Use poetry to run pytest

UMCUGenetics · Oct 11, 2024 · 740e504 · 740e504
1 parent da9f31d
commit 740e504
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Showing 3 changed files with 66 additions and 4 deletions.
diff --git a/.github/workflows/gendercheck_test.yml b/.github/workflows/gendercheck_test.yml
@@ -59,5 +59,4 @@ jobs:
       #----------------------------------------------
       - name: Run tests
         run: |
-          source .venv/bin/activate
-          pytest .
+          poetry run pytest .
diff --git a/.github/workflows/moisaichunter_test.yml b/.github/workflows/moisaichunter_test.yml
@@ -59,5 +59,4 @@ jobs:
       #----------------------------------------------
       - name: Run tests
         run: |
-          source .venv/bin/activate
-          pytest .
+          poetry run pytest .
diff --git a/CheckQC/checkqc_giabeval_settings.yaml b/CheckQC/checkqc_giabeval_settings.yaml
@@ -0,0 +1,64 @@
+metrics:
+  - filename: "summary_snp.*truth.txt"
+    qc_col: "Sensitivity"
+    threshold: 0.98
+    operator: "<="
+    report_cols: ["sample_1", "Sensitivity"]
+    sample_cols: ["sample_1"]
+    title: "PK_C_SNPs"
+  - filename: "summary_indel.*truth.txt"
+    qc_col: "Sensitivity"
+    threshold: 0.90
+    operator: "<="
+    report_cols: ["sample_1", "Sensitivity"]
+    sample_cols: ["sample_1"]
+    title: "PK_C_INDELs"
+  - filename: "summary_snp.*truth.txt"
+    qc_col: "Precision"
+    threshold: 0.98
+    operator: "<="
+    report_cols: ["sample_1", "Precision"]
+    sample_cols: ["sample_1"]
+    title: "PK_D_SNPs"
+  - filename: "summary_indel.*truth.txt"
+    qc_col: "Precision"
+    threshold: 0.85
+    operator: "<="
+    report_cols: ["sample_1", "Precision"]
+    sample_cols: ["sample_1"]
+    title: "PK_D_INDELs"
+  - filename: "summary_snp_.*_((?!truth).)*$"
+    qc_col: "Sensitivity"
+    threshold: 0.98
+    operator: "<="
+    report_cols: ["sample_1", "sample_2", "Sensitivity"]
+    sample_cols: ["sample_1", "sample_2"]
+    title: "PK_E_SNPs"
+  - filename: "summary_indel_.*_((?!truth).)*$"
+    qc_col: "Sensitivity"
+    threshold: 0.90
+    operator: "<="
+    report_cols: ["sample_1", "sample_2", "Sensitivity"]
+    sample_cols: ["sample_1", "sample_2"]
+    title: "PK_E_INDELs"
+  - filename: "summary_high_conf_snp.*truth.txt"
+    qc_col: "Sensitivity"
+    threshold: 0.98
+    operator: "<="
+    report_cols: ["sample_1", "Sensitivity"]
+    sample_cols: ["sample_1"]
+    title: "PK_C_SNPs_high_conf"
+  - filename: "summary_high_conf_snp.*truth.txt"
+    qc_col: "Precision"
+    threshold: 0.98
+    operator: "<="
+    report_cols: ["sample_1", "Precision"]
+    sample_cols: ["sample_1"]
+    title: "PK_D_SNPs_high_conf"
+  - filename: "summary_high_conf_snp_.*_((?!truth).)*$"
+    qc_col: "Sensitivity"
+    threshold: 0.98
+    operator: "<="
+    report_cols: ["sample_1", "sample_2", "Sensitivity"]
+    sample_cols: ["sample_1", "sample_2"]
+    title: "PK_E_SNPs_high_conf"