diff --git a/cg/models/nallo/nallo.py b/cg/models/nallo/nallo.py index c5463d5fe1..46f164ae4a 100644 --- a/cg/models/nallo/nallo.py +++ b/cg/models/nallo/nallo.py @@ -7,6 +7,12 @@ from cg.models.nf_analysis import WorkflowParameters +class NalloQCMetrics(BaseModel): + """Nallo QC metrics""" + + median_coverage: float | None + + class NalloSampleSheetEntry(BaseModel): """Nallo sample model is used when building the sample sheet.""" diff --git a/tests/conftest.py b/tests/conftest.py index f39f96f124..784d0f98bf 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -2567,7 +2567,6 @@ def nallo_context( case_id_not_enough_reads: str, sample_id_not_enough_reads: str, total_sequenced_reads_not_pass: int, - mocker: MockFixture, ) -> CGConfig: """context to use in cli""" cg_context.housekeeper_api_ = nf_analysis_housekeeper diff --git a/tests/fixtures/analysis/nallo/multiqc_data.json b/tests/fixtures/analysis/nallo/multiqc_data.json index aedb6c7c1d..ef0c3b817e 100644 --- a/tests/fixtures/analysis/nallo/multiqc_data.json +++ b/tests/fixtures/analysis/nallo/multiqc_data.json @@ -3,19 +3,6 @@ "report_general_stats_data": [ { "ADM1": { - "mean_coverage": 32.18, - "min_coverage": 0.0, - "max_coverage": 63906.0, - "coverage_bases": 99366056494, - "length": 3088286377, - "1_x_pc": 94.0, - "5_x_pc": 94.0, - "10_x_pc": 93.0, - "30_x_pc": 65.0, - "50_x_pc": 2.0, - "median_coverage": 13 - }, - "ADM2": { "mean_coverage": 32.18, "min_coverage": 0.0, "max_coverage": 63906.0,