Clinical-Genomics / cg / 12004616018

86%

Build Type

push

github

Committed by web-flow

Commit Message

patch - Concatenate Microbial fastq files (#3958)(patch)

## Description
Addresses https://github.com/Clinical-Genomics/bug-reports/issues/17
The Microbial fastq orders currently behave in the backend as a normal fastq order, while in reality, they should have a hybrid functionality between Microsalt and fastq. This is, the raw data fastq files should be concatenated for a sample (the replicates in multiple lanes) as it is done in Microsalt, but no analysis should start, as in fastq orders.

This PR overwrites the Workflow of Microbial-fastq cases from Workflow.RAW_DATA to Workflow.MICROSALT just for the delivery service.

### Added

- Static method `_convert_workflow` in `DeliveryServiceFactory` that patches the workflow of microbial fastq cases as Microsalt
- Unit test for new function

### Changed

- The parameters of the public function `build_delivery_service` from `DeliveryServiceFactory` to receive case and delivery_type instead of Workflow and delivery_type

### Fixed

- All calls to `build_delivery_service` with the new parameters
- Tests for `build_delivery_service`

Run Details

49 of 53 new or added lines in 6 files covered. (92.45%)

2 existing lines in 2 files now uncovered.

23437 of 27742 relevant lines covered (84.48%)

0.84 hits per line