From 55a35c7c32cc0ad8fdb7ca1c90fd7683da0ac485 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Thu, 7 Dec 2023 11:47:07 +0100 Subject: [PATCH] update config case function --- cg/meta/workflow/raredisease.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/cg/meta/workflow/raredisease.py b/cg/meta/workflow/raredisease.py index 399da1c0fb..c831a1f701 100644 --- a/cg/meta/workflow/raredisease.py +++ b/cg/meta/workflow/raredisease.py @@ -7,7 +7,7 @@ from cg.meta.workflow.nf_analysis import NfAnalysisAPI from cg.models.cg_config import CGConfig from cg.models.raredisease.raredisease import RarediseaseSampleSheetEntry, RarediseaseParameters -from cg.store.models import Case, Sample +from cg.store.models import Case, Sample, CaseSample LOG = logging.getLogger(__name__) @@ -54,7 +54,7 @@ def config_case( self.write_params_file(case_id=case_id, pipeline_parameters=pipeline_parameters.dict()) def get_sample_sheet_content_per_sample( - self, sample: Sample, case: Case = "" + self, sample: Sample, case: Case = "", case_sample: CaseSample = "" ) -> list[list[str]]: """Get sample sheet content per sample.""" sample_metadata: list[str] = self.gather_file_metadata_for_sample(sample) @@ -71,9 +71,9 @@ def get_sample_sheet_content_per_sample( fastq_forward_read_paths=fastq_forward_read_paths, fastq_reverse_read_paths=fastq_reverse_read_paths, sex=sample.sex, - phenotype=sample.status, - paternal_id=sample.father, - maternal_id=sample.mother, + phenotype=case_sample.status, + paternal_id=case_sample.father, + maternal_id=case_sample.mother, case_id=case, ) return sample_sheet_entry.reformat_sample_content()