Clinical-Genomics / cg / 17091851797

86%

push

github

Rework subprocess submitter (#4549)(patch)

## Description
Closes https://github.com/Clinical-Genomics/pipeline-integration/issues/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>

8 of 8 new or added lines in 2 files covered. (100.0%)

27837 of 32441 relevant lines covered (85.81%)

0.86 hits per line