wfcommons.wfchef

wfcommons.wfchef.recipes.blast.recipe

class wfcommons.wfchef.recipes.blast.recipe.BlastRecipe(data_footprint: int | None = 0, num_tasks: int | None = 3, exclude_graphs: Set[str] | None = None, runtime_factor: float | None = 1.0, input_file_size_factor: float | None = 1.0, output_file_size_factor: float | None = 1.0, logger: Logger | None = None, base_method: BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)

Bases: WfChefWorkflowRecipe

A Blast workflow recipe class for creating synthetic workflow instances.

Parameters:

  • data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).

  • num_tasks (int) – The upper bound for the total number of tasks in the workflow.

  • exclude_graphs (Set)

  • runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.

  • input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.

  • output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.

  • logger (Logger) – The logger where to log information/warning or errors (optional).

wfcommons.wfchef.recipes.bwa.recipe

class wfcommons.wfchef.recipes.bwa.recipe.BwaRecipe(data_footprint: int | None = 0, num_tasks: int | None = 3, exclude_graphs: Set[str] | None = None, runtime_factor: float | None = 1.0, input_file_size_factor: float | None = 1.0, output_file_size_factor: float | None = 1.0, logger: Logger | None = None, base_method: BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)

Bases: WfChefWorkflowRecipe

A Bwa workflow recipe class for creating synthetic workflow instances.

Parameters:

  • data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).

  • num_tasks (int) – The upper bound for the total number of tasks in the workflow.

  • exclude_graphs (Set)

  • runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.

  • input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.

  • output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.

  • logger (Logger) – The logger where to log information/warning or errors (optional).

wfcommons.wfchef.recipes.cycles.recipe

class wfcommons.wfchef.recipes.cycles.recipe.CyclesRecipe(data_footprint: int | None = 0, num_tasks: int | None = 3, exclude_graphs: Set[str] | None = None, runtime_factor: float | None = 1.0, input_file_size_factor: float | None = 1.0, output_file_size_factor: float | None = 1.0, logger: Logger | None = None, base_method: BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)

Bases: WfChefWorkflowRecipe

A Cycles workflow recipe class for creating synthetic workflow instances.

Parameters:

  • data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).

  • num_tasks (int) – The upper bound for the total number of tasks in the workflow.

  • exclude_graphs (Set)

  • runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.

  • input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.

  • output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.

  • logger (Logger) – The logger where to log information/warning or errors (optional).

wfcommons.wfchef.recipes.epigenomics.recipe

class wfcommons.wfchef.recipes.epigenomics.recipe.EpigenomicsRecipe(data_footprint: int | None = 0, num_tasks: int | None = 3, exclude_graphs: Set[str] | None = None, runtime_factor: float | None = 1.0, input_file_size_factor: float | None = 1.0, output_file_size_factor: float | None = 1.0, logger: Logger | None = None, base_method: BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)

Bases: WfChefWorkflowRecipe

A Epigenomics workflow recipe class for creating synthetic workflow instances.

Parameters:

  • data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).

  • num_tasks (int) – The upper bound for the total number of tasks in the workflow.

  • exclude_graphs (Set)

  • runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.

  • input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.

  • output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.

  • logger (Logger) – The logger where to log information/warning or errors (optional).

wfcommons.wfchef.recipes.genome.recipe

class wfcommons.wfchef.recipes.genome.recipe.GenomeRecipe(data_footprint: int | None = 0, num_tasks: int | None = 3, exclude_graphs: Set[str] | None = None, runtime_factor: float | None = 1.0, input_file_size_factor: float | None = 1.0, output_file_size_factor: float | None = 1.0, logger: Logger | None = None, base_method: BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)

Bases: WfChefWorkflowRecipe

A Genome workflow recipe class for creating synthetic workflow instances.

Parameters:

  • data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).

  • num_tasks (int) – The upper bound for the total number of tasks in the workflow.

  • exclude_graphs (Set)

  • runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.

  • input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.

  • output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.

  • logger (Logger) – The logger where to log information/warning or errors (optional).

wfcommons.wfchef.recipes.montage.recipe

class wfcommons.wfchef.recipes.montage.recipe.MontageRecipe(data_footprint: int | None = 0, num_tasks: int | None = 3, exclude_graphs: Set[str] | None = None, runtime_factor: float | None = 1.0, input_file_size_factor: float | None = 1.0, output_file_size_factor: float | None = 1.0, logger: Logger | None = None, base_method: BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)

Bases: WfChefWorkflowRecipe

A Montage workflow recipe class for creating synthetic workflow instances.

Parameters:

  • data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).

  • num_tasks (int) – The upper bound for the total number of tasks in the workflow.

  • exclude_graphs (Set)

  • runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.

  • input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.

  • output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.

  • logger (Logger) – The logger where to log information/warning or errors (optional).

wfcommons.wfchef.recipes.rnaseq.recipe

class wfcommons.wfchef.recipes.rnaseq.recipe.RnaseqRecipe(data_footprint: int | None = 0, num_tasks: int | None = 3, exclude_graphs: Set[str] | None = None, runtime_factor: float | None = 1.0, input_file_size_factor: float | None = 1.0, output_file_size_factor: float | None = 1.0, logger: Logger | None = None, base_method: BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)

Bases: WfChefWorkflowRecipe

A Rnaseq workflow recipe class for creating synthetic workflow instances.

Parameters:

  • data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).

  • num_tasks (int) – The upper bound for the total number of tasks in the workflow.

  • exclude_graphs (Set)

  • runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.

  • input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.

  • output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.

  • logger (Logger) – The logger where to log information/warning or errors (optional).

wfcommons.wfchef.recipes.seismology.recipe

class wfcommons.wfchef.recipes.seismology.recipe.SeismologyRecipe(data_footprint: int | None = 0, num_tasks: int | None = 3, exclude_graphs: Set[str] = None, runtime_factor: float | None = 1.0, input_file_size_factor: float | None = 1.0, output_file_size_factor: float | None = 1.0, logger: Logger | None = None, base_method: BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)

Bases: WfChefWorkflowRecipe

A Seismology workflow recipe class for creating synthetic workflow instances.

Parameters:

  • data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).

  • num_tasks (int) – The upper bound for the total number of tasks in the workflow.

  • exclude_graphs (Set)

  • runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.

  • input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.

  • output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.

  • logger (Logger) – The logger where to log information/warning or errors (optional).

wfcommons.wfchef.recipes.soykb.recipe

class wfcommons.wfchef.recipes.soykb.recipe.SoykbRecipe(data_footprint: int | None = 0, num_tasks: int | None = 3, exclude_graphs: Set[str] | None = None, runtime_factor: float | None = 1.0, input_file_size_factor: float | None = 1.0, output_file_size_factor: float | None = 1.0, logger: Logger | None = None, base_method: BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)

Bases: WfChefWorkflowRecipe

A Soykb workflow recipe class for creating synthetic workflow instances.

Parameters:

  • data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).

  • num_tasks (int) – The upper bound for the total number of tasks in the workflow.

  • exclude_graphs (Set)

  • runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.

  • input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.

  • output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.

  • logger (Logger) – The logger where to log information/warning or errors (optional).

wfcommons.wfchef.recipes.srasearch.recipe

class wfcommons.wfchef.recipes.srasearch.recipe.SrasearchRecipe(data_footprint: int | None = 0, num_tasks: int | None = 3, exclude_graphs: Set[str] | None = None, runtime_factor: float | None = 1.0, input_file_size_factor: float | None = 1.0, output_file_size_factor: float | None = 1.0, logger: Logger | None = None, base_method: BaseMethod = BaseMethod.ERROR_TABLE, **kwargs)

Bases: WfChefWorkflowRecipe

A Srasearch workflow recipe class for creating synthetic workflow instances.

Parameters:

  • data_footprint (int) – The upper bound for the workflow total data footprint (in bytes).

  • num_tasks (int) – The upper bound for the total number of tasks in the workflow.

  • exclude_graphs (Set)

  • runtime_factor (float) – The factor of which tasks runtime will be increased/decreased.

  • input_file_size_factor (float) – The factor of which tasks input files size will be increased/decreased.

  • output_file_size_factor (float) – The factor of which tasks output files size will be increased/decreased.

  • logger (Logger) – The logger where to log information/warning or errors (optional).