fix: support configured nextflow directories - #5298
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Description
This PR prepares
cgfor Mammut stage testing by allowing Nextflow workflows to use configured launch and work directories fromcg-config.The change is intentionally small and keeps the existing default behavior when these fields are not configured.
Changed
case_run_directoryandwork_dirfields to Nextflow workflow config models.case_run_directory/<case_id>for generated Nextflow launch files when configured.work_dir/<case_id>as the Seqera work directory when configured.root/<case_id>root/<case_id>/workValidation
pytest tests/services/analysis_starter/test_nextflow_configurator.pyruff checkruff format --check