OCDocker.Workbench.Preflight module

Read-only preflight checks for Workbench specs before execution.

OCDocker.Workbench.Preflight.preflight_spec(spec, *, spec_path=None, ocdocker_executable='ocdocker', snakemake_executable='snakemake')[source]

Build a read-only preflight report for a validated Workbench spec.

Parameters:

  • spec (WorkbenchSpec) – Validated Workbench spec.

  • spec_path (str or pathlib.Path or None) – Optional source spec path used to resolve relative paths.

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

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

Returns:

Read-only preflight report.

Return type:

PreflightReport

OCDocker.Workbench.Preflight.preflight_spec_file(path, *, ocdocker_executable='ocdocker', snakemake_executable='snakemake')[source]

Build a read-only preflight report from a Workbench spec file.

Parameters:

  • path (str or pathlib.Path) – Workbench spec path.

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

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

Returns:

Read-only preflight report.

Return type:

PreflightReport