small arg fixes

cg/apps/scout/scoutapi.py

@@ -278,10 +278,7 @@ def upload_rna_coverage_bigwig(
                 "Something went wrong when uploading rna coverage bigwig file"
             ) from error
 
-
-    def upload_rna_fraser(
-        self, file_path: str, case_id: str, customer_sample_id: str
-    ) -> None:
+    def upload_rna_fraser(self, file_path: str, case_id: str, customer_sample_id: str) -> None:
         """Load a rna fraser file into a case in the database."""
 
         upload_command: list[str] = [
@@ -298,13 +295,9 @@ def upload_rna_fraser(
             LOG.info(f"Uploading rna fraser file {file_path} to case {case_id}")
             self.process.run_command(upload_command)
         except CalledProcessError as error:
-            raise ScoutUploadError(
-                "Something went wrong when uploading rna fraser file"
-            ) from error
+            raise ScoutUploadError("Something went wrong when uploading rna fraser file") from error
 
-    def upload_rna_outrider(
-        self, file_path: str, case_id: str, customer_sample_id: str
-    ) -> None:
+    def upload_rna_outrider(self, file_path: str, case_id: str, customer_sample_id: str) -> None:
         """Load a rna outrider file into a case in the database."""
 
         upload_command: list[str] = [
@@ -325,7 +318,6 @@ def upload_rna_outrider(
                 "Something went wrong when uploading rna outrider file"
             ) from error
 
-
     def upload_rna_alignment_file(
         self, case_id: str, customer_sample_id: str, file_path: str
     ) -> None:

cg/cli/upload/base.py

@@ -89,8 +89,8 @@ def upload(context: click.Context, case_id: str | None, restart: bool):
             upload_api = RarediseaseUploadAPI(config_object)
         elif case.data_analysis in {
             Workflow.RNAFUSION,
-            Workflow.TOMTE,
             Workflow.TAXPROFILER,
+            Workflow.TOMTE,
         }:
             upload_api = NfAnalysisUploadAPI(config_object, case.data_analysis)
 

cg/cli/upload/scout.py

@@ -174,8 +174,10 @@ def validate_case_samples_are_rna(context: CGConfig, case_id: str) -> None:
 @click.option("-r", "--research", is_flag=True, help="Upload research report instead of clinical")
 @click.argument("case_id")
 @click.pass_context
-def upload_rna_to_scout(context, case_id: str, dry_run: bool, research: bool, analysis: str) -> None:
-    """Upload an RNA case's gene fusion report and junction splice files for all samples connect via subject ID."""
+def upload_rna_to_scout(
+    context, case_id: str, dry_run: bool, research: bool, analysis: str
+) -> None:
+    """Upload an RNA case's gene fusion report and junction splice files for all samples connected via subject ID."""
     LOG.info("----------------- UPLOAD RNA TO SCOUT -----------------------")
 
     context.invoke(validate_case_samples_are_rna, case_id=case_id)
@@ -244,7 +246,6 @@ def upload_omics_to_scout(context: CGConfig, case_id: str, dry_run: bool) -> Non
     scout_upload_api.upload_omics_to_scout(dry_run=dry_run, case_id=case_id)
 
 
-
 @click.command(name="multiqc-to-scout")
 @DRY_RUN
 @click.argument("case_id")

cg/meta/report/templates/macros/uploaded_files/tomte_uploaded_files.html

@@ -0,0 +1,30 @@
+{% macro tomte_scout_files(scout_files, case_id, case_name) %}
+  <table class="table w-auto align-middle" aria-describedby="tomte-scout-table">
+    <tbody>
+      {% if scout_files.snv_vcf != "N/A" %}
+        <tr>
+          <th scope="row">Kliniskt relevanta SNVs och INDELs</th>
+          <td>{{ scout_files.snv_vcf.replace(case_id, case_name) }}</td>
+        </tr>
+      {% endif %}
+      {% if scout_files.snv_research_vcf != "N/A" %}
+        <tr>
+          <th scope="row">SNVs och INDELs för forskning</th>
+          <td>{{ scout_files.snv_research_vcf.replace(case_id, case_name) }}</td>
+        </tr>
+      {% endif %}
+      {% if scout_files.fraser_tsv != "N/A" %}
+        <tr>
+          <th scope="row">Kliniskt avvikande splitsningar</th>
+          <td>{{ scout_files.fraser_tsv.replace(case_id, case_name) }}</td>
+        </tr>
+      {% endif %}
+      {% if scout_files.outrider_tsv != "N/A" %}
+        <tr>
+          <th scope="row">Kliniskt avvikande genuttryck</th>
+          <td>{{ scout_files.outrider_tsv.replace(case_id, case_name) }}</td>
+        </tr>
+      {% endif %}
+    </tbody>
+  </table>
+{% endmacro %}

cg/meta/upload/nf_analysis.py

@@ -48,7 +48,9 @@ def upload(self, ctx: click.Context, case: Case, restart: bool) -> None:
         # Scout specific upload
         if DataDelivery.SCOUT in case.data_delivery:
             if case.data_analysis == Workflow.TOMTE:
-                ctx.invoke(upload_rna_to_scout, case_id=case.internal_id, re_upload=restart, analysis=case.data_analysis)
+                ctx.invoke(
+                    upload_rna_to_scout, case_id=case.internal_id, analysis=case.data_analysis
+                )
             else:
                 ctx.invoke(upload_to_scout, case_id=case.internal_id, re_upload=restart)
         LOG.info(

cg/meta/upload/scout/uploadscoutapi.py

@@ -159,19 +159,16 @@ def get_rna_coverage_bigwig(self, case_id: str, sample_id: str) -> File | None:
         tags: set[str] = {AnalysisTag.COVERAGE, AnalysisTag.BIGWIG, sample_id}
         return self.housekeeper.get_file_from_latest_version(bundle_name=case_id, tags=tags)
 
-
     def get_rna_omics_fraser(self, case_id: str, sample_id: str) -> File | None:
         """Return an fraser file for a case in Housekeeper."""
         tags: set[str] = {AnalysisTag.COVERAGE, AnalysisTag.FRASER, sample_id}
         return self.housekeeper.get_file_from_latest_version(bundle_name=case_id, tags=tags)
 
-
     def get_rna_omics_outrider(self, case_id: str, sample_id: str) -> File | None:
         """Return an outrider file for a case in Housekeeper."""
         tags: set[str] = {AnalysisTag.COVERAGE, AnalysisTag.OUTRIDER, sample_id}
         return self.housekeeper.get_file_from_latest_version(bundle_name=case_id, tags=tags)
 
-
     def get_unique_dna_cases_related_to_rna_case(self, case_id: str) -> set[str]:
         """Return a set of unique DNA cases related to an RNA case."""
         case: Case = self.status_db.get_case_by_internal_id(case_id)
@@ -337,7 +334,6 @@ def upload_rna_coverage_bigwig_to_scout(self, case_id: str, dry_run: bool) -> No
             LOG.info(upload_statement)
         LOG.info("Upload RNA coverage bigwig file finished!")
 
-
     def upload_rna_fraser_to_scout(self, dry_run: bool, case_id: str) -> None:
         """Upload omics fraser file for a case to Scout."""
         status_db: Store = self.status_db
@@ -375,7 +371,6 @@ def upload_rna_fraser_to_scout(self, dry_run: bool, case_id: str) -> None:
             LOG.info(upload_statement)
         LOG.info("Upload RNA fraser file finished!")
 
-
     def upload_rna_outrider_to_scout(self, dry_run: bool, case_id: str) -> None:
         """Upload omics outrider file for a case to Scout."""
         status_db: Store = self.status_db
@@ -411,8 +406,6 @@ def upload_rna_outrider_to_scout(self, dry_run: bool, case_id: str) -> None:
             LOG.info(upload_statement)
         LOG.info("Upload RNA outrider file finished!")
 
-
-
     def upload_splice_junctions_bed_to_scout(self, dry_run: bool, case_id: str) -> None:
         """Upload splice_junctions_bed file for a case to Scout."""
 
@@ -516,13 +509,11 @@ def upload_rna_junctions_to_scout(self, dry_run: bool, case_id: str) -> None:
         self.upload_splice_junctions_bed_to_scout(dry_run=dry_run, case_id=case_id)
         self.upload_rna_coverage_bigwig_to_scout(case_id=case_id, dry_run=dry_run)
 
-
     def upload_omics_to_scout(self, dry_run: bool, case_id: str) -> None:
         """Upload RNA omics files to Scout."""
         self.upload_rna_fraser_to_scout(dry_run=dry_run, case_id=case_id)
         self.upload_rna_outrider_to_scout(case_id=case_id, dry_run=dry_run)
 
-
     def get_config_builder(self, analysis, hk_version) -> ScoutConfigBuilder:
         config_builders = {
             Workflow.BALSAMIC: BalsamicConfigBuilder(
@@ -548,6 +539,13 @@ def get_config_builder(self, analysis, hk_version) -> ScoutConfigBuilder:
             Workflow.RNAFUSION: RnafusionConfigBuilder(
                 hk_version_obj=hk_version, analysis_obj=analysis, lims_api=self.lims
             ),
+            Workflow.TOMTE: TomteConfigBuilder(
+                hk_version_obj=hk_version,
+                analysis_obj=analysis,
+                mip_analysis_api=self.mip_analysis_api,
+                lims_api=self.lims,
+                madeline_api=self.madeline_api,
+            ),
         }
 
         return config_builders[analysis.workflow]