Clinical-Genomics / cg / 8630237318

86%

Build Type

push

github

Committed by web-flow

Commit Message

feat - Remove bcl2fastq from automation (#3088)

This PR makes any `bcl2fastq` sample sheet fail validation and forces the creation of a new sample sheet of type `BCLConvert`. 

NOTE: This is not the full deprecation of the demultiplexing using `bcl2fastq` as the manual option will still be available.

### Added

- Tests for the new functionality.

### Changed

- The validation of the sample sheet is now bcl-converter-specific. The commands like demultiplex all and create all sample sheets use `BCLConverter` by default, so `bcl2fastq` sample sheets will fail validation in the automation. If cought in the creation phase, the sample sheets will be updated to a `BCLConvert` sample sheet. If caught in the demultiplexing phase, the demultiplexing will fail after the slurm job has been submitted so the error can be easily tracked.
- `bcl2fastq` sample sheets can still be created, validated and used in demultiplexing by explicitly specifying the converter as a CLI parameter. 

### Fixed

- The `SampleSheetAPI` attribute `bcl_converter` was removed and the bcl converter of the flow cell is used instead to avoid ambiguity.

Run Details

20 of 24 new or added lines in 2 files covered. (83.33%)

1 existing line in 1 file now uncovered.

19697 of 23254 relevant lines covered (84.7%)

0.85 hits per line