diff --git a/BALSAMIC/constants/quality_check_reporting.py b/BALSAMIC/constants/quality_check_reporting.py index aead36c00..dba06df8e 100644 --- a/BALSAMIC/constants/quality_check_reporting.py +++ b/BALSAMIC/constants/quality_check_reporting.py @@ -55,14 +55,14 @@ "default": { "MEAN_INSERT_SIZE": {"condition": None}, "PERCENT_DUPLICATION": {"condition": None}, - "MEDIAN_TARGET_COVERAGE": {"condition": None}, + "MEDIAN_TARGET_COVERAGE": {"condition": {"norm": "gt", "threshold": 500}}, "PCT_TARGET_BASES_50X": {"condition": None}, "PCT_TARGET_BASES_100X": {"condition": None}, "PCT_TARGET_BASES_250X": {"condition": None}, "PCT_TARGET_BASES_500X": {"condition": None}, "PCT_TARGET_BASES_1000X": {"condition": None}, "MEAN_TARGET_COVERAGE": {"condition": None}, - "FOLD_80_BASE_PENALTY": {"condition": None}, + "FOLD_80_BASE_PENALTY": {"condition": {"norm": "lt", "threshold": 1.8}}, "PCT_OFF_BAIT": {"condition": None}, }, "gicfdna": { diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 7053dbb54..5fa79e25f 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -7,6 +7,7 @@ Added: * Snakemake workflow to create canfam3 reference #843 * Call umi variants using TNscope in bed defined regions #821 * UMI duplication metrics to report in multiqc_picard_dups.json #844 +* QC default validation conditions (for not defined capture kits) #855 Changed: ^^^^^^^^ diff --git a/tests/conftest.py b/tests/conftest.py index 454d3b83e..cff2d544a 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -523,6 +523,7 @@ def qc_requested_metrics(): }, "panel_2": { "METRIC_1": {"condition": {"norm": "gt", "threshold": 1}}, + "METRIC_2": {"condition": {"norm": "gt", "threshold": 22}}, "METRIC_4": {"condition": {"norm": "gt", "threshold": 4}}, }, }, diff --git a/tests/scripts/test_collect_qc_metrics.py b/tests/scripts/test_collect_qc_metrics.py index f0035d0c1..9b2cb7e16 100644 --- a/tests/scripts/test_collect_qc_metrics.py +++ b/tests/scripts/test_collect_qc_metrics.py @@ -45,13 +45,13 @@ def test_get_requested_metrics_targeted(qc_requested_metrics): # GIVEN a sequencing type and a capture kit seq_type = "targeted" - capture_kit = "panel_1_v1.0_hg19_design.bed" + capture_kit = "panel_2_v1.0_hg19_design.bed" # GIVEN the expected output expected_output = { - "METRIC_1": {"condition": None}, - "METRIC_2": {"condition": {"norm": "gt", "threshold": 2}}, - "METRIC_3": {"condition": {"norm": "gt", "threshold": 3}}, + "METRIC_1": {"condition": {"norm": "gt", "threshold": 1}}, + "METRIC_2": {"condition": {"norm": "gt", "threshold": 22}}, + "METRIC_4": {"condition": {"norm": "gt", "threshold": 4}}, } # WHEN calling the function