Clinical-Genomics / cg / 11380755148

78%

Build Type

push

github

Committed by web-flow

Commit Message

new post process all (#3845)(minor)

## Description
Closes https://github.com/Clinical-Genomics/add-new-tech/issues/118
Create a command `post-process all` that will post-process all instrument runs regardless of the instrument. Currently only works for Pacbio. The instrument can be added as a flag so that only runs of a given instrument are post-processed.

### Added

- Cli command function `post_process_all_runs` in `cg/cli/post_process/post_process.py`.
- Utils functions and a model to get and filter the runs to post-process in `cg/cli/post_process/utils.py`
- Tests and fixtures for these utils functions
- Abstract service family ` RunNamesService` with the child `PacbioRunNamesService` in charge of generating sequencing run names
- Tests and fixtures for this new service
- New property `run_names_services` in the `CGConfig` class to access the run names service from the config
- New check function `is_run_processed` defined abstractly in the post-processing class and in implemented in the Pacbio child class that checks if a run has been post-processed

Run Details

100 of 120 new or added lines in 14 files covered. (83.33%)

1 existing line in 1 file now uncovered.

23002 of 27213 relevant lines covered (84.53%)

0.85 hits per line