fovus pipeline resume¶

Resume a remote pipeline execution.

Provide PIPELINE_DIRECTORY to resume using the pipeline id stored for that pipeline directory (and optionally re-upload files from that directory).

If no pipeline id is found for the pipeline directory, specify the pipeline id to resume with –pipeline-id. It will be saved to the provided pipeline directory after a successful command execution.

If PIPELINE_DIRECTORY is omitted, pass –pipeline-id explicitly. If both are provided and the ids differ, explicit confirmation is required before the stored pipeline id is overwritten. In non-interactive mode (–silence), overwrite is the default.

Only writable fields are configuration.setupCommand and configuration.runCommand. When configuration is provided, runCommand is required; setupCommand is optional. Any other fields are ignored by backend.

Usage

fovus pipeline resume [OPTIONS] [PIPELINE_DIRECTORY]

Options

--pipeline-id <pipeline_id>¶: The ID of the pipeline to resume. Required when PIPELINE_DIRECTORY is omitted or has no stored id yet. If both are provided and the ids differ, explicit confirmation is required before the stored pipeline id for the pipeline directory is overwritten. In non-interactive mode (–silence), overwrite is the default.

-c, --config <config_path>¶: Path to pipeline config JSON for optional overrides. Only configuration.setupCommand and configuration.runCommand are writable (runCommand is required when configuration is provided).

--setup-command <setup_command>¶: Setup command for remote execution. Overrides config if provided.

--run-command <run_command>¶: Run command for remote execution. Overrides config if provided.

--include-paths <include_paths>¶: Include only these paths when uploading pipeline directory. Relative paths inside PIPELINE_DIRECTORY. Use * and ? for wildcards. Only one of –include-paths or –exclude-paths.

--exclude-paths <exclude_paths>¶: Exclude these paths when uploading pipeline directory. Relative paths inside PIPELINE_DIRECTORY. Use * and ? for wildcards. Only one of –include-paths or –exclude-paths.

Arguments

PIPELINE_DIRECTORY¶: Optional argument