cytosnake.cli.exec package#

Submodules#

cytosnake.cli.exec.workflow_exec module#

workflow_exec.py

Module containing functions to execute workflows via cytopipe’s CLI interface

cytosnake.cli.exec.workflow_exec.workflow_executor(workflow, n_cores: int | None = 1, allow_unlock: bool | None = False, force_run: bool | None = False) → int#

Wrapper for executing cytopipe workflows

Parameters:

  • n_cores (int, optional) – max number of cores to use in the workflow, by default 1

  • allow_unlock (bool, optional) – Locks working directory when running cytopipe if interrupted. If set to True, cytopipe will automatically unlock the working directory. by default False

  • force_run (bool, optional) – If set to True, when re-running cytopipe’s workflow will start from the beginning. If False, the workflow will start where it last stopped. by default False

Module contents#