Clinical-Genomics / cg / 9676632168

86%

Build Type

push

github

Committed by web-flow

Commit Message

fix validate to admit manually modified sample sheets (#3355)(patch)

## Description
Fixes #3288 
This PR introduces a distinction between a sample sheet failing validation by structural failures (most likely Bcl2Fastq or other old sample sheets) and failing by content (manually modified sample sheets). For this, two new exceptions replace the `SampleSheetError`: `SampleSheetFormatError` and `SampleSheetContentError`, respectively. Sample sheets failing validation for format will be regenerated as usual, but sample sheets failing for content will not.

### Added

- New exceptions `SampleSheetFormatError` and `SampleSheetContentError`

### Changed

- Replaced all occurrences of `SampleSheetError` for either `SampleSheetFormatError` and `SampleSheetContentError`
- Fixed the try-except clauses to perform different conditions for the two different exceptions
- Sample sheet Error only used in Nextflow code renamed to `NfSampleSheetError`

Run Details

36 of 63 new or added lines in 7 files covered. (57.14%)

2 existing lines in 2 files now uncovered.

20573 of 24329 relevant lines covered (84.56%)

0.85 hits per line