4.7 Task Execution Lifecycle

4.7.1 Identify and plan

Confirm the objective, input location, and required documentation. Discover Flows with fkit flow list, inspect their ports, parameters, and graph with fkit flow inspect, and check BioLine inputs with fkit ls. A dry-run plan presents the real Flow/Version ID, bindings, defaults, and impact.

4.7.2 Submission gate

After the plan is saved, enter awaiting_plan_confirmation. Show the Flow/Version ID, input paths, bindings, defaults, risks, and downstream objective. Do not create a Job without user confirmation. After submission, record the Job ID returned by BioLine before entering submitted and running.

4.7.3 Poll and finalize

Poll with fkit job get and retain each response, timestamp, and state. Only success permits succeeded and finalized: download outputs, organize stage, and record input/output and reproducibility evidence. Failures remain in explicit phases such as plan_failed, submit_failed, upstream_failed, or finalize_failed.

4.7.4 Downstream execution

After finalization, discover a suitable BioLine Tool and pin it to an exact NAME:VERSION. Export and inspect that version’s summary/config. The summary must declare analysis_lane: downstream and fixed_command: false, and the config must contain no fixed analysis command. Pull the version on demand only after confirmation, generate and save a task script, and run it with network none. Stage and task reproducibility material are read-only; analysis is writable.

Record the Tool name and version, summary/config snapshot or hash, pre-existing and post-pull image identity, actual command, script, logs, and outputs. Cleanup follows the task pull ledger: non-forced removal is eligible only when the image was absent beforehand, its identity is unchanged, and it is not shared or in use.

4.7.5 Authoring is never implicit in execution

An execution task does not automatically create or publish a Tool, Tool Version, or Flow. If no suitable existing capability is available, use a separate authoring workspace. Build, publish, and register each require confirmation, and handoff follows successful read-back verification.