diff --git a/.github/workflows/gendercheck_test.yml b/.github/workflows/gendercheck_test.yml index b5083d4..dc3d279 100644 --- 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 index f1906d0..6cd3467 100644 --- 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 new file mode 100644 index 0000000..39bf986 --- /dev/null +++ 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" \ No newline at end of file