pytest-wdl
1.1.0
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User manual
pytest_wdl
pytest-wdl
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C
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I
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W
A
alias() (pytest_wdl.url_schemes.UrlHandler method)
assert_bam_files_equal() (in module pytest_wdl.data_types.bam)
assert_binary_files_equal() (in module pytest_wdl.data_types)
assert_contents_equal() (pytest_wdl.data_types.DataFile method)
assert_text_files_equal() (in module pytest_wdl.data_types)
B
bam_to_sam() (in module pytest_wdl.data_types.bam)
BamDataFile (class in pytest_wdl.data_types.bam)
BaseResponse (class in pytest_wdl.url_schemes)
C
chdir() (in module pytest_wdl.utils)
cleanup() (pytest_wdl.config.UserConfiguration method)
compare_gzip() (in module pytest_wdl.data_types)
compare_output_values() (in module pytest_wdl.executors)
context_dir() (in module pytest_wdl.utils)
COORDINATE (pytest_wdl.data_types.bam.Sorting attribute)
create_data_file() (in module pytest_wdl.core)
create_executor() (in module pytest_wdl.core)
CromwellExecutor (class in pytest_wdl.executors.cromwell)
D
DATA_TYPES (in module pytest_wdl.core)
DataDirs (class in pytest_wdl.core)
DataFile (class in pytest_wdl.data_types)
DataManager (class in pytest_wdl.core)
DataResolver (class in pytest_wdl.core)
default_executors() (in module pytest_wdl.fixtures)
DefaultDataFile (class in pytest_wdl.data_types)
diff_bam_columns() (in module pytest_wdl.data_types.bam)
diff_default() (in module pytest_wdl.data_types)
diff_vcf_columns() (in module pytest_wdl.data_types.vcf)
download_file() (in module pytest_wdl.localizers)
(pytest_wdl.url_schemes.BaseResponse method)
(pytest_wdl.url_schemes.dx.DxResponse method)
(pytest_wdl.url_schemes.Response method)
DxResponse (class in pytest_wdl.url_schemes.dx)
DxUrlHandler (class in pytest_wdl.url_schemes.dx)
E
ensure_path() (in module pytest_wdl.utils)
env_map() (in module pytest_wdl.utils)
Executor (class in pytest_wdl.executors)
EXECUTORS (in module pytest_wdl.core)
F
find_executable_path() (in module pytest_wdl.utils)
find_in_classpath() (in module pytest_wdl.utils)
find_project_path() (in module pytest_wdl.utils)
G
get_content_length() (pytest_wdl.url_schemes.BaseResponse method)
(pytest_wdl.url_schemes.ResponseWrapper method)
get_cromwell_outputs() (pytest_wdl.executors.cromwell.CromwellExecutor static method)
get_dict() (pytest_wdl.core.DataManager method)
get_executor_defaults() (pytest_wdl.config.UserConfiguration method)
get_list() (pytest_wdl.core.DataManager method)
get_workflow_imports() (pytest_wdl.executors.cromwell.CromwellExecutor method)
get_workflow_inputs() (in module pytest_wdl.executors)
H
handles() (pytest_wdl.url_schemes.dx.DxUrlHandler property)
(pytest_wdl.url_schemes.UrlHandler property)
http_headers() (pytest_wdl.localizers.UrlLocalizer property)
I
import_dirs() (in module pytest_wdl.fixtures)
import_paths() (in module pytest_wdl.fixtures)
install_schemes() (in module pytest_wdl.url_schemes)
is_executable() (in module pytest_wdl.utils)
J
JsonDataFile (class in pytest_wdl.data_types.json)
JsonLocalizer (class in pytest_wdl.localizers)
L
LinkLocalizer (class in pytest_wdl.localizers)
localize() (pytest_wdl.localizers.JsonLocalizer method)
(pytest_wdl.localizers.LinkLocalizer method)
(pytest_wdl.localizers.Localizer method)
(pytest_wdl.localizers.StringLocalizer method)
(pytest_wdl.localizers.UrlLocalizer method)
Localizer (class in pytest_wdl.localizers)
log_source() (in module pytest_wdl.executors.miniwdl)
M
make_serializable() (in module pytest_wdl.executors)
Method (class in pytest_wdl.url_schemes)
MiniwdlExecutor (class in pytest_wdl.executors.miniwdl)
N
NAME (pytest_wdl.data_types.bam.Sorting attribute)
NONE (pytest_wdl.data_types.bam.Sorting attribute)
O
OPEN (pytest_wdl.url_schemes.Method attribute)
P
path() (pytest_wdl.data_types.DataFile property)
paths() (pytest_wdl.core.DataDirs property)
plugin_factory_map() (in module pytest_wdl.utils)
PluginFactory (class in pytest_wdl.utils)
project_root() (in module pytest_wdl.fixtures)
project_root_files() (in module pytest_wdl.fixtures)
proxies() (pytest_wdl.localizers.UrlLocalizer property)
pytest_wdl (module)
pytest_wdl.config (module)
pytest_wdl.core (module)
pytest_wdl.data_types (module)
pytest_wdl.data_types.bam (module)
pytest_wdl.data_types.json (module)
pytest_wdl.data_types.vcf (module)
pytest_wdl.executors (module)
pytest_wdl.executors.cromwell (module)
pytest_wdl.executors.miniwdl (module)
pytest_wdl.fixtures (module)
pytest_wdl.localizers (module)
pytest_wdl.url_schemes (module)
pytest_wdl.url_schemes.dx (module)
pytest_wdl.utils (module)
R
read() (pytest_wdl.url_schemes.BaseResponse method)
(pytest_wdl.url_schemes.ResponseWrapper method)
REQUEST (pytest_wdl.url_schemes.Method attribute)
request() (pytest_wdl.url_schemes.UrlHandler method)
resolve() (pytest_wdl.core.DataResolver method)
resolve_file() (in module pytest_wdl.utils)
resolve_value_descriptor() (in module pytest_wdl.utils)
Response (class in pytest_wdl.url_schemes)
RESPONSE (pytest_wdl.url_schemes.Method attribute)
response() (pytest_wdl.url_schemes.UrlHandler method)
ResponseWrapper (class in pytest_wdl.url_schemes)
run_workflow() (pytest_wdl.executors.cromwell.CromwellExecutor method)
(pytest_wdl.executors.Executor method)
(pytest_wdl.executors.miniwdl.MiniwdlExecutor method)
S
safe_string() (in module pytest_wdl.utils)
scheme() (pytest_wdl.url_schemes.dx.DxUrlHandler property)
(pytest_wdl.url_schemes.UrlHandler property)
set_compare_opts() (pytest_wdl.data_types.DataFile method)
Sorting (class in pytest_wdl.data_types.bam)
StringLocalizer (class in pytest_wdl.localizers)
T
tempdir() (in module pytest_wdl.utils)
U
UrlHandler (class in pytest_wdl.url_schemes)
UrlLocalizer (class in pytest_wdl.localizers)
urlopen() (pytest_wdl.url_schemes.dx.DxUrlHandler method)
(pytest_wdl.url_schemes.UrlHandler method)
user_config() (in module pytest_wdl.fixtures)
user_config_file() (in module pytest_wdl.fixtures)
UserConfiguration (class in pytest_wdl.config)
V
validate_outputs() (in module pytest_wdl.executors)
VcfDataFile (class in pytest_wdl.data_types.vcf)
W
workflow_data() (in module pytest_wdl.fixtures)
workflow_data_descriptor_file() (in module pytest_wdl.fixtures)
workflow_data_descriptors() (in module pytest_wdl.fixtures)
workflow_data_resolver() (in module pytest_wdl.fixtures)
workflow_runner() (in module pytest_wdl.fixtures)
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