fovus pipeline resume

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.

Setup command, run command, and storage connectors can be changed. When configuration is provided, the run command is required if setup command is given; storage connectors can be changed independently. Any other fields are ignored.

–storage-connectors REPLACES the pipeline’s declared connector set wholesale, not additively. Omitting –storage-connectors leaves the pipeline’s currently-declared connectors untouched. Pass –clear-storage-connectors to remove all of them.

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 setup and run commands can be changed (run command 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.

--storage-connectors <storage_connectors_tuple>

Replace the pipeline’s declared storage connector names with this set. A storage connector gives both the pipeline host (the machine running pipeline orchestration, e.g. Nextflow) and the pipeline’s jobs access to a storage location outside Fovus storage. Names may contain only letters, digits, and hyphens. Repeat the option for multiple connectors. Omit this option entirely to leave the pipeline’s currently-declared connectors unchanged; use –clear-storage-connectors to remove all of them. Cannot be combined with –clear-storage-connectors.

--clear-storage-connectors

Remove all storage connectors declared on the pipeline. Cannot be combined with –storage-connectors.

--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