.022627’, ‘job_id’: None, ‘workflow_step_id’: ‘8b0bee1f52868c9e’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘inp1’, ‘workflow_step_uuid’: ‘f29f33c4-4fdd-493b-bc97-1710b2921b6a’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘8b0bee1f52868c9e’, ‘update_time’: ‘2026-03-09T02:53:27.022629’, ‘job_id’: None, ‘workflow_step_id’: ‘b5065b03be4c41dc’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘inp2’, ‘workflow_step_uuid’: ‘6d6c7505-b7ef-42ed-8c85-b6f90f44a3ff’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘b5065b03be4c41dc’, ‘update_time’: ‘2026-03-09T02:53:27.022631’, ‘job_id’: None, ‘workflow_step_id’: ‘2c41b8145f7ed85e’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘step1’, ‘workflow_step_uuid’: ‘9fec82ec-b679-4e46-a407-0329cdfc87cf’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘0’: {‘id’: ‘f356c15ec7800da0’, ‘workflow_step_id’: ‘8b0bee1f52868c9e’, ‘label’: ‘inp1’, ‘src’: ‘hdca’}, ‘1’: {‘id’: ‘22d3c31104d9102b’, ‘workflow_step_id’: ‘b5065b03be4c41dc’, ‘label’: ‘inp2’, ‘src’: ‘hdca’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: ‘Cannot match collection types.’, ‘workflow_step_id’: 2}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_valuefrom_wf_step - AssertionError: Job {‘model_class’: ‘Job’, ‘id’: ‘917af94b51aeccc8’, ‘history_id’: ‘cb6e11b662890a90’, ‘tool_id’: ‘:e03d628a-edcc-45c3-bcbb-eb3eea7c003d’, ‘state’: ‘paused’, ‘exit_code’: None, ‘create_time’: ‘2026-03-09T02:53:31.634554’, ‘update_time’: ‘2026-03-09T02:53:31.853519’, ‘galaxy_version’: ‘26.1’, ‘external_id’: None, ‘handler’: None, ‘job_runner_name’: None, ‘command_line’: None, ‘user_email’: None, ‘user_id’: None} not in expected state
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_wf_scatter_twoparam_nested_crossproduct_valuefrom - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘9d37e53072ff9fa4’, ‘create_time’: ‘2026-03-09T02:53:39.981826’, ‘update_time’: ‘2026-03-09T02:53:40.442240’, ‘workflow_id’: ‘9d37e53072ff9fa4’, ‘history_id’: ‘9d37e53072ff9fa4’, ‘uuid’: ‘2d3b324e-1b63-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘4b455cfa602b54cb’, ‘update_time’: ‘2026-03-09T02:53:40.444347’, ‘job_id’: None, ‘workflow_step_id’: ‘9564811bfb69c81e’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘inp1’, ‘workflow_step_uuid’: ‘c35b6351-9798-47e0-8d5d-8200f910067b’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘9564811bfb69c81e’, ‘update_time’: ‘2026-03-09T02:53:40.444350’, ‘job_id’: None, ‘workflow_step_id’: ‘917af94b51aeccc8’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘inp2’, ‘workflow_step_uuid’: ‘2764b8b2-27d9-44c3-9995-214bfc49dcc4’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘917af94b51aeccc8’, ‘update_time’: ‘2026-03-09T02:53:40.444351’, ‘job_id’: None, ‘workflow_step_id’: ‘4b455cfa602b54cb’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘step1’, ‘workflow_step_uuid’: ‘70c86af6-de4f-4731-a9c3-a9ef86dd9f9f’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘0’: {‘id’: ‘5a77dbba84d2acbb’, ‘workflow_step_id’: ‘9564811bfb69c81e’, ‘label’: ‘inp1’, ‘src’: ‘hdca’}, ‘1’: {‘id’: ‘2c41b8145f7ed85e’, ‘workflow_step_id’: ‘917af94b51aeccc8’, ‘label’: ‘inp2’, ‘src’: ‘hdca’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: None, ‘workflow_step_id’: None}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_wf_scatter_twoparam_flat_crossproduct_valuefrom - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘da92407cb46a61f3’, ‘create_time’: ‘2026-03-09T02:53:48.807576’, ‘update_time’: ‘2026-03-09T02:53:49.005464’, ‘workflow_id’: ‘da92407cb46a61f3’, ‘history_id’: ‘da92407cb46a61f3’, ‘uuid’: ‘327de828-1b63-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘149c5ffa3420467d’, ‘update_time’: ‘2026-03-09T02:53:49.013197’, ‘job_id’: None, ‘workflow_step_id’: ‘807c96c72578b3a5’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘inp1’, ‘workflow_step_uuid’: ‘8b1657c6-fff2-4a81-ad89-dee85c37db64’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘807c96c72578b3a5’, ‘update_time’: ‘2026-03-09T02:53:49.013201’, ‘job_id’: None, ‘workflow_step_id’: ‘decab5ee1e95b10b’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘inp2’, ‘workflow_step_uuid’: ‘42f141a2-9850-4a4c-8e09-9d2576f8a177’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘decab5ee1e95b10b’, ‘update_time’: ‘2026-03-09T02:53:49.013205’, ‘job_id’: None, ‘workflow_step_id’: ‘149c5ffa3420467d’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘step1’, ‘workflow_step_uuid’: ‘f8821fdc-715f-4e6f-ba43-95db1e2ca4c5’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘0’: {‘id’: ‘8b0bee1f52868c9e’, ‘workflow_step_id’: ‘807c96c72578b3a5’, ‘label’: ‘inp1’, ‘src’: ‘hdca’}, ‘1’: {‘id’: ‘b5065b03be4c41dc’, ‘workflow_step_id’: ‘decab5ee1e95b10b’, ‘label’: ‘inp2’, ‘src’: ‘hdca’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: None, ‘workflow_step_id’: None}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_wf_scatter_twoparam_dotproduct_valuefrom - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘f06d708dacad69d8’, ‘create_time’: ‘2026-03-09T02:53:57.958047’, ‘update_time’: ‘2026-03-09T02:53:58.044393’, ‘workflow_id’: ‘f06d708dacad69d8’, ‘history_id’: ‘f06d708dacad69d8’, ‘uuid’: ‘37f2312e-1b63-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘75cfda0e4b8063b8’, ‘update_time’: ‘2026-03-09T02:53:58.046476’, ‘job_id’: None, ‘workflow_step_id’: ‘b351d620879d6814’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘inp1’, ‘workflow_step_uuid’: ‘672b75d0-867d-4bba-bf90-42b9d3567954’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘b351d620879d6814’, ‘update_time’: ‘2026-03-09T02:53:58.046478’, ‘job_id’: None, ‘workflow_step_id’: ‘91c89b6f01b9f2ae’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘inp2’, ‘workflow_step_uuid’: ‘ed46e6b4-ae59-4d8a-99cc-87a3982ef8ba’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘91c89b6f01b9f2ae’, ‘update_time’: ‘2026-03-09T02:53:58.046480’, ‘job_id’: None, ‘workflow_step_id’: ‘75cfda0e4b8063b8’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘step1’, ‘workflow_step_uuid’: ‘05503467-de85-46b1-9090-c5e047329cda’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘0’: {‘id’: ‘8cf91205f2f737f4’, ‘workflow_step_id’: ‘b351d620879d6814’, ‘label’: ‘inp1’, ‘src’: ‘hdca’}, ‘1’: {‘id’: ‘3393d74dbae390cc’, ‘workflow_step_id’: ‘91c89b6f01b9f2ae’, ‘label’: ‘inp2’, ‘src’: ‘hdca’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: None, ‘workflow_step_id’: None}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_dockeroutputdir - AssertionError: Final state - error - not okay. Full response: {‘model_class’: ‘Job’, ‘id’: ‘07492bd4c94b3435’, ‘history_id’: ‘22d3c31104d9102b’, ‘tool_id’: ‘docker-output-dir.cwl’, ‘state’: ‘error’, ‘exit_code’: 1, ‘create_time’: ‘2026-03-09T02:54:24.501388’, ‘update_time’: ‘2026-03-09T02:54:32.813549’, ‘galaxy_version’: ‘26.1’, ‘external_id’: ‘3453’, ‘handler’: None, ‘job_runner_name’: None, ‘command_line’: ‘touch /other/thing’, ‘user_email’: ‘test@bx.psu.edu’, ‘user_id’: ‘adb5f5c93f827949’, ‘command_version’: ”, ‘params’: {‘chromInfo’: ’“/home/runner/work/galaxy/galaxy/galaxy root/tool-data/shared/ucsc/chrom/?.len”’, ‘dbkey’: ’”?”’, ‘__input_ext’: ‘“input”’}, ‘inputs’: {}, ‘outputs’: {‘thing’: {‘id’: ‘2e810b1cd3515059’, ‘src’: ‘hda’, ‘uuid’: ‘1b2e7a08-cbba-476e-9983-39eaf91ca260’}}, ‘copied_from_job_id’: None, ‘output_collections’: {}, ‘tool_stdout’: ”, ‘tool_stderr’: “touch: cannot touch ‘/other/thing’: No such file or directory\n”, ‘job_stdout’: ”, ‘job_stderr’: ‘ERROR:galaxy_ext.cwl.handle_outputs:Failed to relocate CWL dynamic outputs\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1423, in collect_output\n raise WorkflowException(\ncwl_utils.errors.WorkflowException: Did not find output file with glob pattern: [‘thing’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1254, in collect_output_ports\n ret[fragment] = self.collect_output(\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1421, in collect_output\n with SourceLine(binding, “glob”, WorkflowException, debug):\n File “schema_salad/sourceline.py”, line 255, in exit\ncwl_utils.errors.WorkflowException: .:1:140: Did not find output file with glob pattern: [‘thing’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy_ext/cwl/handle_outputs.py”, line 18, in relocate_dynamic_outputs\n handle_outputs()\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/runtime_actions.py”, line 184, in handle_outputs\n outputs = job_proxy.collect_outputs(tool_working_directory, tool_exit_code)\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/parser.py”, line 647, in collect_outputs\n return cwl_job.collect_outputs(tool_working_directory, rcode)\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1247, in collect_output_ports\n with SourceLine(\n File “schema_salad/sourceline.py”, line 255, in exit\ncwltool.command_line_tool.ParameterOutputWorkflowException: (“Error collecting output for parameter ‘thing’: .:1:140: Did not find output file with glob pattern: [‘thing’].”, {})\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1423, in collect_output\n raise WorkflowException(\ncwl_utils.errors.WorkflowException: Did not find output file with glob pattern: [‘thing’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1254, in collect_output_ports\n ret[fragment] = self.collect_output(\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1421, in collect_output\n with SourceLine(binding, “glob”, WorkflowException, debug):\n File “schema_salad/sourceline.py”, line 255, in exit\ncwl_utils.errors.WorkflowException: .:1:140: Did not find output file with glob pattern: [‘thing’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/tmp/tmpvaflugfu/tmpczu4nhmx/tmp3tu4rv8u/database/job_working_directory1/000/39/relocate_dynamic_outputs.py”, line 1, in \n from galaxy_ext.cwl.handle_outputs import relocate_dynamic_outputs; relocate_dynamic_outputs()\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy_ext/cwl/handle_outputs.py”, line 18, in relocate_dynamic_outputs\n handle_outputs()\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/runtime_actions.py”, line 184, in handle_outputs\n outputs = job_proxy.collect_outputs(tool_working_directory, tool_exit_code)\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/parser.py”, line 647, in collect_outputs\n return cwl_job.collect_outputs(tool_working_directory, rcode)\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1247, in collect_output_ports\n with SourceLine(\n File “schema_salad/sourceline.py”, line 255, in exit\ncwltool.command_line_tool.ParameterOutputWorkflowException: (“Error collecting output for parameter ‘thing’: .:1:140: Did not find output file with glob pattern: [‘thing’].”, {})\n’, ‘stdout’: ”, ‘stderr’: ‘touch: cannot touch ‘/other/thing’: No such file or directory\n\nERROR:galaxy_ext.cwl.handle_outputs:Failed to relocate CWL dynamic outputs\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1423, in collect_output\n raise WorkflowException(\ncwl_utils.errors.WorkflowException: Did not find output file with glob pattern: [‘thing’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1254, in collect_output_ports\n ret[fragment] = self.collect_output(\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1421, in collect_output\n with SourceLine(binding, “glob”, WorkflowException, debug):\n File “schema_salad/sourceline.py”, line 255, in exit\ncwl_utils.errors.WorkflowException: .:1:140: Did not find output file with glob pattern: [‘thing’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy_ext/cwl/handle_outputs.py”, line 18, in relocate_dynamic_outputs\n handle_outputs()\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/runtime_actions.py”, line 184, in handle_outputs\n outputs = job_proxy.collect_outputs(tool_working_directory, tool_exit_code)\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/parser.py”, line 647, in collect_outputs\n return cwl_job.collect_outputs(tool_working_directory, rcode)\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1247, in collect_output_ports\n with SourceLine(\n File “schema_salad/sourceline.py”, line 255, in exit\ncwltool.command_line_tool.ParameterOutputWorkflowException: (“Error collecting output for parameter ‘thing’: .:1:140: Did not find output file with glob pattern: [‘thing’].”, {})\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1423, in collect_output\n raise WorkflowException(\ncwl_utils.errors.WorkflowException: Did not find output file with glob pattern: [‘thing’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1254, in collect_output_ports\n ret[fragment] = self.collect_output(\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1421, in collect_output\n with SourceLine(binding, “glob”, WorkflowException, debug):\n File “schema_salad/sourceline.py”, line 255, in exit\ncwl_utils.errors.WorkflowException: .:1:140: Did not find output file with glob pattern: [‘thing’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/tmp/tmpvaflugfu/tmpczu4nhmx/tmp3tu4rv8u/database/job_working_directory1/000/39/relocate_dynamic_outputs.py”, line 1, in \n from galaxy_ext.cwl.handle_outputs import relocate_dynamic_outputs; relocate_dynamic_outputs()\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy_ext/cwl/handle_outputs.py”, line 18, in relocate_dynamic_outputs\n handle_outputs()\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/runtime_actions.py”, line 184, in handle_outputs\n outputs = job_proxy.collect_outputs(tool_working_directory, tool_exit_code)\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/parser.py”, line 647, in collect_outputs\n return cwl_job.collect_outputs(tool_working_directory, rcode)\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1247, in collect_output_ports\n with SourceLine(\n File “schema_salad/sourceline.py”, line 255, in exit\ncwltool.command_line_tool.ParameterOutputWorkflowException: (“Error collecting output for parameter ‘thing’: .:1:140: Did not find output file with glob pattern: [‘thing’].”, {})\n’, ‘job_messages’: [{‘desc’: ‘Fatal error: Exit code 1 ()’, ‘code_desc’: ”, ‘error_level’: 3.0, ‘type’: ‘exit_code’, ‘exit_code’: 1}], ‘dependencies’: [], ‘job_metrics’: [{‘title’: ‘Cores Allocated’, ‘value’: ‘1’, ‘plugin’: ‘core’, ‘name’: ‘galaxy_slots’, ‘raw_value’: ‘1.0000000’}, {‘title’: ‘Job Start Time’, ‘value’: ‘2026-03-09 02:54:25’, ‘plugin’: ‘core’, ‘name’: ‘start_epoch’, ‘raw_value’: ‘1773024865.0000000’}, {‘title’: ‘Job End Time’, ‘value’: ‘2026-03-09 02:54:32’, ‘plugin’: ‘core’, ‘name’: ‘end_epoch’, ‘raw_value’: ‘1773024872.0000000’}, {‘title’: ‘Job Runtime (Wall Clock)’, ‘value’: ‘7 seconds’, ‘plugin’: ‘core’, ‘name’: ‘runtime_seconds’, ‘raw_value’: ‘7.0000000’}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_resreq_step_overrides_wf - cwltest.compare.CompareFail: expected: {
“checksum”: “sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e”,
“class”: “File”,
“location”: “cores.txt”,
“size”: 2
}
got: {
“basename”: “cores.txt”,
“checksum”: “sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a”,
“class”: “File”,
“format”: “http://edamontology.org/format_1915”,
“location”: “file:///tmp/tmpj5i1emit/cores.txt”,
“nameext”: “.txt”,
“nameroot”: “cores”,
“path”: “/tmp/tmpj5i1emit/cores.txt”,
“size”: 2
}
caused by: Output file checksums do not match: actual ‘sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a’ is not equal to expected ‘sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e’
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_docker_entrypoint - AssertionError: Final state - error - not okay. Full response: {‘model_class’: ‘Job’, ‘id’: ‘9a58064fb2c43d99’, ‘history_id’: ‘9564811bfb69c81e’, ‘tool_id’: ‘docker-run-cmd.cwl’, ‘state’: ‘error’, ‘exit_code’: 127, ‘create_time’: ‘2026-03-09T02:57:22.255212’, ‘update_time’: ‘2026-03-09T02:57:30.887148’, ‘galaxy_version’: ‘26.1’, ‘external_id’: ‘4487’, ‘handler’: None, ‘job_runner_name’: None, ‘command_line’: ‘-c ‘echo ’”’“‘moo’”’”’ > cow”, ‘user_email’: ‘test@bx.psu.edu’, ‘user_id’: ‘adb5f5c93f827949’, ‘command_version’: ”, ‘params’: {‘chromInfo’: ’“/home/runner/work/galaxy/galaxy/galaxy root/tool-data/shared/ucsc/chrom/?.len”’, ‘dbkey’: ’”?”’, ‘__input_ext’: ‘“input”’}, ‘inputs’: {}, ‘outputs’: {‘cow’: {‘id’: ‘b7076a144d094a18’, ‘src’: ‘hda’, ‘uuid’: ‘5240a261-e88a-4b4c-9a64-e113a52592ad’}}, ‘copied_from_job_id’: None, ‘output_collections’: {}, ‘tool_stdout’: ”, ‘tool_stderr’: ‘/tmp/tmpvaflugfu/tmpczu4nhmx/tmp3tu4rv8u/database/job_working_directory1/000/67/tool_script.sh: line 10: -c: command not found\n’, ‘job_stdout’: ”, ‘job_stderr’: ‘ERROR:galaxy_ext.cwl.handle_outputs:Failed to relocate CWL dynamic outputs\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1423, in collect_output\n raise WorkflowException(\ncwl_utils.errors.WorkflowException: Did not find output file with glob pattern: [‘cow’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1254, in collect_output_ports\n ret[fragment] = self.collect_output(\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1421, in collect_output\n with SourceLine(binding, “glob”, WorkflowException, debug):\n File “schema_salad/sourceline.py”, line 255, in exit\ncwl_utils.errors.WorkflowException: .:1:140: Did not find output file with glob pattern: [‘cow’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy_ext/cwl/handle_outputs.py”, line 18, in relocate_dynamic_outputs\n handle_outputs()\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/runtime_actions.py”, line 184, in handle_outputs\n outputs = job_proxy.collect_outputs(tool_working_directory, tool_exit_code)\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/parser.py”, line 647, in collect_outputs\n return cwl_job.collect_outputs(tool_working_directory, rcode)\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1247, in collect_output_ports\n with SourceLine(\n File “schema_salad/sourceline.py”, line 255, in exit\ncwltool.command_line_tool.ParameterOutputWorkflowException: (“Error collecting output for parameter ‘cow’: .:1:140: Did not find output file with glob pattern: [‘cow’].”, {})\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1423, in collect_output\n raise WorkflowException(\ncwl_utils.errors.WorkflowException: Did not find output file with glob pattern: [‘cow’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1254, in collect_output_ports\n ret[fragment] = self.collect_output(\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1421, in collect_output\n with SourceLine(binding, “glob”, WorkflowException, debug):\n File “schema_salad/sourceline.py”, line 255, in exit\ncwl_utils.errors.WorkflowException: .:1:140: Did not find output file with glob pattern: [‘cow’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/tmp/tmpvaflugfu/tmpczu4nhmx/tmp3tu4rv8u/database/job_working_directory1/000/67/relocate_dynamic_outputs.py”, line 1, in \n from galaxy_ext.cwl.handle_outputs import relocate_dynamic_outputs; relocate_dynamic_outputs()\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy_ext/cwl/handle_outputs.py”, line 18, in relocate_dynamic_outputs\n handle_outputs()\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/runtime_actions.py”, line 184, in handle_outputs\n outputs = job_proxy.collect_outputs(tool_working_directory, tool_exit_code)\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/parser.py”, line 647, in collect_outputs\n return cwl_job.collect_outputs(tool_working_directory, rcode)\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1247, in collect_output_ports\n with SourceLine(\n File “schema_salad/sourceline.py”, line 255, in exit\ncwltool.command_line_tool.ParameterOutputWorkflowException: (“Error collecting output for parameter ‘cow’: .:1:140: Did not find output file with glob pattern: [‘cow’].”, {})\n’, ‘stdout’: ”, ‘stderr’: ‘/tmp/tmpvaflugfu/tmpczu4nhmx/tmp3tu4rv8u/database/job_working_directory1/000/67/tool_script.sh: line 10: -c: command not found\n\nERROR:galaxy_ext.cwl.handle_outputs:Failed to relocate CWL dynamic outputs\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1423, in collect_output\n raise WorkflowException(\ncwl_utils.errors.WorkflowException: Did not find output file with glob pattern: [‘cow’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1254, in collect_output_ports\n ret[fragment] = self.collect_output(\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1421, in collect_output\n with SourceLine(binding, “glob”, WorkflowException, debug):\n File “schema_salad/sourceline.py”, line 255, in exit\ncwl_utils.errors.WorkflowException: .:1:140: Did not find output file with glob pattern: [‘cow’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy_ext/cwl/handle_outputs.py”, line 18, in relocate_dynamic_outputs\n handle_outputs()\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/runtime_actions.py”, line 184, in handle_outputs\n outputs = job_proxy.collect_outputs(tool_working_directory, tool_exit_code)\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/parser.py”, line 647, in collect_outputs\n return cwl_job.collect_outputs(tool_working_directory, rcode)\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1247, in collect_output_ports\n with SourceLine(\n File “schema_salad/sourceline.py”, line 255, in exit\ncwltool.command_line_tool.ParameterOutputWorkflowException: (“Error collecting output for parameter ‘cow’: .:1:140: Did not find output file with glob pattern: [‘cow’].”, {})\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1423, in collect_output\n raise WorkflowException(\ncwl_utils.errors.WorkflowException: Did not find output file with glob pattern: [‘cow’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1254, in collect_output_ports\n ret[fragment] = self.collect_output(\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1421, in collect_output\n with SourceLine(binding, “glob”, WorkflowException, debug):\n File “schema_salad/sourceline.py”, line 255, in exit\ncwl_utils.errors.WorkflowException: .:1:140: Did not find output file with glob pattern: [‘cow’].\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File “/tmp/tmpvaflugfu/tmpczu4nhmx/tmp3tu4rv8u/database/job_working_directory1/000/67/relocate_dynamic_outputs.py”, line 1, in \n from galaxy_ext.cwl.handle_outputs import relocate_dynamic_outputs; relocate_dynamic_outputs()\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy_ext/cwl/handle_outputs.py”, line 18, in relocate_dynamic_outputs\n handle_outputs()\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/runtime_actions.py”, line 184, in handle_outputs\n outputs = job_proxy.collect_outputs(tool_working_directory, tool_exit_code)\n File “/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tool_util/cwl/parser.py”, line 647, in collect_outputs\n return cwl_job.collect_outputs(tool_working_directory, rcode)\n File “/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.10/site-packages/cwltool/command_line_tool.py”, line 1247, in collect_output_ports\n with SourceLine(\n File “schema_salad/sourceline.py”, line 255, in exit\ncwltool.command_line_tool.ParameterOutputWorkflowException: (“Error collecting output for parameter ‘cow’: .:1:140: Did not find output file with glob pattern: [‘cow’].”, {})\n’, ‘job_messages’: [{‘desc’: ‘Fatal error: Exit code 127 ()’, ‘code_desc’: ”, ‘error_level’: 3.0, ‘type’: ‘exit_code’, ‘exit_code’: 127}], ‘dependencies’: [], ‘job_metrics’: [{‘title’: ‘Cores Allocated’, ‘value’: ‘1’, ‘plugin’: ‘core’, ‘name’: ‘galaxy_slots’, ‘raw_value’: ‘1.0000000’}, {‘title’: ‘Job Start Time’, ‘value’: ‘2026-03-09 02:57:22’, ‘plugin’: ‘core’, ‘name’: ‘start_epoch’, ‘raw_value’: ‘1773025042.0000000’}, {‘title’: ‘Job End Time’, ‘value’: ‘2026-03-09 02:57:29’, ‘plugin’: ‘core’, ‘name’: ‘end_epoch’, ‘raw_value’: ‘1773025049.0000000’}, {‘title’: ‘Job Runtime (Wall Clock)’, ‘value’: ‘7 seconds’, ‘plugin’: ‘core’, ‘name’: ‘runtime_seconds’, ‘raw_value’: ‘7.0000000’}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_secondary_files_in_named_records - AssertionError: Final state - error - not okay. Full response: {‘model_class’: ‘Job’, ‘id’: ‘2c06ae359f50c276’, ‘history_id’: ‘917af94b51aeccc8’, ‘tool_id’: ‘record-sd-secondaryFiles.cwl’, ‘state’: ‘error’, ‘exit_code’: None, ‘create_time’: ‘2026-03-09T02:57:38.241675’, ‘update_time’: ‘2026-03-09T02:57:38.612793’, ‘galaxy_version’: ‘26.1’, ‘external_id’: None, ‘handler’: None, ‘job_runner_name’: None, ‘command_line’: None, ‘user_email’: ‘test@bx.psu.edu’, ‘user_id’: ‘adb5f5c93f827949’, ‘command_version’: None, ‘params’: {‘record_input’: ’{“id”: 28, “src”: “hdca”}’, ‘chromInfo’: ’“/home/runner/work/galaxy/galaxy/galaxy root/tool-data/shared/ucsc/chrom/?.len”’, ‘dbkey’: ’”?”’, ‘__input_ext’: ‘“input”’}, ‘inputs’: {}, ‘outputs’: {}, ‘copied_from_job_id’: None, ‘output_collections’: {}, ‘tool_stdout’: ”, ‘tool_stderr’: ”, ‘job_stdout’: None, ‘job_stderr’: None, ‘stdout’: ”, ‘stderr’: ”, ‘job_messages’: None, ‘dependencies’: [], ‘job_metrics’: []}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_record_output_file_entry_format - AssertionError: Final state - error - not okay. Full response: {‘model_class’: ‘History’, ‘id’: ‘149c5ffa3420467d’, ‘name’: ‘API Test History’, ‘deleted’: False, ‘purged’: False, ‘archived’: False, ‘url’: ‘/api/histories/149c5ffa3420467d’, ‘published’: False, ‘count’: 9, ‘annotation’: None, ‘tags’: [], ‘update_time’: ‘2026-03-09T02:57:54.226658’, ‘preferred_object_store_id’: None, ‘contents_url’: ‘/api/histories/149c5ffa3420467d/contents’, ‘size’: 0, ‘user_id’: ‘adb5f5c93f827949’, ‘create_time’: ‘2026-03-09T02:57:41.099381’, ‘importable’: False, ‘slug’: None, ‘username’: ‘test—bx—psu—edu’, ‘username_and_slug’: None, ‘genome_build’: None, ‘state’: ‘error’, ‘state_ids’: {‘new’: [], ‘upload’: [], ‘queued’: [], ‘running’: [], ‘ok’: [‘aea569350f89bf84’, ‘b44c74861d094619’, ‘15a3f866c4811e6a’], ‘empty’: [], ‘error’: [], ‘paused’: [], ‘setting_metadata’: [], ‘failed_metadata’: [‘fcefc3cde5ffd71c’, ‘82aae0a8ec0b5ec7’], ‘deferred’: [], ‘discarded’: []}, ‘state_details’: {‘new’: 0, ‘upload’: 0, ‘queued’: 0, ‘running’: 0, ‘ok’: 3, ‘empty’: 0, ‘error’: 0, ‘paused’: 0, ‘setting_metadata’: 0, ‘failed_metadata’: 2, ‘deferred’: 0, ‘discarded’: 0}}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_workflow_input_inputBinding_loadContents - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘91c89b6f01b9f2ae’, ‘create_time’: ‘2026-03-09T02:57:59.823151’, ‘update_time’: ‘2026-03-09T02:57:59.945300’, ‘workflow_id’: ‘91c89b6f01b9f2ae’, ‘history_id’: ‘807c96c72578b3a5’, ‘uuid’: ‘c81bea60-1b63-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘17af7ba02be4dc6a’, ‘update_time’: ‘2026-03-09T02:57:59.947344’, ‘job_id’: None, ‘workflow_step_id’: ‘c34129969476e859’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘my_file’, ‘workflow_step_uuid’: ‘5485d761-f121-4a21-affe-8793cbbeb6e6’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘c34129969476e859’, ‘update_time’: ‘2026-03-09T02:57:59.947347’, ‘job_id’: None, ‘workflow_step_id’: ‘17af7ba02be4dc6a’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘one’, ‘workflow_step_uuid’: ‘b0d0a7a3-49bd-4cea-9320-d6e43f96deef’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘0’: {‘id’: ‘7d2a4a8eeb06732e’, ‘workflow_step_id’: ‘c34129969476e859’, ‘label’: ‘my_file’, ‘src’: ‘hda’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: ‘1 validation error for _:037d9dc4-a9ed-4bc6-8ddf-230d07220a7b (workflow step)\nmy_number\n Input should be a valid integer [type=int_type, input_value=None, input_type=NoneType]\n For further information visit https://errors.pydantic.dev/2.12/v/int_type’, ‘workflow_step_id’: 1}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_workflow_input_loadContents_without_inputBinding - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘66701dbe65507c8c’, ‘create_time’: ‘2026-03-09T02:58:03.127442’, ‘update_time’: ‘2026-03-09T02:58:03.277160’, ‘workflow_id’: ‘66701dbe65507c8c’, ‘history_id’: ‘decab5ee1e95b10b’, ‘uuid’: ‘ca142904-1b63-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘aea569350f89bf84’, ‘update_time’: ‘2026-03-09T02:58:03.285502’, ‘job_id’: None, ‘workflow_step_id’: ‘b44c74861d094619’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘my_file’, ‘workflow_step_uuid’: ‘286ef21a-ce21-4028-9747-22271cae4df9’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘b44c74861d094619’, ‘update_time’: ‘2026-03-09T02:58:03.285505’, ‘job_id’: None, ‘workflow_step_id’: ‘aea569350f89bf84’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘one’, ‘workflow_step_uuid’: ‘f7d6b219-2767-4d9f-9086-676fa288a1a3’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘0’: {‘id’: ‘37903b84bafe1288’, ‘workflow_step_id’: ‘b44c74861d094619’, ‘label’: ‘my_file’, ‘src’: ‘hda’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: ‘1 validation error for _:1c967166-788a-4dc9-88d9-c1f1f334dba1 (workflow step)\nmy_number\n Input should be a valid integer [type=int_type, input_value=None, input_type=NoneType]\n For further information visit https://errors.pydantic.dev/2.12/v/int_type’, ‘workflow_step_id’: 1}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_workflow_step_in_loadContents - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘855802e3b44452e1’, ‘create_time’: ‘2026-03-09T02:58:06.443574’, ‘update_time’: ‘2026-03-09T02:58:06.513143’, ‘workflow_id’: ‘855802e3b44452e1’, ‘history_id’: ‘75cfda0e4b8063b8’, ‘uuid’: ‘cc0e1e90-1b63-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘15a3f866c4811e6a’, ‘update_time’: ‘2026-03-09T02:58:06.515140’, ‘job_id’: None, ‘workflow_step_id’: ‘fcefc3cde5ffd71c’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘my_file’, ‘workflow_step_uuid’: ‘bf623075-0a0d-4ebe-be75-2fef9ef4f300’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘fcefc3cde5ffd71c’, ‘update_time’: ‘2026-03-09T02:58:06.515143’, ‘job_id’: None, ‘workflow_step_id’: ‘15a3f866c4811e6a’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘one’, ‘workflow_step_uuid’: ‘01590576-ffd5-4371-a1ed-1c4260a4eb1f’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘0’: {‘id’: ‘0a296d7461b1f475’, ‘workflow_step_id’: ‘fcefc3cde5ffd71c’, ‘label’: ‘my_file’, ‘src’: ‘hda’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: ‘1 validation error for _:b7c22d84-5d98-4fbf-b6c1-5331325ee47c (workflow step)\nmy_number\n Input should be a valid integer [type=int_type, input_value=None, input_type=NoneType]\n For further information visit https://errors.pydantic.dev/2.12/v/int_type’, ‘workflow_step_id’: 1}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_timelimit_expressiontool - AssertionError: Final state - error - not okay. Full response: {‘model_class’: ‘Job’, ‘id’: ‘7d2a4a8eeb06732e’, ‘history_id’: ‘b351d620879d6814’, ‘tool_id’: ‘timelimit5.cwl’, ‘state’: ‘error’, ‘exit_code’: None, ‘create_time’: ‘2026-03-09T02:58:09.546787’, ‘update_time’: ‘2026-03-09T02:58:13.114321’, ‘galaxy_version’: ‘26.1’, ‘external_id’: ‘4620’, ‘handler’: None, ‘job_runner_name’: None, ‘command_line’: ‘true’, ‘user_email’: ‘test@bx.psu.edu’, ‘user_id’: ‘adb5f5c93f827949’, ‘command_version’: None, ‘params’: {‘chromInfo’: ’“/home/runner/work/galaxy/galaxy/galaxy root/tool-data/shared/ucsc/chrom/?.len”’, ‘dbkey’: ’”?”’, ‘__input_ext’: ‘“input”’}, ‘inputs’: {}, ‘outputs’: {‘status’: {‘id’: ‘fe8affe5d81f4f8b’, ‘src’: ‘hda’, ‘uuid’: ‘08ad4953-ca48-4845-9c13-a7ec6d9b976a’}}, ‘copied_from_job_id’: None, ‘output_collections’: {}, ‘tool_stdout’: ”, ‘tool_stderr’: ”, ‘job_stdout’: None, ‘job_stderr’: None, ‘stdout’: ”, ‘stderr’: ”, ‘job_messages’: None, ‘dependencies’: [], ‘job_metrics’: [{‘title’: ‘Cores Allocated’, ‘value’: ‘1’, ‘plugin’: ‘core’, ‘name’: ‘galaxy_slots’, ‘raw_value’: ‘1.0000000’}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_networkaccess_disabled - Exception: Expected run to fail but it didn’t.
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_initial_work_dir_for_null_and_arrays - json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_initial_work_dir_for_array_dirs - AssertionError: Final state - error - not okay. Full response: {‘model_class’: ‘Job’, ‘id’: ‘ad3326667f76b816’, ‘history_id’: ‘855802e3b44452e1’, ‘tool_id’: ‘stage-array-dirs.cwl#stage_array_dirs’, ‘state’: ‘error’, ‘exit_code’: None, ‘create_time’: ‘2026-03-09T02:58:47.307363’, ‘update_time’: ‘2026-03-09T02:58:47.470789’, ‘galaxy_version’: ‘26.1’, ‘external_id’: None, ‘handler’: None, ‘job_runner_name’: None, ‘command_line’: None, ‘user_email’: ‘test@bx.psu.edu’, ‘user_id’: ‘adb5f5c93f827949’, ‘command_version’: None, ‘params’: {‘input_list’: ’{“id”: 33, “src”: “hdca”}’, ‘chromInfo’: ’“/home/runner/work/galaxy/galaxy/galaxy root/tool-data/shared/ucsc/chrom/?.len”’, ‘dbkey’: ’”?”’, ‘__input_ext’: ‘“input”’}, ‘inputs’: {}, ‘outputs’: {}, ‘copied_from_job_id’: None, ‘output_collections’: {‘output’: {‘src’: ‘hdca’, ‘id’: ‘e00d4fc8bba8b6c5’}}, ‘tool_stdout’: ”, ‘tool_stderr’: ”, ‘job_stdout’: None, ‘job_stderr’: None, ‘stdout’: ”, ‘stderr’: ”, ‘job_messages’: None, ‘dependencies’: [], ‘job_metrics’: []}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_cwl_requirements_addition - cwltest.compare.CompareFail: expected: {
“checksum”: “sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519”,
“class”: “File”,
“location”: “out”,
“size”: 15
}
got: {
“basename”: “out”,
“checksum”: “sha1$adc83b19e793491b1c6ea0fd8b46cd9f32e592fc”,
“class”: “File”,
“format”: “http://edamontology.org/format_1915”,
“location”: “file:///tmp/tmpmsp2uc05/out”,
“nameext”: "",
“nameroot”: “out”,
“path”: “/tmp/tmpmsp2uc05/out”,
“size”: 1
}
caused by: Output file checksums do not match: actual ‘sha1$adc83b19e793491b1c6ea0fd8b46cd9f32e592fc’ is not equal to expected ‘sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519’
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_cwl_requirements_override_expression - cwltest.compare.CompareFail: expected: {
“checksum”: “sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519”,
“class”: “File”,
“location”: “out”,
“size”: 15
}
got: {
“basename”: “out”,
“checksum”: “sha1$893a885b3785c8e9bfe0721a4149b129ac0f21f9”,
“class”: “File”,
“format”: “http://edamontology.org/format_1915”,
“location”: “file:///tmp/tmpznw91izh/out”,
“nameext”: "",
“nameroot”: “out”,
“path”: “/tmp/tmpznw91izh/out”,
“size”: 18
}
caused by: Output file checksums do not match: actual ‘sha1$893a885b3785c8e9bfe0721a4149b129ac0f21f9’ is not equal to expected ‘sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519’
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_cwl_requirements_override_static - cwltest.compare.CompareFail: expected: {
“checksum”: “sha1$715e62184492851512a020c36ab7118eca114a59”,
“class”: “File”,
“location”: “out”,
“size”: 23
}
got: {
“basename”: “out”,
“checksum”: “sha1$adc83b19e793491b1c6ea0fd8b46cd9f32e592fc”,
“class”: “File”,
“format”: “http://edamontology.org/format_1915”,
“location”: “file:///tmp/tmp1rxzgogv/out”,
“nameext”: "",
“nameroot”: “out”,
“path”: “/tmp/tmp1rxzgogv/out”,
“size”: 1
}
caused by: Output file checksums do not match: actual ‘sha1$adc83b19e793491b1c6ea0fd8b46cd9f32e592fc’ is not equal to expected ‘sha1$715e62184492851512a020c36ab7118eca114a59’
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_illegal_symlink - Exception: Expected run to fail but it didn’t.
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_modify_directory_content - cwltest.compare.CompareFail: expected: [
{
“basename”: “blurb”,
“class”: “File”,
“location”: “blurb”
}
]
got: [
{
“basename”: “.galaxy_empty_directory”,
“checksum”: “sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709”,
“class”: “File”,
“format”: “http://edamontology.org/format_1915”,
“location”: “file:///tmp/tmptzi4dpz5/.galaxy_empty_directory”,
“nameext”: "",
“nameroot”: “.galaxy_empty_directory”,
“path”: “/tmp/tmptzi4dpz5/.galaxy_empty_directory”,
“size”: 0
},
{
“basename”: “blurb”,
“checksum”: “sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709”,
“class”: “File”,
“format”: “http://edamontology.org/format_1915”,
“location”: “file:///tmp/tmptzi4dpz5/blurb”,
“nameext”: "",
“nameroot”: “blurb”,
“path”: “/tmp/tmptzi4dpz5/blurb”,
“size”: 0
}
]
caused by: lengths don’t match
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_pass_through_required_false_when - cwltest.compare.CompareFail: expected: “Direct”
got: null
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_first_non_null_first_non_null - cwltest.compare.CompareFail: expected: “foo 0”
got: [
“foo 0”,
null
]
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_first_non_null_all_null - Exception: Expected run to fail but it didn’t.
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_first_non_null_second_non_null - cwltest.compare.CompareFail: expected: “foo 3”
got: [
null,
“foo 3”
]
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_pass_through_required_the_only_non_null - cwltest.compare.CompareFail: expected: “Direct”
got: null
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_pass_through_required_fail - Exception: Expected run to fail but it didn’t.
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_the_only_non_null_single_true - cwltest.compare.CompareFail: expected: “bar 1”
got: [
null,
“bar 1”
]
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_the_only_non_null_multi_true - Exception: Expected run to fail but it didn’t.
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_all_non_null_all_null - cwltest.compare.CompareFail: expected: []
got: [
null,
null
]
caused by: lengths don’t match
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_all_non_null_one_non_null - cwltest.compare.CompareFail: expected: [
“bar 1”
]
got: [
null,
“bar 1”
]
caused by: lengths don’t match
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_condifional_scatter_on_nonscattered_false - cwltest.compare.CompareFail: expected: []
got: [
null,
null,
null,
null,
null,
null
]
caused by: lengths don’t match
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_scatter_on_scattered_conditional - cwltest.compare.CompareFail: expected: [
“foo 4”,
“foo 5”,
“foo 6”
]
got: [
null,
null,
null,
“foo 4”,
“foo 5”,
“foo 6”
]
caused by: lengths don’t match
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_conditionals_nested_cross_scatter - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘d2efe60a42a7f78c’, ‘create_time’: ‘2026-03-09T03:04:03.940600’, ‘update_time’: ‘2026-03-09T03:04:04.213405’, ‘workflow_id’: ‘d2efe60a42a7f78c’, ‘history_id’: ‘12d23f2cc1e13d05’, ‘uuid’: ‘a123a456-1b64-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘9802c787bf009fe2’, ‘update_time’: ‘2026-03-09T03:04:04.215812’, ‘job_id’: None, ‘workflow_step_id’: ‘8b6f46c593d35e12’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘in1’, ‘workflow_step_uuid’: ‘4bc22452-d0a1-42ec-84ce-006aa87d02b8’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘8b6f46c593d35e12’, ‘update_time’: ‘2026-03-09T03:04:04.215814’, ‘job_id’: None, ‘workflow_step_id’: ‘763817bba969bb3b’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘in2’, ‘workflow_step_uuid’: ‘e21bb39a-79a1-45d2-8564-2014cbf8e98a’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘763817bba969bb3b’, ‘update_time’: ‘2026-03-09T03:04:04.215816’, ‘job_id’: None, ‘workflow_step_id’: ‘f4df8294d9246e23’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘in3’, ‘workflow_step_uuid’: ‘477c7a68-1f29-4120-a1f8-b2d321358045’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘f4df8294d9246e23’, ‘update_time’: ‘2026-03-09T03:04:04.215818’, ‘job_id’: None, ‘workflow_step_id’: ‘9802c787bf009fe2’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 3, ‘workflow_step_label’: ‘step1’, ‘workflow_step_uuid’: ‘56514196-7240-4ef2-9b3d-3a30d49b6687’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘0’: {‘id’: ‘b0b7020ba769517f’, ‘workflow_step_id’: ‘8b6f46c593d35e12’, ‘label’: ‘in1’, ‘src’: ‘hdca’}, ‘1’: {‘id’: ‘d732dd4c887f1b39’, ‘workflow_step_id’: ‘763817bba969bb3b’, ‘label’: ‘in2’, ‘src’: ‘hdca’}, ‘2’: {‘id’: ‘08e7818090ba2620’, ‘workflow_step_id’: ‘f4df8294d9246e23’, ‘label’: ‘in3’, ‘src’: ‘hdca’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: ‘Cannot match collection types.’, ‘workflow_step_id’: 3}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_conditionals_multi_scatter - cwltest.compare.CompareFail: expected: [
“foo 2”,
“foo 4”,
“foo 6”,
“bar 1”,
“bar 3”,
“bar 5”
]
got: [
[
“bar 1”,
null,
“bar 3”,
null,
“bar 5”,
null
],
[
null,
“foo 2”,
null,
“foo 4”,
null,
“foo 6”
]
]
caused by: lengths don’t match
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_pass_through_required_false_when_nojs - cwltest.compare.CompareFail: expected: “Direct”
got: null
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_first_non_null_first_non_null_nojs - cwltest.compare.CompareFail: expected: “foo 23”
got: [
“foo 23”,
null
]
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_first_non_null_all_null_nojs - Exception: Expected run to fail but it didn’t.
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_first_non_null_second_non_null_nojs - cwltest.compare.CompareFail: expected: “foo 23”
got: [
null,
“foo 23”
]
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_pass_through_required_the_only_non_null_nojs - cwltest.compare.CompareFail: expected: “Direct”
got: null
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_pass_through_required_fail_nojs - Exception: Expected run to fail but it didn’t.
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_the_only_non_null_single_true_nojs - cwltest.compare.CompareFail: expected: “bar 23”
got: [
null,
“bar 23”
]
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_the_only_non_null_multi_true_nojs - Exception: Expected run to fail but it didn’t.
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_all_non_null_all_null_nojs - cwltest.compare.CompareFail: expected: []
got: [
null,
null
]
caused by: lengths don’t match
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_all_non_null_one_non_null_nojs - cwltest.compare.CompareFail: expected: [
“bar 23”
]
got: [
null,
“bar 23”
]
caused by: lengths don’t match
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_condifional_scatter_on_nonscattered_false_nojs - AssertionError: Request status code (400) was not expected value 200. Body was {‘err_msg’: “Workflow cannot be run because input step ‘186’ (data) is not optional and no input provided.”, ‘err_code’: 0}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_condifional_scatter_on_nonscattered_true_nojs - AssertionError: Request status code (400) was not expected value 200. Body was {‘err_msg’: “Workflow cannot be run because input step ‘189’ (data) is not optional and no input provided.”, ‘err_code’: 0}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_scatter_on_scattered_conditional_nojs - AssertionError: Request status code (400) was not expected value 200. Body was {‘err_msg’: “Workflow cannot be run because input step ‘192’ (val) is not optional and no input provided.”, ‘err_code’: 0}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_conditionals_nested_cross_scatter_nojs - AssertionError: Request status code (400) was not expected value 200. Body was {‘err_msg’: “Workflow cannot be run because input step ‘195’ (in1) is not optional and no input provided.”, ‘err_code’: 0}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_conditionals_multi_scatter_nojs - AssertionError: Request status code (400) was not expected value 200. Body was {‘err_msg’: “Workflow cannot be run because input step ‘201’ (in1) is not optional and no input provided.”, ‘err_code’: 0}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_cond_with_defaults_1 - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘c9e8d9c227967b6e’, ‘create_time’: ‘2026-03-09T03:07:24.728672’, ‘update_time’: ‘2026-03-09T03:07:25.194548’, ‘workflow_id’: ‘243bad2e41a5f04f’, ‘history_id’: ‘aea569350f89bf84’, ‘uuid’: ‘18d18568-1b65-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘111726bf3c6a45d3’, ‘update_time’: ‘2026-03-09T03:07:24.984645’, ‘job_id’: None, ‘workflow_step_id’: ‘4270eecb221138ef’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘forward_reads’, ‘workflow_step_uuid’: ‘7ad50cd6-f552-4afa-8981-2f5cb60cb562’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘50e4708495b937c0’, ‘update_time’: ‘2026-03-09T03:07:24.984647’, ‘job_id’: None, ‘workflow_step_id’: ‘f3bf93b37f84569d’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘reverse_reads’, ‘workflow_step_uuid’: ‘942e2ed3-4215-4b4b-af8d-1ce0896cfe0c’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘a35442b0f60ded3a’, ‘update_time’: ‘2026-03-09T03:07:24.984649’, ‘job_id’: None, ‘workflow_step_id’: ‘9c95ca0e2eddcc89’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘single_reads’, ‘workflow_step_uuid’: ‘168541ff-6b92-4978-bffe-9cf0c7592fc4’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘42097d570d9591e6’, ‘update_time’: ‘2026-03-09T03:07:25.197147’, ‘job_id’: None, ‘workflow_step_id’: ‘1a660fbe2b2b7a3b’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 3, ‘workflow_step_label’: ‘step_paired’, ‘workflow_step_uuid’: ‘4a1be081-524b-41b2-8131-ce45499fbd18’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: ‘f356c15ec7800da0’}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘585cfd9e8ccc8e94’, ‘update_time’: ‘2026-03-09T03:07:25.197640’, ‘job_id’: None, ‘workflow_step_id’: ‘7bddf50e5e8cc3d2’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 4, ‘workflow_step_label’: ‘step_single’, ‘workflow_step_uuid’: ‘4805ce5d-77de-48e0-98e8-b8ddc9e2a17b’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘0’: {‘id’: ‘5b21726bdc64ed9d’, ‘workflow_step_id’: ‘4270eecb221138ef’, ‘label’: ‘forward_reads’, ‘src’: ‘hda’}, ‘1’: {‘id’: ‘a50c61d9c2d2a913’, ‘workflow_step_id’: ‘f3bf93b37f84569d’, ‘label’: ‘reverse_reads’, ‘src’: ‘hda’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {‘out_file’: {‘id’: ‘cd0d5ebe0d6c0496’, ‘workflow_step_id’: ‘1a660fbe2b2b7a3b’, ‘src’: ‘hdca’}}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: “1 validation error for _:1e27232b-0ea1-49d3-b46c-5e0526cb6884 (workflow step)\ninitial_file\n Field required [type=missing, input_value={‘out_file_name’: ‘filename_single’}, input_type=dict]\n For further information visit https://errors.pydantic.dev/2.1”, ‘workflow_step_id’: 4}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_cond_with_defaults_2 - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘a18f7a3ebd8971a8’, ‘create_time’: ‘2026-03-09T03:07:30.048844’, ‘update_time’: ‘2026-03-09T03:07:30.256513’, ‘workflow_id’: ‘9a58064fb2c43d99’, ‘history_id’: ‘b44c74861d094619’, ‘uuid’: ‘1bfd5410-1b65-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘36c733bbe04d922b’, ‘update_time’: ‘2026-03-09T03:07:30.206853’, ‘job_id’: None, ‘workflow_step_id’: ‘23a7132c2fbfac9d’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘forward_reads’, ‘workflow_step_uuid’: ‘f5469ced-b4e7-4d81-b18b-d018b25183d9’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘fc9e97b20be64817’, ‘update_time’: ‘2026-03-09T03:07:30.206855’, ‘job_id’: None, ‘workflow_step_id’: ‘02f10775c6928b18’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘reverse_reads’, ‘workflow_step_uuid’: ‘134e5a77-bab5-400c-ba22-5d180099bdeb’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘d8f7bb3c54c0c8d8’, ‘update_time’: ‘2026-03-09T03:07:30.206857’, ‘job_id’: None, ‘workflow_step_id’: ‘b114bfef23b8f61b’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘single_reads’, ‘workflow_step_uuid’: ‘5476cbf4-ed6c-4978-97e0-b80efae22ac1’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘e18dab2fd02e476d’, ‘update_time’: ‘2026-03-09T03:07:30.258869’, ‘job_id’: ‘32316a503e776ac9’, ‘workflow_step_id’: ‘ce17744fc0592198’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 3, ‘workflow_step_label’: ‘step_single’, ‘workflow_step_uuid’: ‘c03ef31c-f2d0-48d5-929b-76939f26a6fc’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘5e785654862ddf8a’, ‘update_time’: ‘2026-03-09T03:07:30.259387’, ‘job_id’: None, ‘workflow_step_id’: ‘3f808cae74b53534’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 4, ‘workflow_step_label’: ‘step_paired’, ‘workflow_step_uuid’: ‘b3e64bf9-cb19-4909-a5bc-89f712270851’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘2’: {‘id’: ‘3553fe5c6be74a24’, ‘workflow_step_id’: ‘b114bfef23b8f61b’, ‘label’: ‘single_reads’, ‘src’: ‘hda’}}, ‘input_step_parameters’: {}, ‘outputs’: {‘out_file’: {‘id’: ‘a788a74d5e06d777’, ‘workflow_step_id’: ‘ce17744fc0592198’, ‘src’: ‘hda’}}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: None, ‘workflow_step_id’: None}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_mixed_version_v12_wf - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘7dd217ef537226a7’, ‘create_time’: ‘2026-03-09T03:07:33.538759’, ‘update_time’: ‘2026-03-09T03:07:33.886007’, ‘workflow_id’: ‘a93804b20b5f5e87’, ‘history_id’: ‘15a3f866c4811e6a’, ‘uuid’: ‘1e11f7ba-1b65-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘57d37d28709b342e’, ‘update_time’: ‘2026-03-09T03:07:33.890476’, ‘job_id’: None, ‘workflow_step_id’: ‘3deef165d6b75a7f’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘inp1’, ‘workflow_step_uuid’: ‘10abecc6-58f8-4ee2-84b5-8dd1b687b44a’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘7d839e83caed8683’, ‘update_time’: ‘2026-03-09T03:07:33.891367’, ‘job_id’: None, ‘workflow_step_id’: ‘40ce3c753772438e’, ‘subworkflow_invocation_id’: None, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘toolv12’, ‘workflow_step_uuid’: ‘300bf512-2ce6-4f81-acda-c5307d253a01’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {}, ‘input_step_parameters’: {‘inp1’: {‘parameter_value’: {‘class’: ‘File’, ‘location’: ‘https://raw.githubusercontent.com/common-workflow-language/cwl-v1.2/main/tests/mixed-versions/hello.txt’}, ‘label’: ‘inp1’, ‘workflow_step_id’: ‘3deef165d6b75a7f’}}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘dataset_failed’, ‘workflow_step_index_path’: None, ‘workflow_step_id’: 1, ‘hda_id’: ‘841695c2790dfb0d’, ‘dependent_workflow_step_id’: None}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_iwd_container_entryname1 - AssertionError: Final state - error - not okay. Full response: {‘model_class’: ‘Job’, ‘id’: ‘dd93bb8edc42a50e’, ‘history_id’: ‘7d2a4a8eeb06732e’, ‘tool_id’: ‘iwd-container-entryname1.cwl’, ‘state’: ‘error’, ‘exit_code’: None, ‘create_time’: ‘2026-03-09T03:08:01.127628’, ‘update_time’: ‘2026-03-09T03:08:01.384958’, ‘galaxy_version’: ‘26.1’, ‘external_id’: None, ‘handler’: None, ‘job_runner_name’: None, ‘command_line’: None, ‘user_email’: ‘test@bx.psu.edu’, ‘user_id’: ‘adb5f5c93f827949’, ‘command_version’: None, ‘params’: {‘chromInfo’: ’“/home/runner/work/galaxy/galaxy/galaxy root/tool-data/shared/ucsc/chrom/?.len”’, ‘dbkey’: ’”?”’, ‘__input_ext’: ‘“input”’}, ‘inputs’: {‘filelist’: {‘id’: ‘b200e6c76cf8becc’, ‘src’: ‘hda’, ‘uuid’: ‘3ec2915e-3419-41b7-a1f6-2ad8306c2351’}}, ‘outputs’: {‘head’: {‘id’: ‘5d462ac951e738a2’, ‘src’: ‘hda’, ‘uuid’: ‘3b01f6c9-35d0-4352-83d8-a50b9afbf552’}}, ‘copied_from_job_id’: None, ‘output_collections’: {}, ‘tool_stdout’: ”, ‘tool_stderr’: ”, ‘job_stdout’: None, ‘job_stderr’: None, ‘stdout’: ”, ‘stderr’: ”, ‘job_messages’: None, ‘dependencies’: [], ‘job_metrics’: []}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_simple_simple_scatter - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘fca558564a37f41b’, ‘create_time’: ‘2026-03-09T03:08:17.895338’, ‘update_time’: ‘2026-03-09T03:08:18.093341’, ‘workflow_id’: ‘b7076a144d094a18’, ‘history_id’: ‘37903b84bafe1288’, ‘uuid’: ‘388170bc-1b65-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘2a722b25a41c5bbb’, ‘update_time’: ‘2026-03-09T03:08:18.097753’, ‘job_id’: None, ‘workflow_step_id’: ‘2cf235fc3a3387c3’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘letters’, ‘workflow_step_uuid’: ‘c2c30edd-361d-4c2d-8474-06b1f2e956d2’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘10d1d7ddf14d8ae5’, ‘update_time’: ‘2026-03-09T03:08:18.097756’, ‘job_id’: None, ‘workflow_step_id’: ‘a53aa9d4dc32b5ed’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘numbers’, ‘workflow_step_uuid’: ‘901150d7-d00e-4e30-ba97-9a9df8bc0932’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘ebdef174148ecc74’, ‘update_time’: ‘2026-03-09T03:08:18.097758’, ‘job_id’: None, ‘workflow_step_id’: ‘466cbf94f4cef7cb’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘start_line’, ‘workflow_step_uuid’: ‘10383728-447f-414b-8bcb-66411f73f587’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘26825b89e51f34bd’, ‘update_time’: ‘2026-03-09T03:08:18.097759’, ‘job_id’: None, ‘workflow_step_id’: ‘16a64ee190b13473’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 3, ‘workflow_step_label’: ‘end_line’, ‘workflow_step_uuid’: ‘fbbfe7af-1436-4253-ba98-6288a51a37e4’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘40c460aba6bd1189’, ‘update_time’: ‘2026-03-09T03:08:18.097761’, ‘job_id’: None, ‘workflow_step_id’: ‘1bea71e3d0564fc1’, ‘subworkflow_invocation_id’: ‘90f4880903567f43’, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 4, ‘workflow_step_label’: ‘scatterletters’, ‘workflow_step_uuid’: ‘bd6fc8ab-863d-42c3-be6c-1487e01ddb52’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘2’: {‘id’: ‘7fd6f4699bfd7b41’, ‘workflow_step_id’: ‘466cbf94f4cef7cb’, ‘label’: ‘start_line’, ‘src’: ‘hda’}, ‘3’: {‘id’: ‘244952b317a2aad0’, ‘workflow_step_id’: ‘16a64ee190b13473’, ‘label’: ‘end_line’, ‘src’: ‘hda’}, ‘0’: {‘id’: ‘48fb965ab29def62’, ‘workflow_step_id’: ‘2cf235fc3a3387c3’, ‘label’: ‘letters’, ‘src’: ‘hdca’}, ‘1’: {‘id’: ‘e76810231f869016’, ‘workflow_step_id’: ‘a53aa9d4dc32b5ed’, ‘label’: ‘numbers’, ‘src’: ‘hdca’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: [4], ‘details’: “1 validation error for _:13b510c5-ad1c-4356-9c85-a4c3564dca00 (workflow step)\nletter\n Input should be a valid string [type=string_type, input_value={‘src’: ‘hdca’, ‘id’: 58}, input_type=dict]\n For further information visit https://errors.pydantic.dev/”, ‘workflow_step_id’: 4}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_dotproduct_simple_scatter - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘243bad2e41a5f04f’, ‘create_time’: ‘2026-03-09T03:08:44.114674’, ‘update_time’: ‘2026-03-09T03:08:44.478938’, ‘workflow_id’: ‘17af7ba02be4dc6a’, ‘history_id’: ‘0a296d7461b1f475’, ‘uuid’: ‘4821ff8c-1b65-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘4270eecb221138ef’, ‘update_time’: ‘2026-03-09T03:08:44.484759’, ‘job_id’: None, ‘workflow_step_id’: ‘90365542fb21d6ae’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘letters’, ‘workflow_step_uuid’: ‘9efecf69-fd22-48a0-8146-6d80c3077a65’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘f3bf93b37f84569d’, ‘update_time’: ‘2026-03-09T03:08:44.484761’, ‘job_id’: None, ‘workflow_step_id’: ‘58155a7d797d11a9’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘letters2’, ‘workflow_step_uuid’: ‘dd84eabf-6a9a-4594-afb3-5fcf6395abb2’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘ce17744fc0592198’, ‘update_time’: ‘2026-03-09T03:08:44.484763’, ‘job_id’: None, ‘workflow_step_id’: ‘81c691bf4bdcf708’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘numbers’, ‘workflow_step_uuid’: ‘34af0de8-0b97-4d5a-b185-d68bcd15db88’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘3f808cae74b53534’, ‘update_time’: ‘2026-03-09T03:08:44.484765’, ‘job_id’: None, ‘workflow_step_id’: ‘32316a503e776ac9’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 3, ‘workflow_step_label’: ‘start_line’, ‘workflow_step_uuid’: ‘1576566f-4b6c-4773-9238-d4d556308fd7’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘b114bfef23b8f61b’, ‘update_time’: ‘2026-03-09T03:08:44.484767’, ‘job_id’: None, ‘workflow_step_id’: ‘71b8873b565cf55f’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 4, ‘workflow_step_label’: ‘end_line’, ‘workflow_step_uuid’: ‘f11a0bb4-9f76-4e97-b223-7fb949c656dd’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘23a7132c2fbfac9d’, ‘update_time’: ‘2026-03-09T03:08:44.484769’, ‘job_id’: None, ‘workflow_step_id’: ‘ec01fa7648822888’, ‘subworkflow_invocation_id’: ‘9a58064fb2c43d99’, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 5, ‘workflow_step_label’: ‘scatterletters’, ‘workflow_step_uuid’: ‘8c6d979f-3beb-4f5b-b076-397554d798a0’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘3’: {‘id’: ‘0db44d233493850c’, ‘workflow_step_id’: ‘32316a503e776ac9’, ‘label’: ‘start_line’, ‘src’: ‘hda’}, ‘4’: {‘id’: ‘74a44aed1c1c226c’, ‘workflow_step_id’: ‘71b8873b565cf55f’, ‘label’: ‘end_line’, ‘src’: ‘hda’}, ‘0’: {‘id’: ‘1d4fd2396356c147’, ‘workflow_step_id’: ‘90365542fb21d6ae’, ‘label’: ‘letters’, ‘src’: ‘hdca’}, ‘1’: {‘id’: ‘c9e8d9c227967b6e’, ‘workflow_step_id’: ‘58155a7d797d11a9’, ‘label’: ‘letters2’, ‘src’: ‘hdca’}, ‘2’: {‘id’: ‘a18f7a3ebd8971a8’, ‘workflow_step_id’: ‘81c691bf4bdcf708’, ‘label’: ‘numbers’, ‘src’: ‘hdca’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: [5], ‘details’: “2 validation errors for _:1c3038b3-9c25-4256-ba19-d095863b495d (workflow step)\nletter\n Input should be a valid string [type=string_type, input_value={‘src’: ‘hdca’, ‘id’: 60}, input_type=dict]\n For further information visit https://errors.pydantic.dev”, ‘workflow_step_id’: 5}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_simple_dotproduct_scatter - cwltest.compare.CompareFail: expected: [
[
“^15a$”,
“^26a$”,
“^37a$”,
“^48a$”
],
[
“^15b$”,
“^26b$”,
“^37b$”,
“^48b$”
],
[
“^15c$”,
“^26c$”,
“^37c$”,
“^48c$”
],
[
“^15d$”,
“^26d$”,
“^37d$”,
“^48d$”
]
]
got: [
“^15a$”,
“^26b$”,
“^37c$”,
“^48d$”
]
caused by: expected: [
“^15a$”,
“^26a$”,
“^37a$”,
“^48a$”
]
got: “^15a$”
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_dotproduct_dotproduct_scatter - cwltest.compare.CompareFail: expected: [
[
“^15aw$”,
“^26aw$”,
“^37aw$”,
“^48aw$”
],
[
“^15bx$”,
“^26bx$”,
“^37bx$”,
“^48bx$”
],
[
“^15cy$”,
“^26cy$”,
“^37cy$”,
“^48cy$”
],
[
“^15dz$”,
“^26dz$”,
“^37dz$”,
“^48dz$”
]
]
got: [
“^15aw$”,
“^26bx$”,
“^37cy$”,
“^48dz$”
]
caused by: expected: [
“^15aw$”,
“^26aw$”,
“^37aw$”,
“^48aw$”
]
got: “^15aw$”
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_flat_crossproduct_simple_scatter - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘17af7ba02be4dc6a’, ‘create_time’: ‘2026-03-09T03:10:46.030473’, ‘update_time’: ‘2026-03-09T03:10:46.196564’, ‘workflow_id’: ‘82aae0a8ec0b5ec7’, ‘history_id’: ‘4e6d5b049d5a4a27’, ‘uuid’: ‘90ccfc64-1b65-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘ed5e20b94b2af525’, ‘update_time’: ‘2026-03-09T03:10:46.198810’, ‘job_id’: None, ‘workflow_step_id’: ‘076343ab9522b737’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘letters’, ‘workflow_step_uuid’: ‘eb6b832c-9ebb-4795-914d-44ff580cb4e7’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘5b21726bdc64ed9d’, ‘update_time’: ‘2026-03-09T03:10:46.198813’, ‘job_id’: None, ‘workflow_step_id’: ‘cda8ec5455a55990’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘letters2’, ‘workflow_step_uuid’: ‘e37fe14e-5a1d-4485-89ff-5a3029bf6aa7’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘a50c61d9c2d2a913’, ‘update_time’: ‘2026-03-09T03:10:46.198815’, ‘job_id’: None, ‘workflow_step_id’: ‘3d0ca2420d1410fd’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘numbers’, ‘workflow_step_uuid’: ‘ea52220c-2def-43d0-8375-20904ebf1b93’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘242ef73637ebc525’, ‘update_time’: ‘2026-03-09T03:10:46.198817’, ‘job_id’: None, ‘workflow_step_id’: ‘84dd6cf348316376’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 3, ‘workflow_step_label’: ‘start_line’, ‘workflow_step_uuid’: ‘b54e77dc-6f03-4fa8-beaa-d6358283cb0d’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘333add226b1f5083’, ‘update_time’: ‘2026-03-09T03:10:46.198818’, ‘job_id’: None, ‘workflow_step_id’: ‘2265c92be2d3286e’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 4, ‘workflow_step_label’: ‘end_line’, ‘workflow_step_uuid’: ‘7c0d9e2e-2cc0-463d-a6aa-eb59ffdc4622’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘3553fe5c6be74a24’, ‘update_time’: ‘2026-03-09T03:10:46.198820’, ‘job_id’: None, ‘workflow_step_id’: ‘2597d4d63959be71’, ‘subworkflow_invocation_id’: ‘c34129969476e859’, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 5, ‘workflow_step_label’: ‘scatterletters’, ‘workflow_step_uuid’: ‘17e37821-9f04-425f-9e4e-9bd43e9a482e’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘3’: {‘id’: ‘ef23fcda9b1b5588’, ‘workflow_step_id’: ‘84dd6cf348316376’, ‘label’: ‘start_line’, ‘src’: ‘hda’}, ‘4’: {‘id’: ‘182c368f02c3b1d2’, ‘workflow_step_id’: ‘2265c92be2d3286e’, ‘label’: ‘end_line’, ‘src’: ‘hda’}, ‘0’: {‘id’: ‘17af7ba02be4dc6a’, ‘workflow_step_id’: ‘076343ab9522b737’, ‘label’: ‘letters’, ‘src’: ‘hdca’}, ‘1’: {‘id’: ‘c34129969476e859’, ‘workflow_step_id’: ‘cda8ec5455a55990’, ‘label’: ‘letters2’, ‘src’: ‘hdca’}, ‘2’: {‘id’: ‘aea569350f89bf84’, ‘workflow_step_id’: ‘3d0ca2420d1410fd’, ‘label’: ‘numbers’, ‘src’: ‘hdca’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: None, ‘workflow_step_id’: None}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_simple_flat_crossproduct_scatter - cwltest.compare.CompareFail: expected: [
[
“^15a$”,
“^16a$”,
“^17a$”,
“^18a$”,
“^25a$”,
“^26a$”,
“^27a$”,
“^28a$”,
“^35a$”,
“^36a$”,
“^37a$”,
“^38a$”,
“^45a$”,
“^46a$”,
“^47a$”,
“^48a$”
],
[
“^15b$”,
“^16b$”,
“^17b$”,
“^18b$”,
“^25b$”,
“^26b$”,
“^27b$”,
“^28b$”,
“^35b$”,
“^36b$”,
“^37b$”,
“^38b$”,
“^45b$”,
“^46b$”,
“^47b$”,
“^48b$”
],
[
“^15c$”,
“^16c$”,
“^17c$”,
“^18c$”,
“^25c$”,
“^26c$”,
“^27c$”,
“^28c$”,
“^35c$”,
“^36c$”,
“^37c$”,
“^38c$”,
“^45c$”,
“^46c$”,
“^47c$”,
“^48c$”
],
[
“^15d$”,
“^16d$”,
“^17d$”,
“^18d$”,
“^25d$”,
“^26d$”,
“^27d$”,
“^28d$”,
“^35d$”,
“^36d$”,
“^37d$”,
“^38d$”,
“^45d$”,
“^46d$”,
“^47d$”,
“^48d$”
]
]
got: [
“^15a$”,
“^26b$”,
“^37c$”,
“^48d$”
]
caused by: expected: [
“^15a$”,
“^16a$”,
“^17a$”,
“^18a$”,
“^25a$”,
“^26a$”,
“^27a$”,
“^28a$”,
“^35a$”,
“^36a$”,
“^37a$”,
“^38a$”,
“^45a$”,
“^46a$”,
“^47a$”,
“^48a$”
]
got: “^15a$”
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_flat_crossproduct_flat_crossproduct_scatter - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘15a3f866c4811e6a’, ‘create_time’: ‘2026-03-09T03:12:06.135367’, ‘update_time’: ‘2026-03-09T03:12:06.386706’, ‘workflow_id’: ‘fe8affe5d81f4f8b’, ‘history_id’: ‘ad3326667f76b816’, ‘uuid’: ‘c08ba6bc-1b65-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘98f497de7995a7ed’, ‘update_time’: ‘2026-03-09T03:12:06.388994’, ‘job_id’: None, ‘workflow_step_id’: ‘f04ab3b54f050a4e’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘letters’, ‘workflow_step_uuid’: ‘f50e2ff0-05ba-4d17-b567-af4946ea5c3e’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘b492c5865e953d13’, ‘update_time’: ‘2026-03-09T03:12:06.388996’, ‘job_id’: None, ‘workflow_step_id’: ‘9fdcb3fa20f21079’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘letters2’, ‘workflow_step_uuid’: ‘c2e1bb2a-9792-4c1e-9f7d-b1cc11bcd371’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘432c010d0dfe7ff4’, ‘update_time’: ‘2026-03-09T03:12:06.388998’, ‘job_id’: None, ‘workflow_step_id’: ‘cc77f1bad5e2da88’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘numbers’, ‘workflow_step_uuid’: ‘e238a4f1-4ba2-4b99-be10-7b19886be1a7’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘e56924ee0dd89f8c’, ‘update_time’: ‘2026-03-09T03:12:06.389000’, ‘job_id’: None, ‘workflow_step_id’: ‘b7697daffd8baebd’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 3, ‘workflow_step_label’: ‘numbers2’, ‘workflow_step_uuid’: ‘829a7588-4ca1-422f-a961-8054096582ee’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘7fd6f4699bfd7b41’, ‘update_time’: ‘2026-03-09T03:12:06.389002’, ‘job_id’: None, ‘workflow_step_id’: ‘cf50bafd8b3bdf25’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 4, ‘workflow_step_label’: ‘start_line’, ‘workflow_step_uuid’: ‘288f71f4-d8e2-4c88-a6a0-248a3cfe124e’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘244952b317a2aad0’, ‘update_time’: ‘2026-03-09T03:12:06.389004’, ‘job_id’: None, ‘workflow_step_id’: ‘47dd087789ea7ece’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 5, ‘workflow_step_label’: ‘end_line’, ‘workflow_step_uuid’: ‘9dfecd8c-3da2-4b55-96e3-55964c65deac’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘f484a1fc984af5bf’, ‘update_time’: ‘2026-03-09T03:12:06.389006’, ‘job_id’: None, ‘workflow_step_id’: ‘8a7b76a44513e204’, ‘subworkflow_invocation_id’: ‘fcefc3cde5ffd71c’, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 6, ‘workflow_step_label’: ‘scatterletters’, ‘workflow_step_uuid’: ‘620c43a7-b83f-412c-a758-7000671fbcf2’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘4’: {‘id’: ‘ba79273507e6c5ec’, ‘workflow_step_id’: ‘cf50bafd8b3bdf25’, ‘label’: ‘start_line’, ‘src’: ‘hda’}, ‘5’: {‘id’: ‘d5610ea872880878’, ‘workflow_step_id’: ‘47dd087789ea7ece’, ‘label’: ‘end_line’, ‘src’: ‘hda’}, ‘0’: {‘id’: ‘7d2a4a8eeb06732e’, ‘workflow_step_id’: ‘f04ab3b54f050a4e’, ‘label’: ‘letters’, ‘src’: ‘hdca’}, ‘1’: {‘id’: ‘37903b84bafe1288’, ‘workflow_step_id’: ‘9fdcb3fa20f21079’, ‘label’: ‘letters2’, ‘src’: ‘hdca’}, ‘2’: {‘id’: ‘0a296d7461b1f475’, ‘workflow_step_id’: ‘cc77f1bad5e2da88’, ‘label’: ‘numbers’, ‘src’: ‘hdca’}, ‘3’: {‘id’: ‘fe8affe5d81f4f8b’, ‘workflow_step_id’: ‘b7697daffd8baebd’, ‘label’: ‘numbers2’, ‘src’: ‘hdca’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: None, ‘workflow_step_id’: None}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_nested_crossproduct_simple_scatter - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘82aae0a8ec0b5ec7’, ‘create_time’: ‘2026-03-09T03:12:31.382577’, ‘update_time’: ‘2026-03-09T03:12:31.593785’, ‘workflow_id’: ‘4e6d5b049d5a4a27’, ‘history_id’: ‘d3296ea2afb7736d’, ‘uuid’: ‘cf986d70-1b65-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘0216e7a4930a65ed’, ‘update_time’: ‘2026-03-09T03:12:31.596726’, ‘job_id’: None, ‘workflow_step_id’: ‘d8e1b6b77f3f0ef7’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘letters’, ‘workflow_step_uuid’: ‘1894e8b9-55e5-41f0-ac91-9a72de88dd10’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘361f333ed747bdc9’, ‘update_time’: ‘2026-03-09T03:12:31.596728’, ‘job_id’: None, ‘workflow_step_id’: ‘c23c8f26b0d04ff8’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘letters2’, ‘workflow_step_uuid’: ‘b9918e99-cdbc-4716-afb3-f8f1b83399e4’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘2597d4d63959be71’, ‘update_time’: ‘2026-03-09T03:12:31.596730’, ‘job_id’: None, ‘workflow_step_id’: ‘7ab57805a7b4eb2d’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘numbers’, ‘workflow_step_uuid’: ‘8f09e710-2db9-4c93-88a0-8d62ce993de3’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘076343ab9522b737’, ‘update_time’: ‘2026-03-09T03:12:31.596732’, ‘job_id’: None, ‘workflow_step_id’: ‘c85c9cf6b4627e83’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 3, ‘workflow_step_label’: ‘start_line’, ‘workflow_step_uuid’: ‘24f7cd80-a088-4be7-bae2-f64fd8771843’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘cda8ec5455a55990’, ‘update_time’: ‘2026-03-09T03:12:31.596734’, ‘job_id’: None, ‘workflow_step_id’: ‘28cea5330c96c3e0’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 4, ‘workflow_step_label’: ‘end_line’, ‘workflow_step_uuid’: ‘249bcf06-8ada-49a6-a6a0-b15305be65fb’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘3d0ca2420d1410fd’, ‘update_time’: ‘2026-03-09T03:12:31.596736’, ‘job_id’: None, ‘workflow_step_id’: ‘a2c2f53f833a54c5’, ‘subworkflow_invocation_id’: ‘7d2a4a8eeb06732e’, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 5, ‘workflow_step_label’: ‘scatterletters’, ‘workflow_step_uuid’: ‘841b48a8-d166-48f4-9878-77fa99bab6dc’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘3’: {‘id’: ‘acba176cf38a1709’, ‘workflow_step_id’: ‘c85c9cf6b4627e83’, ‘label’: ‘start_line’, ‘src’: ‘hda’}, ‘4’: {‘id’: ‘3607dcbef30930ec’, ‘workflow_step_id’: ‘28cea5330c96c3e0’, ‘label’: ‘end_line’, ‘src’: ‘hda’}, ‘0’: {‘id’: ‘2457aeadef0b103d’, ‘workflow_step_id’: ‘d8e1b6b77f3f0ef7’, ‘label’: ‘letters’, ‘src’: ‘hdca’}, ‘1’: {‘id’: ‘4e6d5b049d5a4a27’, ‘workflow_step_id’: ‘c23c8f26b0d04ff8’, ‘label’: ‘letters2’, ‘src’: ‘hdca’}, ‘2’: {‘id’: ‘33758e25c6d4af44’, ‘workflow_step_id’: ‘7ab57805a7b4eb2d’, ‘label’: ‘numbers’, ‘src’: ‘hdca’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: None, ‘workflow_step_id’: None}]}
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_simple_nested_crossproduct_scatter - cwltest.compare.CompareFail: expected: [
[
[
“^15a$”,
“^16a$”,
“^17a$”,
“^18a$”
],
[
“^25a$”,
“^26a$”,
“^27a$”,
“^28a$”
],
[
“^35a$”,
“^36a$”,
“^37a$”,
“^38a$”
],
[
“^45a$”,
“^46a$”,
“^47a$”,
“^48a$”
]
],
[
[
“^15b$”,
“^16b$”,
“^17b$”,
“^18b$”
],
[
“^25b$”,
“^26b$”,
“^27b$”,
“^28b$”
],
[
“^35b$”,
“^36b$”,
“^37b$”,
“^38b$”
],
[
“^45b$”,
“^46b$”,
“^47b$”,
“^48b$”
]
],
[
[
“^15c$”,
“^16c$”,
“^17c$”,
“^18c$”
],
[
“^25c$”,
“^26c$”,
“^27c$”,
“^28c$”
],
[
“^35c$”,
“^36c$”,
“^37c$”,
“^38c$”
],
[
“^45c$”,
“^46c$”,
“^47c$”,
“^48c$”
]
],
[
[
“^15d$”,
“^16d$”,
“^17d$”,
“^18d$”
],
[
“^25d$”,
“^26d$”,
“^27d$”,
“^28d$”
],
[
“^35d$”,
“^36d$”,
“^37d$”,
“^38d$”
],
[
“^45d$”,
“^46d$”,
“^47d$”,
“^48d$”
]
]
]
got: [
“^15a$”,
“^26b$”,
“^37c$”,
“^48d$”
]
caused by: expected: [
[
“^15a$”,
“^16a$”,
“^17a$”,
“^18a$”
],
[
“^25a$”,
“^26a$”,
“^27a$”,
“^28a$”
],
[
“^35a$”,
“^36a$”,
“^37a$”,
“^38a$”
],
[
“^45a$”,
“^46a$”,
“^47a$”,
“^48a$”
]
]
got: “^15a$”
FAILED lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py::TestCwlConformance::test_conformance_v1_2_nested_crossproduct_nested_crossproduct_scatter - AssertionError: Final state - failed - not okay. Full response: {‘model_class’: ‘WorkflowInvocation’, ‘id’: ‘fe8affe5d81f4f8b’, ‘create_time’: ‘2026-03-09T03:13:51.367150’, ‘update_time’: ‘2026-03-09T03:13:51.687143’, ‘workflow_id’: ‘6be72c87c27f6fb3’, ‘history_id’: ‘86b129d9086083a8’, ‘uuid’: ‘ff44954e-1b65-11f1-bc25-70a8a54142bd’, ‘state’: ‘failed’, ‘landing_uuid’: None, ‘on_complete’: None, ‘steps’: [{‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘bf7111057f4d54a5’, ‘update_time’: ‘2026-03-09T03:13:51.690269’, ‘job_id’: None, ‘workflow_step_id’: ‘182c368f02c3b1d2’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 0, ‘workflow_step_label’: ‘letters’, ‘workflow_step_uuid’: ‘bb66d1c1-57a4-4fb7-b218-0f2e0de4f77b’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘81c347cd5446a563’, ‘update_time’: ‘2026-03-09T03:13:51.690272’, ‘job_id’: None, ‘workflow_step_id’: ‘18836156a89764fd’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 1, ‘workflow_step_label’: ‘letters2’, ‘workflow_step_uuid’: ‘237e0893-3026-4f50-bae7-e3733f57b601’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘2afa08de8348e032’, ‘update_time’: ‘2026-03-09T03:13:51.690296’, ‘job_id’: None, ‘workflow_step_id’: ‘f8c03943a30b249a’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 2, ‘workflow_step_label’: ‘numbers’, ‘workflow_step_uuid’: ‘d27a460b-9311-4483-b333-d12f9cfd1efa’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘83e7db820ef95572’, ‘update_time’: ‘2026-03-09T03:13:51.690298’, ‘job_id’: None, ‘workflow_step_id’: ‘ba4d3e349751c963’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 3, ‘workflow_step_label’: ‘numbers2’, ‘workflow_step_uuid’: ‘659f2adf-ea0e-4a0e-98d9-2a3b7aff28c1’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘b3c249a565447f43’, ‘update_time’: ‘2026-03-09T03:13:51.690300’, ‘job_id’: None, ‘workflow_step_id’: ‘8784ae9fbf97376e’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 4, ‘workflow_step_label’: ‘start_line’, ‘workflow_step_uuid’: ‘f969b9f3-9fff-4e18-888a-ed39728dea40’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘a3326b693363bfa1’, ‘update_time’: ‘2026-03-09T03:13:51.690303’, ‘job_id’: None, ‘workflow_step_id’: ‘ba3fd0677107aa97’, ‘subworkflow_invocation_id’: None, ‘state’: ‘scheduled’, ‘action’: None, ‘order_index’: 5, ‘workflow_step_label’: ‘end_line’, ‘workflow_step_uuid’: ‘68ecaf4a-721d-4771-97a9-6a1f14d0f336’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}, {‘model_class’: ‘WorkflowInvocationStep’, ‘id’: ‘d1767c016f5a3633’, ‘update_time’: ‘2026-03-09T03:13:51.690305’, ‘job_id’: None, ‘workflow_step_id’: ‘ef23fcda9b1b5588’, ‘subworkflow_invocation_id’: ‘2457aeadef0b103d’, ‘state’: ‘new’, ‘action’: None, ‘order_index’: 6, ‘workflow_step_label’: ‘scatterletters’, ‘workflow_step_uuid’: ‘1e1d014d-985f-4c5c-8625-37abaf194521’, ‘outputs’: {}, ‘output_collections’: {}, ‘jobs’: [], ‘implicit_collection_jobs_id’: None}], ‘inputs’: {‘4’: {‘id’: ‘cb675b6f31a3a656’, ‘workflow_step_id’: ‘8784ae9fbf97376e’, ‘label’: ‘start_line’, ‘src’: ‘hda’}, ‘5’: {‘id’: ‘00818accf91f7305’, ‘workflow_step_id’: ‘ba3fd0677107aa97’, ‘label’: ‘end_line’, ‘src’: ‘hda’}, ‘0’: {‘id’: ‘73a1c34e01a9daf5’, ‘workflow_step_id’: ‘182c368f02c3b1d2’, ‘label’: ‘letters’, ‘src’: ‘hdca’}, ‘1’: {‘id’: ‘76bc6b8e6396dad0’, ‘workflow_step_id’: ‘18836156a89764fd’, ‘label’: ‘letters2’, ‘src’: ‘hdca’}, ‘2’: {‘id’: ‘54b488b258521264’, ‘workflow_step_id’: ‘f8c03943a30b249a’, ‘label’: ‘numbers’, ‘src’: ‘hdca’}, ‘3’: {‘id’: ‘b9a6667b46a83b69’, ‘workflow_step_id’: ‘ba4d3e349751c963’, ‘label’: ‘numbers2’, ‘src’: ‘hdca’}}, ‘input_step_parameters’: {}, ‘outputs’: {}, ‘output_collections’: {}, ‘output_values’: {}, ‘messages’: [{‘reason’: ‘unexpected_failure’, ‘workflow_step_index_path’: None, ‘details’: None, ‘workflow_step_id’: None}]}