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added 5 commits
October 9, 2025 16:42
WardDeb
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Oct 13, 2025
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Thanks for the work.
It'd be great to have:
- Infer if aviti or not only once, and perhaps keep it at the config level
- get rid of the code duplicatio for seqfacdir
- have the config updates reflected in the ini template
- ensure the tests pass
- PR title should follow conventional commit
| d = {'flowcell_id': FCID} | ||
| d['sequences'] = json.dumps(msg) | ||
| basePath= config.get("Paths","baseData") | ||
| aviti_check= glob.glob(f"{basePath}/*/RunManifest.csv") |
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Why not directly from the folder name ?
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Thanks for the notice! opted for this approach.
BRB/PushButton.py
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| current_year = "20" + str(lane_dir)[0:2] | ||
| year_postfix = Path("Sequence_Quality_" + current_year) / Path("Illumina_" + current_year) | ||
| sequencing_type=lane_dir.split("_")[1] | ||
| if sequencing_type.startswith("AV"): |
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This is now a second way of discriminating aviti runs from illumina, this should be consistent.
BRB/PushButton.py
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| project = BRB.misc.pacifier(project) | ||
| sampleSheet = f"/dont_touch_this/short_runs/{runID}/RELACS_Project_{project}.txt" | ||
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| # Fallback if exact path doesn't exist |
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Implemented! taken care off redundancies.
| org_yaml = 'GRCh38' | ||
| PE = linkFiles(config, group, project, outputDir, tuples) | ||
| CMD = [config.get('10x', 'RNA'), outputDir, outputDir, org_yaml] | ||
| snakeMakePath= "{}/bin".format(os.path.join(config.get('Options', 'snakemakeWorkflowBaseDir'))) |
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This is not reflected in the ini file
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Thank you for noticing!
Path updated in the ini file
BRB/PushButton.py
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| lane_dir = Path(d).parents[1].stem | ||
| current_year = "20" + str(lane_dir)[0:2] | ||
| year_postfix = Path("Sequence_Quality_" + current_year) / Path("Illumina_" + current_year) | ||
| sequencing_type=lane_dir.split("_")[1] |
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Would be great to get rid of the duplicated code here.
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Removed duplicated part
NavandarM
changed the title
added 5 commits
October 24, 2025 15:57
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