28 lines
844 B
Python
28 lines
844 B
Python
from pathlib import Path
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from genomic_consultant.orchestration.phase1_pipeline import run_phase1_pipeline
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def test_phase1_pipeline_with_existing_tsv():
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root = Path(__file__).resolve().parents[1]
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tsv = root / "sample_data/example_annotated.tsv"
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panel = root / "configs/panel.example.json"
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acmg = root / "configs/acmg_config.example.yaml"
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result = run_phase1_pipeline(
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samples=None,
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reference_fasta=None,
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workdir=root / "runtime",
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output_prefix="demo",
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acmg_config_path=acmg,
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max_af=0.05,
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panel_path=panel,
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phenotype_id=None,
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phenotype_mapping=None,
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report_format="markdown",
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existing_tsv=tsv,
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skip_call=True,
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skip_annotate=True,
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)
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assert "Panel Report" in result.panel_report
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assert result.tsv_path == tsv
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