Initial commit

tests/test_phase1_pipeline.py

@@ -0,0 +1,27 @@
+from pathlib import Path
+
+from genomic_consultant.orchestration.phase1_pipeline import run_phase1_pipeline
+
+
+def test_phase1_pipeline_with_existing_tsv():
+    root = Path(__file__).resolve().parents[1]
+    tsv = root / "sample_data/example_annotated.tsv"
+    panel = root / "configs/panel.example.json"
+    acmg = root / "configs/acmg_config.example.yaml"
+    result = run_phase1_pipeline(
+        samples=None,
+        reference_fasta=None,
+        workdir=root / "runtime",
+        output_prefix="demo",
+        acmg_config_path=acmg,
+        max_af=0.05,
+        panel_path=panel,
+        phenotype_id=None,
+        phenotype_mapping=None,
+        report_format="markdown",
+        existing_tsv=tsv,
+        skip_call=True,
+        skip_annotate=True,
+    )
+    assert "Panel Report" in result.panel_report
+    assert result.tsv_path == tsv