Batch plugin¶

Available since version 1.1.0, the batch plugin runs multiple plugin executions sequentially with the same resolved CWL context. An execution plan in YAML specifies the plugins and their inputs.

Command¶

transpiler-mate batch [OPTIONS] SOURCE

SOURCE is the CWL document, as with other plugin commands. In addition to the shared runtime options, the plugin accepts:

The plugin's BatchOption model defines this option; the runtime generates the CLI option from the model.

Execution file¶

tmom stands for Transpiler Mate Object Model.

Create tmom.yaml in your working directory:

bundle:
  - output: build/workflow.cwl
  - output: build/copy.cwl

Then run:

transpiler-mate batch workflow.cwl

To use a different execution file:

transpiler-mate batch workflow.cwl --file plans/release.yaml

The file must contain a mapping with this structure:

• Each key is a nonblank string naming an installed plugin's entry point.
• Each value is an array of executions for that plugin.
• Each execution is an object whose string keys and values supply the target plugin's options model. Use {} when an execution needs only model defaults.

For multiple plugins, add another key with its own execution array. For example, if you have installed a plugin named report with an output option:

bundle:
  - output: build/workflow.cwl
  - output: build/copy.cwl
report:
  - output: build/report.json

Both bundle executions finish before report starts. report is an illustrative external plugin, not included with this runtime.

Relative execution-file paths resolve from the working directory. Input values are passed to each target model; the batch plugin does not rebase paths relative to the YAML file.

Validation and execution¶

The plugin parses YAML using the existing Ruamel.YAML safe loader and validates the complete file structure before loading or executing any target plugin. Empty documents, duplicate keys, non-mapping roots, non-array execution groups, and non-object execution items are rejected. An empty mapping ({}) is a valid no-op; empty execution arrays are skipped without loading their plugin.

Plugins run in the order their keys appear in the file, and each plugin's executions run in array order. The runtime's existing plugin loader discovers and loads each target. Immediately before each execution, the target's options model validates its inputs, applies defaults, and performs its normal type conversion. Both field names and aliases are accepted.

Every execution receives the same context instance. The CWL source is resolved once by the runtime, and batch does not create a new context for each execution. Nested batch invocations are rejected.

Failures and debug logging¶

Execution stops at the first failure. Earlier executions are not rolled back; option validation for a later execution can fail after earlier executions have already completed.

Unreadable files raise PluginExecutionError. Invalid YAML, invalid plan structure, plugin loading failures, invalid target options, and recursive batch invocations raise PluginFailureError. Exceptions raised by target plugins propagate unchanged to the runtime's error handling.

Debug messages cover file parsing, structure validation, plugin loading, options validation, shared context identity, execution progress, timings, skipped groups, and failures. These debug messages omit input values.