add things to scout config

cg/constants/scout.py

@@ -41,18 +41,20 @@ class ScoutUploadKey(StrEnum):
 
 RAREDISEASE_CASE_TAGS = dict(
     delivery_report={"delivery-report"},
-    multiqc_report={"multiqc-html"},
+    multiqc={"multiqc-html"},
     peddy_check={"ped-check", "peddy"},
     peddy_ped={"ped", "peddy"},
     peddy_sex={"sex-check", "peddy"},
     smn_tsv={"smn-calling"},
-    snv_research_vcf={"vcf-snv-research"},
-    snv_vcf={"vcf-snv-clinical"},
-    str_catalog={"expansionhunter", "variant-catalog"},
-    sv_research_vcf={"vcf-sv-research"},
-    sv_vcf={"vcf-sv-clinical"},
     vcf_mei={"mobile-elements", "clinical", "vcf"},
     vcf_mei_research={"mobile-elements", "research", "vcf"},
+    vcf_snv_research={"vcf-snv-research"},
+    vcf_snv={"vcf-snv-clinical"},
+    vcf_snv_research_mt={"vcf-sv-research", "mitochondria"},
+    vcf_snv_mt={"vcf-sv-clinical", "mitochondria"},
+    str_catalog={"expansionhunter", "variant-catalog"},
+    vcf_sv_research={"vcf-sv-research"},
+    vcf_sv={"vcf-sv-clinical"},
     vcf_str={"vcf-str"},
 )
 
@@ -101,9 +103,9 @@ class ScoutUploadKey(StrEnum):
     vcf_fusion={"vcf-fusion"},
 )
 
-RAREDISEASE_SAMPLE_TAGS = dict(
+RAREDISEASE_SAMPLE_TAGS: dict[str, set[str]] = dict(
     bam_file={"bam"},
-    # alignment_file={"cram"},
+    alignment_file={"cram"},
     vcf2cytosure={"vcf2cytosure"},
     mt_bam={"bam-mt"},
     chromograph_autozyg={"chromograph", "autozyg"},
@@ -116,7 +118,20 @@ class ScoutUploadKey(StrEnum):
     mitodel_file={"mitodel"},
 )
 
-MIP_SAMPLE_TAGS: dict[str, set[str]] = RAREDISEASE_SAMPLE_TAGS
+MIP_SAMPLE_TAGS: dict[str, set[str]] = dict(
+    bam_file={"bam"},
+    alignment_file={"cram"},
+    vcf2cytosure={"vcf2cytosure"},
+    mt_bam={"bam-mt"},
+    chromograph_autozyg={"chromograph", "autozyg"},
+    chromograph_coverage={"chromograph", "tcov"},
+    chromograph_regions={"chromograph", "regions"},
+    chromograph_sites={"chromograph", "sites"},
+    reviewer_alignment={"expansionhunter", "bam"},
+    reviewer_alignment_index={"expansionhunter", "bam-index"},
+    reviewer_vcf={"expansionhunter", "vcf-str"},
+    mitodel_file={"mitodel"},
+)
 
 BALSAMIC_SAMPLE_TAGS = dict(
     bam_file={"bam"},

cg/meta/upload/scout/raredisease_config_builder.py

@@ -60,7 +60,7 @@ def build_load_config(self, rank_score_threshold: int = 5) -> None:
             GenomeBuild,
             self.raredisease_analysis_api.get_genome_build(case_id=self.analysis_obj.case.internal_id),
         )
-        self.load_config.rank_score_threshold = rank_score_threshold
+        # self.load_config.rank_score_threshold = rank_score_threshold
         # self.load_config.rank_model_version = raredisease_analysis_data.rank_model_version
         # self.load_config.sv_rank_model_version = raredisease_analysis_data.sv_rank_model_version
 
@@ -90,8 +90,7 @@ def include_pedigree_picture(self) -> None:
             LOG.info("family of 1 sample - skip pedigree graph")
 
     def build_config_sample(self, case_sample: CaseSample) -> ScoutRarediseaseIndividual:
-        """Build a sample with mip specific information"""
-
+        """Build a sample with specific information"""
         config_sample = ScoutRarediseaseIndividual()
         self.add_common_sample_info(config_sample=config_sample, case_sample=case_sample)
         self.add_common_sample_files(config_sample=config_sample, case_sample=case_sample)
@@ -117,6 +116,7 @@ def include_case_files(self) -> None:
 
     def include_sample_files(self, config_sample: ScoutIndividual = None) -> None:
         for scout_key in RAREDISEASE_SAMPLE_TAGS.keys():
+            scout_key = scout_key.replace("chromograph_", "chromograph_images.")
             self._include_file(scout_key)
 
     def _include_file(self, scout_key) -> None:
@@ -128,16 +128,6 @@ def _include_file(self, scout_key) -> None:
             self.get_file_from_hk(getattr(self.case_tags, scout_key)),
         )
 
-    @staticmethod
-    def extract_generic_filepath(file_path: str | None) -> str | None:
-        """Remove a file's suffix and identifying integer or X/Y
-        Example:
-        `/some/path/gatkcomb_rhocall_vt_af_chromograph_sites_X.png` becomes
-        `/some/path/gatkcomb_rhocall_vt_af_chromograph_sites_`"""
-        if file_path is None:
-            return file_path
-        return re.split("(\d+|X|Y)\.png", file_path)[0]
-
     @staticmethod
     def is_family_case(load_config: ScoutLoadConfig) -> bool:
         """Check if there are any linked individuals in a case"""

cg/models/scout/scout_load_config.py

@@ -70,20 +70,21 @@ class ScoutMipIndividual(ScoutIndividual):
 class ScoutRarediseaseIndividual(ScoutIndividual):
     mt_bam: str | None = None
     bam_file: str | None = None
-    chromograph_autozyg: str | None = None
-    chromograph_coverage: str | None = None
-    chromograph_regions: ChromographImages = ChromographImages()
-    chromograph_sites: ChromographImages = ChromographImages()
-    reviewer_alignment: Reviewer = Reviewer()
-    reviewer_alignment_index: Reviewer = Reviewer()
+    # chromograph_autozyg: str | None = None
+    # chromograph_coverage: str | None = None
+    # chromograph_regions: ChromographImages = ChromographImages()
+    # chromograph_sites: ChromographImages = ChromographImages()
+    # reviewer_alignment: Reviewer = Reviewer()
+    # reviewer_alignment_index: Reviewer = Reviewer()
     rhocall_bed: str | None = None
     rhocall_wig: str | None = None
     tiddit_coverage_wig: str | None = None
     upd_regions_bed: str | None = None
     upd_sites_bed: str | None = None
     vcf2cytosure: str | None = None
     mitodel_file: str | None = None
-
+    chromograph_images: ChromographImages = ChromographImages()
+    reviewer: Reviewer = Reviewer()
 
 class ScoutCancerIndividual(ScoutIndividual):
     tumor_type: str | None = None
@@ -114,7 +115,6 @@ class ScoutLoadConfig(BaseModel):
     coverage_qc_report: str | None = None
     cnv_report: str | None = None
     multiqc: str | None = None
-    multiqc_report: str | None = None
     track: Literal[UploadTrack.RARE_DISEASE.value, UploadTrack.CANCER.value] = (
         UploadTrack.RARE_DISEASE.value
     )
@@ -155,8 +155,8 @@ class MipLoadConfig(ScoutLoadConfig):
 
 
 class RarediseaseLoadConfig(ScoutLoadConfig):
-    chromograph_image_files: list[str] | None = None
-    chromograph_prefixes: list[str] | None = None
+    # chromograph_image_files: list[str] | None = None
+    # chromograph_prefixes: list[str] | None = None
     madeline: str | None = None
     peddy_check: str | None = None
     peddy_ped: str | None = None
@@ -166,12 +166,13 @@ class RarediseaseLoadConfig(ScoutLoadConfig):
     str_catalog: str | None = None
     vcf_mei: str | None = None
     vcf_mei_research: str | None = None
-    snv_vcf: Annotated[str, BeforeValidator(field_not_none)] = None
-    snv_research_vcf: Annotated[str | None, BeforeValidator(field_not_none)] = None
+    vcf_snv: Annotated[str, BeforeValidator(field_not_none)] = None
+    vcf_snv_research: Annotated[str | None, BeforeValidator(field_not_none)] = None
+    vcf_snv_mt: str | None = None
+    vcf_snv_research_mt: str | None = None
+    vcf_sv: Annotated[str | None, BeforeValidator(field_not_none)] = None
+    vcf_sv_research: Annotated[str | None, BeforeValidator(field_not_none)] = None
     vcf_str: str | None = None
-    sv_vcf: Annotated[str | None, BeforeValidator(field_not_none)] = None
-    sv_research_vcf: Annotated[str | None, BeforeValidator(field_not_none)] = None
-
 
 class RnafusionLoadConfig(ScoutLoadConfig):
     multiqc_rna: str | None = None