diff --git a/cg/constants/scout.py b/cg/constants/scout.py index 2507a5abbe..5371f4275c 100644 --- a/cg/constants/scout.py +++ b/cg/constants/scout.py @@ -106,6 +106,7 @@ class ScoutUploadKey(StrEnum): RAREDISEASE_SAMPLE_TAGS: dict[str, set[str]] = dict( alignment_file={AlignmentFileTag.CRAM}, + d4_file={"d4"}, vcf2cytosure={"vcf2cytosure"}, mt_bam={"bam-mt"}, eklipse_path={"eklipse-png"}, diff --git a/cg/meta/upload/scout/hk_tags.py b/cg/meta/upload/scout/hk_tags.py index 8e83daad52..2b65df672c 100644 --- a/cg/meta/upload/scout/hk_tags.py +++ b/cg/meta/upload/scout/hk_tags.py @@ -71,6 +71,7 @@ class SampleTags(BaseModel): bam_file: set[str] | None = None alignment_file: set[str] | None = None alignment_path: set[str] | None = None + d4_file: set[str] | None = None vcf2cytosure: set[str] | None = None eklipse_path: set[str] | None = None mt_bam: set[str] | None = None diff --git a/cg/meta/upload/scout/raredisease_config_builder.py b/cg/meta/upload/scout/raredisease_config_builder.py index 5d8975b70d..68f803ea6e 100644 --- a/cg/meta/upload/scout/raredisease_config_builder.py +++ b/cg/meta/upload/scout/raredisease_config_builder.py @@ -6,11 +6,7 @@ from cg.apps.lims import LimsAPI from cg.apps.madeline.api import MadelineAPI from cg.constants.constants import FileFormat -from cg.constants.housekeeper_tags import ( - HK_DELIVERY_REPORT_TAG, - AnalysisTag, - NFAnalysisTags, -) +from cg.constants.housekeeper_tags import HK_DELIVERY_REPORT_TAG, AnalysisTag, NFAnalysisTags from cg.constants.scout import ( RANK_MODEL_THRESHOLD, RAREDISEASE_CASE_TAGS, @@ -206,3 +202,6 @@ def include_sample_files(self, config_sample: ScoutRarediseaseIndividual) -> Non config_sample.mitodel_file = self.get_sample_file( hk_tags=self.sample_tags.mitodel_file, sample_id=sample_id ) + config_sample.d4_file = self.get_sample_file( + hk_tags=self.sample_tags.d4_file, sample_id=sample_id + ) diff --git a/cg/models/scout/scout_load_config.py b/cg/models/scout/scout_load_config.py index 8075da8be0..3cf2c5eccc 100644 --- a/cg/models/scout/scout_load_config.py +++ b/cg/models/scout/scout_load_config.py @@ -93,6 +93,7 @@ class ScoutRarediseaseIndividual(ScoutIndividual): vcf2cytosure: str | None = None mitodel_file: str | None = None reviewer: Reviewer = Reviewer() + d4_file: str | None = None class ScoutCancerIndividual(ScoutIndividual):