OCDocker.Workbench.Bundle module

Run-bundle builders for prepared Workbench runs.

OCDocker.Workbench.Bundle.build_run_bundle(spec, bundle_dir, *, run_id, overwrite=False, ocdocker_executable='ocdocker', snakemake_executable='snakemake')[source]

Build a prepared run bundle without executing the planned command.

Parameters:

  • spec (WorkbenchSpec) – Validated Workbench spec.

  • bundle_dir (str or pathlib.Path) – Directory that will receive the bundle files.

  • run_id (str) – Stable run identifier for the run manifest.

  • overwrite (bool) – If True, overwrite existing bundle files.

  • ocdocker_executable (str) – OCDocker executable to use in planned OCScore commands.

  • snakemake_executable (str) – Snakemake executable to use in planned VS campaign commands.

Returns:

Prepared bundle summary.

Return type:

RunBundle