Clinical-Genomics / cg / 16339834348

86%

push

github

Refactor sample sheet entry creation (#4510)(patch)

## Description
Closes https://github.com/Clinical-Genomics/pipeline-integration/issues/19
Refactors the Nextflow sample sheet creation in the pipeline integration flow so that it does not need any Pydantic base model for its creation.

### Added

- Taxprofiler sample sheet creator

### Changed

- Validation for existence of fastqfiles relies exclusively on the input fetcher, not in the sample sheet
- The return type of `_get_paired_read_paths` changed to a tuple iterator

27 of 27 new or added lines in 4 files covered. (100.0%)

27744 of 32359 relevant lines covered (85.74%)

0.86 hits per line