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Add d4_file to raredisease scout load config #4154

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merged 2 commits into from
Jan 27, 2025
Merged

Add d4_file to raredisease scout load config #4154

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a54a6e0
add d4 to rd scout load config
rannick Jan 24, 2025
99e71dc
Merge branch 'master' into add_d4_rd
rannick Jan 27, 2025
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1 change: 1 addition & 0 deletions cg/constants/scout.py
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Expand Up @@ -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"},
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1 change: 1 addition & 0 deletions cg/meta/upload/scout/hk_tags.py
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Expand Up @@ -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
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9 changes: 4 additions & 5 deletions cg/meta/upload/scout/raredisease_config_builder.py
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Expand Up @@ -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,
Expand Down Expand Up @@ -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
)
1 change: 1 addition & 0 deletions cg/models/scout/scout_load_config.py
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Expand Up @@ -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):
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