schema_salad.tests.test_real_cwl

Checks loading of some real world tools and workflows found in the wild (e.g. dockstore)

run individually as py.test -k tests/test_real_cwl.py

Module Contents

Classes

TestRealWorldCWL

Attributes

test_dir_name

schema_salad.tests.test_real_cwl.test_dir_name = 'tests/test_real_cwl/'

class schema_salad.tests.test_real_cwl.TestRealWorldCWL

document_loader: schema_salad.ref_resolver.Loader

avsc_names: schema_salad.avro.schema.Names | schema_salad.avro.schema.SchemaParseException | None

schema_metadata: Dict[str, Any] | None

metaschema_loader: schema_salad.ref_resolver.Loader | None

classmethod setup_class()

Return type:

None

load_cwl(src)

Parameters:

src (str) –

Return type:

None

test_topmed_single_doc()

TOPMed Variant Calling Pipeline CWL1

Return type:

None

test_h3agatk_WES()

H3ABioNet GATK Germline Workflow

Return type:

None

test_h3agatk_SNP()

H3ABioNet SNPs Workflow

Return type:

None

test_icgc_pancan()

ICGC PanCan

Return type:

None