toil.test.wdl.wdltoil_test
¶
Module Contents¶
Classes¶
Base test class for WDL tests. |
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WDL conformance tests for Toil. |
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Tests for Toil's MiniWDL-based implementation. |
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Ensure WDL works on the Kubernetes batchsystem. |
- class toil.test.wdl.wdltoil_test.BaseWDLTest(methodName='runTest')¶
Bases:
toil.test.ToilTest
Base test class for WDL tests.
- setUp()¶
Runs anew before each test to create farm fresh temp dirs.
- Return type:
None
- tearDown()¶
Hook method for deconstructing the test fixture after testing it.
- Return type:
None
- class toil.test.wdl.wdltoil_test.WDLConformanceTests(methodName='runTest')¶
Bases:
BaseWDLTest
WDL conformance tests for Toil.
- wdl_dir = 'wdl-conformance-tests'¶
- classmethod setUpClass()¶
Hook method for setting up class fixture before running tests in the class.
- Return type:
None
- test_conformance_tests_v10()¶
- test_conformance_tests_v11()¶
- classmethod tearDownClass()¶
Hook method for deconstructing the class fixture after running all tests in the class.
- Return type:
None
- class toil.test.wdl.wdltoil_test.WDLTests(methodName='runTest')¶
Bases:
BaseWDLTest
Tests for Toil’s MiniWDL-based implementation.
- classmethod setUpClass()¶
Runs once for all tests.
- Return type:
None
- test_MD5sum()¶
Test if Toil produces the same outputs as known good outputs for WDL’s GATK tutorial #1.
- test_missing_output_directory()¶
Test if Toil can run a WDL workflow into a new directory.
- test_miniwdl_self_test(extra_args=None)¶
Test if the MiniWDL self test runs and produces the expected output.
- Parameters:
extra_args (Optional[List[str]])
- Return type:
None
- test_miniwdl_self_test_by_reference()¶
Test if the MiniWDL self test works when passing input files by URL reference.
- Return type:
None
- test_giraffe_deepvariant()¶
Test if Giraffe and GPU DeepVariant run. This could take 25 minutes.
- test_giraffe()¶
Test if Giraffe runs. This could take 12 minutes. Also we scale it down but it still demands lots of memory.
- test_gs_uri()¶
Test if Toil can access Google Storage URIs.
- test_coalesce()¶
Test if WDLSectionJob can coalesce WDL decls.
White box test; will need to be changed or removed if the WDL interpreter changes.
- class toil.test.wdl.wdltoil_test.WDLKubernetesClusterTest(name)¶
Bases:
toil.test.provisioners.clusterTest.AbstractClusterTest
Ensure WDL works on the Kubernetes batchsystem.
- setUp()¶
Set up for the test. Must be overridden to call this method and set self.jobStore.
- Return type:
None
- launchCluster()¶
- Return type:
None
- test_wdl_kubernetes_cluster()¶
Test that a wdl workflow works on a kubernetes cluster. Launches a cluster with 1 worker. This runs a wdl workflow that performs an image pull on the worker. :return: