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0.4.0

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@github-actions github-actions released this 27 Oct 14:32
c07aeab

Changed

  • The plugin calls the Workbench Launcher API itself (WorkbenchApiClient, with the JDK's HTTP client) instead of shelling out to posit-workbench-nf-launcher. Nextflow needs no Python and no CLI to run tasks as Workbench Jobs, in a session, in a headless driver job, or anywhere with WORKBENCH_SERVER/WORKBENCH_API_KEY. Submit, status and kill keep their behaviour; the status mapping moved from the CLI into WorkbenchExecutor.queueStatusOf.
  • workbench.launcherCli is no longer used. It still validates, and logs a warning when set. The examples no longer set it, and have no --launcherCli param.
  • The launcher CLI is optional, for submitting, listing and stopping jobs from a terminal (e.g. a headless driver). It no longer depends on posit-sdk: it uses a built-in client (standard library only), the same as posit-sdk-snakemake's. whoami now checks the credentials with one API call.
  • A Workbench session without a readable RPC cookie falls back to WORKBENCH_SERVER/WORKBENCH_API_KEY, where posit-sdk failed.
  • The plugin and launcher are now 0.4.0. Update plugins { id 'nf-workbench@0.4.0' } in pipeline configs.
  • Verified on Posit Workbench with the Positron Nextflow extension.

Added

  • e2e/run.sh: the real Nextflow with the built plugin against e2e/fake_workbench.py, a stand-in for the Launcher API that runs each job as a local process. It checks a completed run (the job spec: script, work dir, cpus, memory, resource profile) and a run stopped while its tasks run (status polled, jobs stopped).
  • CI: plugin tests and build, the end-to-end run, and the launcher tests.