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Upload saltshaker report to Scout for raredisease #5234

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133bcd0
Add saltshaker report handling to RarediseaseLoadConfig
diitaz93 Aug 6, 2026
21b7c1f
Update saltshaker report handling to use 'saltshaker-classify' tag
diitaz93 Aug 6, 2026
af76f50
Merge branch 'master' into add-saltshaker-to-scout
diitaz93 Aug 6, 2026
c4be8c2
Merge branch 'master' into add-saltshaker-to-scout
diitaz93 Aug 11, 2026
bc07bf6
Merge branch 'master' into add-saltshaker-to-scout
diitaz93 Aug 13, 2026
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3 changes: 3 additions & 0 deletions cg/meta/upload/scout/raredisease_config_builder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,9 @@ def build_load_config(self, hk_version: Version, analysis: Analysis) -> Raredise
)
load_config.sv_rank_model_url = sv_rank_model.path
load_config.sv_rank_model_version = sv_rank_model.version
load_config.saltshaker_report = self.get_file_from_hk(
hk_tags={"saltshaker-classify"}, hk_version=hk_version
)
Comment on lines +77 to +79

@islean islean Aug 6, 2026

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Did we consider adding this tag to the RAREDISEASE_CASE_TAGS? I do find the old pattern very confusing but I wonder if it will not be confusing as well to have the HK fetching done in a new way here?

@diitaz93 diitaz93 Aug 6, 2026

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I don't find the old pattern useful. Although it is nice to have the tags listed centrally in one place, the use of that dictionary is confusing, and it entangles many parts of the code. I suspect its use was intended for something else

@islean islean Aug 10, 2026

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I am not certain that the intent was anything but collecting all the tags in the same place (which I think might be nice preserving), but if you do not find it useful, feel free to do it like this.

return load_config

def _get_rank_model(self, hk_version: Version, variant_type: Variants) -> RankModel:
Expand Down
7 changes: 4 additions & 3 deletions cg/models/scout/scout_load_config.py
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Expand Up @@ -183,22 +183,23 @@ class NalloLoadConfig(ScoutLoadConfig):


class RarediseaseLoadConfig(ScoutLoadConfig):
custom_images: CustomImages | None = None
madeline: str | None = None
peddy_check: str | None = None
peddy_ped: str | None = None
peddy_sex: str | None = None
saltshaker_report: str | None = None
samples: list[ScoutRarediseaseIndividual] = []
custom_images: CustomImages | None = None
smn_tsv: str | None = None
vcf_mei: str | None = None
vcf_mei_research: str | None = None
vcf_snv: Annotated[str | None, AfterValidator(field_not_none)] = None
vcf_snv_research: Annotated[str | None, AfterValidator(field_not_none)] = None
vcf_snv_mt: str | None = None
vcf_snv_research: Annotated[str | None, AfterValidator(field_not_none)] = None
vcf_snv_research_mt: str | None = None
vcf_str: str | None = None
vcf_sv: Annotated[str | None, AfterValidator(field_not_none)] = None
vcf_sv_research: Annotated[str | None, AfterValidator(field_not_none)] = None
vcf_str: str | None = None


class RnafusionLoadConfig(ScoutLoadConfig):
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4 changes: 4 additions & 0 deletions tests/meta/upload/scout/test_scout_config_builder.py
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Expand Up @@ -598,6 +598,7 @@ def test_raredisease_config_builder(mocker: MockerFixture):
chromograph_autozyg: File = create_autospec(File, full_path="chromograph_autozyg_chr9.png")
chromograph_coverage: File = create_autospec(File, full_path="chromograph_coverage_chr9.png")
saltshaker_path: File = create_autospec(File, full_path="saltshaker.png")
saltshaker_report: File = create_autospec(File, full_path="saltshaker_report.html")
chromograph_regions: File = create_autospec(File, full_path="chromograph_regions.bed")
chromograph_sites: File = create_autospec(File, full_path="chromograph_sites.bed")
reviewer_alignment: File = create_autospec(File, full_path="reviewer_alignment.vcf")
Expand All @@ -620,6 +621,8 @@ def mock_get_file_from_version(version: Version, tags: set[str]) -> File | None:
return peddy_check
if tags == {"ped", "peddy"}:
return peddy_ped
if tags == {"saltshaker-classify"}:
return saltshaker_report
if tags == {"sex-check", "peddy"}:
return peddy_sex
if tags == {"smn-calling"}:
Expand Down Expand Up @@ -749,6 +752,7 @@ def mock_get_file_from_version(version: Version, tags: set[str]) -> File | None:
rank_model_url=snv_rank_model.full_path,
sv_rank_model_version="2.0",
sv_rank_model_url=sv_rank_model.full_path,
saltshaker_report=saltshaker_report.full_path,
analysis_date=datetime.now(),
samples=[
ScoutRarediseaseIndividual(
Expand Down
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