toil.test.wdl.wdltoil_test

Module Contents

Classes

BaseWDLTest	Base test class for WDL tests.
WDLConformanceTests	WDL conformance tests for Toil.
WDLTests	Tests for Toil's MiniWDL-based implementation.

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

Bases: toil.test.ToilTest

digraph inheritance437c369ff3 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "BaseWDLTest" [URL="#toil.test.wdl.wdltoil_test.BaseWDLTest",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" -> "BaseWDLTest" [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)"]; }

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

digraph inheritanceef18241562 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "BaseWDLTest" [URL="#toil.test.wdl.wdltoil_test.BaseWDLTest",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" -> "BaseWDLTest" [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)"]; "WDLConformanceTests" [URL="#toil.test.wdl.wdltoil_test.WDLConformanceTests",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="WDL conformance tests for Toil."]; "BaseWDLTest" -> "WDLConformanceTests" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

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

digraph inheritance03e1ab02b7 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "BaseWDLTest" [URL="#toil.test.wdl.wdltoil_test.BaseWDLTest",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" -> "BaseWDLTest" [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)"]; "WDLTests" [URL="#toil.test.wdl.wdltoil_test.WDLTests",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="Tests for Toil's MiniWDL-based implementation."]; "BaseWDLTest" -> "WDLTests" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

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_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.