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@clingen-sthlm clingen-sthlm released this 20 Aug 07:39
v75.0.6
1464db4

Rework subprocess submitter (#4549)(patch)

Description

Closes Clinical-Genomics/pipeline-integration#56

In the pipeline integration flow, this PR creates the start command for non-Nextflow pipelines in a CaseConfig model method, instead of fetching it from formatting a dictionary in the Submitter.

Added

  • get_start_command method in MicrosaltCaseConfig
  • Test for the new method

Changed

  • Remove WORKFLOW_LAUNCH_COMMAND_MAP.

Co-authored-by: Rasmus Burge 80392398+RasmusBurge-CG@users.noreply.github.com
Co-authored-by: Sebastian Diaz juan.sebastian.diaz.boada@scilifelab.se

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