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Ran 26 Jun 2024 08:58AM UTC

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Committed 26 Jun 2024 08:56AM UTC coverage: 84.562% (-0.03%) from 84.589%

Job # 9676632168.1

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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`

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master: 86%

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