{"id":27894456,"url":"https://github.com/multimeric/miniwdlbug","last_synced_at":"2026-01-22T13:49:02.284Z","repository":{"id":285850121,"uuid":"959555776","full_name":"multimeric/MiniWdlBug","owner":"multimeric","description":null,"archived":false,"fork":false,"pushed_at":"2025-04-03T01:21:21.000Z","size":14,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-05-05T14:52:11.659Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"WDL","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/multimeric.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2025-04-03T01:18:30.000Z","updated_at":"2025-04-03T01:21:24.000Z","dependencies_parsed_at":"2025-04-03T02:26:11.521Z","dependency_job_id":"fd09547d-7860-4562-be38-c6656bb8c586","html_url":"https://github.com/multimeric/MiniWdlBug","commit_stats":null,"previous_names":["multimeric/miniwdlbug"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/multimeric/MiniWdlBug","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2FMiniWdlBug","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2FMiniWdlBug/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2FMiniWdlBug/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2FMiniWdlBug/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/multimeric","download_url":"https://codeload.github.com/multimeric/MiniWdlBug/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2FMiniWdlBug/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28664036,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-22T01:17:37.254Z","status":"online","status_checked_at":"2026-01-22T02:00:07.137Z","response_time":144,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-05-05T14:41:37.719Z","updated_at":"2026-01-22T13:49:02.268Z","avatar_url":"https://github.com/multimeric.png","language":"WDL","funding_links":[],"categories":[],"sub_categories":[],"readme":"```bash\nuv run miniwdl run wf.wdl --cfg conf.cfg\n```\n\n```\n2025-04-03 12:20:25.917 wdl.w:wf NOTICE workflow start :: name: \"wf\", source: \"wf.wdl\", line: 10, column: 1, dir: \"/vast/scratch/users/milton.m/MiniWdlBug/20250403_122025_wf\"\n2025-04-03 12:20:25.931 wdl.w:wf NOTICE miniwdl :: version: \"v1.12.1\", uname: \"Linux slurm-login02.hpc.wehi.edu.au 5.14.0-362.24.1.el9_3.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Feb 15 07:18:13 EST 2024 x86_64\"\n2025-04-03 12:20:25.938 wdl.w:wf NOTICE ready :: job: \"call-my_task\", callee: \"my_task\"\n2025-04-03 12:20:25.945 wdl.w:wf.t:call-my_task NOTICE task setup :: name: \"my_task\", source: \"wf.wdl\", line: 1, column: 1, dir: \"/vast/scratch/users/milton.m/MiniWdlBug/20250403_122025_wf/call-my_task\", thread: 22525751285312\n2025-04-03 12:20:26.368 wdl.w:wf.t:call-my_task NOTICE Singularity runtime initialized (BETA) :: singularity_version: \"apptainer version 1.3.3\"\n2025-04-03 12:20:26.376 wdl.w:wf.t:call-my_task ERROR task my_task (wf.wdl Ln 1 Col 1) failed :: dir: \"/vast/scratch/users/milton.m/MiniWdlBug/20250403_122025_wf/call-my_task\", error: \"KeyError\", message: \"'docker'\", traceback: [\"Traceback (most recent call last):\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task.py\\\", line 207, in run_local_task\", \"    _try_task(cfg, task, logger, container, command, terminating)\", \"    ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task.py\\\", line 608, in _try_task\", \"    return container.run(logger, command)\", \"           ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task_container.py\\\", line 323, in run\", \"    exit_code = self._run(logger, terminating, command)\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/cli_subprocess.py\\\", line 67, in _run\", \"    image = self._pull(logger, cleanup)\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/cli_subprocess.py\\\", line 186, in _pull\", \"    image, invocation = self._pull_invocation(logger, cleanup)\", \"                        ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/singularity.py\\\", line 62, in _pull_invocation\", \"    image, invocation = super()._pull_invocation(logger, cleanup)\", \"                        ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/cli_subprocess.py\\\", line 132, in _pull_invocation\", \"    \\\"docker\\\", self.cfg.get_dict(\\\"task_runtime\\\", \\\"defaults\\\")[\\\"docker\\\"]\", \"              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^\", \"KeyError: 'docker'\"]\n2025-04-03 12:20:26.394 wdl.w:wf ERROR call failure propagating :: from: \"call-my_task\", dir: \"/vast/scratch/users/milton.m/MiniWdlBug/20250403_122025_wf\"\n2025-04-03 12:20:26.394 wdl.w:wf NOTICE aborting workflow\n2025-04-03 12:20:26.400 miniwdl-run ERROR 'docker' :: error: \"KeyError\", traceback: [\"Traceback (most recent call last):\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task.py\\\", line 207, in run_local_task\", \"    _try_task(cfg, task, logger, container, command, terminating)\", \"    ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task.py\\\", line 608, in _try_task\", \"    return container.run(logger, command)\", \"           ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task_container.py\\\", line 323, in run\", \"    exit_code = self._run(logger, terminating, command)\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/cli_subprocess.py\\\", line 67, in _run\", \"    image = self._pull(logger, cleanup)\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/cli_subprocess.py\\\", line 186, in _pull\", \"    image, invocation = self._pull_invocation(logger, cleanup)\", \"                        ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/singularity.py\\\", line 62, in _pull_invocation\", \"    image, invocation = super()._pull_invocation(logger, cleanup)\", \"                        ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/backend/cli_subprocess.py\\\", line 132, in _pull_invocation\", \"    \\\"docker\\\", self.cfg.get_dict(\\\"task_runtime\\\", \\\"defaults\\\")[\\\"docker\\\"]\", \"              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^\", \"KeyError: 'docker'\", \"\", \"The above exception was the direct cause of the following exception:\", \"\", \"Traceback (most recent call last):\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/workflow.py\\\", line 1046, in _workflow_main_loop\", \"    __, outputs = future.result()\", \"                  ~~~~~~~~~~~~~^^\", \"  File \\\"/home/users/allstaff/milton.m/.local/share/uv/python/cpython-3.13.1-linux-x86_64-gnu/lib/python3.13/concurrent/futures/_base.py\\\", line 449, in result\", \"    return self.__get_result()\", \"           ~~~~~~~~~~~~~~~~~^^\", \"  File \\\"/home/users/allstaff/milton.m/.local/share/uv/python/cpython-3.13.1-linux-x86_64-gnu/lib/python3.13/concurrent/futures/_base.py\\\", line 401, in __get_result\", \"    raise self._exception\", \"  File \\\"/home/users/allstaff/milton.m/.local/share/uv/python/cpython-3.13.1-linux-x86_64-gnu/lib/python3.13/concurrent/futures/thread.py\\\", line 59, in run\", \"    result = self.fn(*self.args, **self.kwargs)\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/task.py\\\", line 275, in run_local_task\", \"    raise wrapper from exn\", \"WDL.runtime.error.RunFailed: task my_task (wf.wdl Ln 1 Col 1) failed\", \"\", \"The above exception was the direct cause of the following exception:\", \"\", \"Traceback (most recent call last):\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/CLI.py\\\", line 821, in runner\", \"    rundir, output_env = runtime.run(cfg, target, input_env, run_dir=run_dir, _cache=cache)\", \"                         ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/__init__.py\\\", line 63, in run\", \"    return entrypoint(cfg, exe, inputs, **run_kwargs)  # type: ignore\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/workflow.py\\\", line 934, in run_local_workflow\", \"    outputs = _workflow_main_loop(\", \"        cfg,\", \"    ...\u003c9 lines\u003e...\", \"        _test_pickle,\", \"    )\", \"  File \\\"/vast/scratch/users/milton.m/MiniWdlBug/.venv/lib/python3.13/site-packages/WDL/runtime/workflow.py\\\", line 1113, in _workflow_main_loop\", \"    raise wrapper from exn\", \"WDL.runtime.error.RunFailed: workflow wf (wf.wdl Ln 10 Col 1) failed\"], dir: \"/vast/scratch/users/milton.m/MiniWdlBug/20250403_122025_wf\", from_dir: \"/vast/scratch/users/milton.m/MiniWdlBug/20250403_122025_wf/call-my_task\"\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmultimeric%2Fminiwdlbug","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmultimeric%2Fminiwdlbug","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmultimeric%2Fminiwdlbug/lists"}