Add SH machine type #12
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Pull Request Overview
This PR adds support for SH machine type instruments in the Illumina parsing logic. The SH instrument code is treated as another MiSeq model variant within the existing framework.
- Adds SH instrument code mapping to "Illumina-MiSeq" machine type
- Creates test fixture data for SH runs with proper directory structure and FASTQ content
- Refactors flowcell ID parsing logic to use instrument codes directly instead of machine type strings
Reviewed Changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| seqBackupLib/illumina.py | Adds SH to MACHINE_TYPES mapping and refactors flowcell parsing logic |
| test/conftest.py | Creates sh_dir fixture with sample SH run data |
| test/test_illumina.py | Maps SH instrument code to sh_dir fixture for testing |
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Summary
Testing
pytest -qhttps://chatgpt.com/codex/tasks/task_e_687aaf9375888323b870e418a3db04c0