wfcommons.wfbench

wfcommons.wfbench.bench

class wfcommons.wfbench.translator.nextflow.NextflowTranslator(workflow: Workflow | Path, logger: Logger | None = None)

Bases: Translator

A WfFormat parser for creating Nextflow workflow applications.

Parameters:

workflow (Union[Workflow, pathlib.Path],) – Workflow benchmark object or path to the workflow benchmark JSON instance.
logger (Logger) – The logger where to log information/warning or errors (optional).

static _create_task_script(output_folder: Path, task: Task)

Generate the bash script for invoking a task.

Parameters:

Returns:

The code.

Return type:

str

_create_workflow_script(tasks: list[Task])

Create the Nextflow script.

_generate_arg_parsing_code()

Generate the code to parse command-line argument.

_generate_task_code(task: Task) → str

Generate the code for a task, as a Nextflow process.

_generate_task_function(task: Task) → str

Generate the code for a starting a task’s Nextflow process, as a Nextflow function.

_generate_workflow_code(sorted_tasks: List[Task]) → str

Generate the code for the workflow.

_get_tasks_in_topological_order() → List[Task]

Sort the workflow tasks in topological order.

_write_readme_file(output_folder: Path) → None

Write the README file.

Parameters:: output_folder (pathlib.Path) – The path of the output folder.

translate(output_folder: Path) → None

Translate a workflow benchmark description(WfFormat) into a Nextflow workflow application.

Parameters:: output_folder (pathlib.Path) – The path to the folder in which the workflow benchmark will be generated.