module config.enums¶
Configuration enumerators.
class DependencyEmbeddingStrategies¶
Supported dependency embedding strategies.
Attributes:
CONDA: Use binaries from Conda.SINGULARITY: Use Singularity containers.
class ExecModes¶
Execution modes.
Attributes:
DRY_RUN: Do not download any files, infer parameters or start the analysis workflow.PREPARE_RUN: Download files and infer parameters, but do not start the analysis workflow.RUN: Download files, infer parameters and start the analysis workflow.
class LogLevels¶
Log level enumerator.
Attributes:
DEBUG: Logging level for debug messages.INFO: Logging level for info messages.WARNING: Logging level for warning messages.ERROR: Logging level for error messages.CRITICAL: Logging level for critical error messages.
class FieldNameMappingDirection¶
Field name direction enumerator.
Attributes:
TO_MODEL_PROPERTIES: Map from ZARP sample table column to model property names.TO_TABLE_COL_NAMES: Map from model property to ZARP sample table column names.
class ReadOrientation¶
Read orientation types.
Cf. https://salmon.readthedocs.io/en/latest/library_type.html
Attributes:
STRANDED_FORWARD: Reads are stranded and come from the forward strand.STRANDED_REVERSE: Reads are stranded and come from the reverse strand.UNSTRANDED: Reads are unstranded.INWARD_STRANDED_FORWARD: Mates are oriented toward each other, the library is stranded, and first mates come from the forward strand.INWARD_STRANDED_REVERSE: Mates are oriented toward each other, the library is stranded, and first mates come from the reverse strand.INWARD_UNSTRANDED: Mates are oriented toward each other and the library is unstranded.
class SampleReferenceTypes¶
Types of sample references.
Attributes:
LOCAL_LIB_SINGLE: Local single-ended sequencing library.LOCAL_LIB_PAIRED: Local paired-ended sequencing library.REMOTE_LIB_SRA: Sequencing library available at read archive.TABLE: ZARP sample table.INVALID: Reference type invalid.
class SnakemakeRunState¶
Snakemake run states.
Attributes:
UNKNOWN: The Snakemake run state is unknown. This is typically the case when a run was initialized but the state has not yet been updated to a definite state.SUCCESS: The Snakemake run completed successfully.ERROR: The Snakemake run failed.