toil.test.wdl.wdltoil_test

Module Contents

Classes

ToilConformanceTests	New WDL conformance tests for Toil
WdlToilTest	Version of the old Toil WDL tests that tests the new MiniWDL-based implementation.

class toil.test.wdl.wdltoil_test.ToilConformanceTests(methodName='runTest')

Bases: toil.test.wdl.toilwdlTest.BaseToilWdlTest

digraph inheritance1743ad378d { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "BaseToilWdlTest" [URL="../toilwdlTest/index.html#toil.test.wdl.toilwdlTest.BaseToilWdlTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Base test class for WDL tests"]; "ToilTest" -> "BaseToilWdlTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilConformanceTests" [URL="#toil.test.wdl.wdltoil_test.ToilConformanceTests",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="New WDL conformance tests for Toil"]; "BaseToilWdlTest" -> "ToilConformanceTests" [arrowsize=0.5,style="setlinewidth(0.5)"]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

New WDL conformance tests for Toil

wdl_dir = 'wdl-conformance-tests'

classmethod setUpClass()

Runs once for all tests.

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.WdlToilTest(methodName='runTest')

Bases: toil.test.wdl.toilwdlTest.ToilWdlTest

digraph inheritance3f8891d249 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "BaseToilWdlTest" [URL="../toilwdlTest/index.html#toil.test.wdl.toilwdlTest.BaseToilWdlTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Base test class for WDL tests"]; "ToilTest" -> "BaseToilWdlTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "ToilWdlTest" [URL="../toilwdlTest/index.html#toil.test.wdl.toilwdlTest.ToilWdlTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="General tests for Toil WDL"]; "BaseToilWdlTest" -> "ToilWdlTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "WdlToilTest" [URL="#toil.test.wdl.wdltoil_test.WdlToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Version of the old Toil WDL tests that tests the new MiniWDL-based implementation."]; "ToilWdlTest" -> "WdlToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Version of the old Toil WDL tests that tests the new MiniWDL-based implementation.

classmethod setUpClass()

Runs once for all tests.

Return type

None

testMD5sum()

Test if Toil produces the same outputs as known good outputs for WDL’s GATK tutorial #1.

test_empty_file_path()

Test if empty File type inputs are protected against

test_miniwdl_self_test()

Test if the MiniWDL self test runs and produces the expected output.

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_empty_file_path()

Test if empty File type inputs are protected against

test_coalesce()

Test if WDLSectionJob can coalesce WDL decls.

White box test; will need to be changed or removed if the WDL interpreter changes.