Merge branch 'main' into version_4.89

CHANGELOG.md

@@ -14,6 +14,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Subject id search from caseS page (supporting multiple sample types e.g.) - adding indexes to speed up caseS queries
 - Advanced cases search to narrow down results using more than one search parameter
 - Coverage report available for any case with samples containing d4 files, even if case has no associated gene panels
+- RNA delivery reports
 ### Changed
 - Documentation for OMICS variants and updating a case
 - Include both creation and deletion dates in gene panels pages

docs/admin-guide/load-config.md

@@ -47,6 +47,7 @@ Below are available configuration parameters for a Scout case. Names marked with
 - **RNAfusion_report** _String_ Path to HTML [nf-core/rnafusion report][rnafusion-report] containing only clinical fusions (a subset of all detected fusions).
 - **RNAfusion_report_research** _String_ Path to HTML [nf-core/rnafusion report][rnafusion-report] containing all detected fusions.
 - **rna_human_genome_build** _String_ Version of reference genome used for RNA components of build. "37" or "38", default "38".
+- **rna_delivery_report** _String_: Path to HTML RNA delivery report.
 - **samples** _List_ List of samples included in the case:
     - **alignment_path** _String_ Path to BAM/CRAM file to view alignments.
     - **analysis_type** _String_ Specifies the analysis type for the sample. Options: {wgs, wes, panel, unknown, external}.

scout/adapter/mongo/case.py

@@ -1082,6 +1082,7 @@ def update_case(self, case_obj, keep_date=False):
             - RNAfusion_inspector_research: path to the research RNA fusion inspector report
             - RNAfusion_report: path to the RNA fusion report
             - RNAfusion_report_research: path to the research RNA fusion report
+            - rna_delivery_report: path to the RNA delivery report
             - smn_tsv: path to static SMN TSV file
             - status: case status
             - sv_rank_model_version: If there is a new sv rank model
@@ -1155,6 +1156,7 @@ def update_case(self, case_obj, keep_date=False):
                 "RNAfusion_inspector_research": case_obj.get("RNAfusion_inspector_research"),
                 "RNAfusion_report": case_obj.get("RNAfusion_report"),
                 "RNAfusion_report_research": case_obj.get("RNAfusion_report_research"),
+                "rna_delivery_report": case_obj.get("rna_delivery_report"),
                 "smn_tsv": case_obj.get("smn_tsv"),
                 "status": case_obj.get("status"),
                 "sv_rank_model_version": case_obj.get("sv_rank_model_version"),
@@ -1203,6 +1205,7 @@ def update_case(self, case_obj, keep_date=False):
             "RNAfusion_inspector_research",
             "RNAfusion_report",
             "RNAfusion_report_research",
+            "rna_delivery_report",
             "smn_tsv",
             "sv_rank_model_version",
         ]:

scout/build/case.py

@@ -289,6 +289,7 @@ def build_case(case_data, adapter):
     case_obj["vcf_files"] = case_data.get("vcf_files", {})
     case_obj["omics_files"] = case_data.get("omics_files", {})
     case_obj["delivery_report"] = case_data.get("delivery_report")
+    case_obj["rna_delivery_report"] = case_data.get("rna_delivery_report")
 
     _populate_pipeline_info(case_obj, case_data)
 

scout/constants/case_tags.py

@@ -3,6 +3,11 @@
 # keys are used in the load report cli, while key_name is saved in case database documents
 CUSTOM_CASE_REPORTS = {
     "delivery": {"key_name": "delivery_report", "format": "HTML", "pdf_export": True},
+    "rna_delivery_report": {
+        "key_name": "rna_delivery_report",
+        "format": "HTML",
+        "pdf_export": True,
+    },
     "cnv": {"key_name": "cnv_report", "format": "PDF", "pdf_export": False},
     "cov_qc": {"key_name": "coverage_qc_report", "format": "HTML", "pdf_export": True},
     "exe_ver": {"key_name": "pipeline_version", "format": "YAML", "pdf_export": True},

scout/demo/643594.config.yaml

@@ -142,6 +142,7 @@ peddy_sex: scout/demo/643594.sex_check.csv
 
 delivery_report: scout/demo/delivery_report.html
 gene_fusion_report: scout/demo/draw-fusions-example.pdf
+rna_delivery_report: scout/demo/delivery_report.html
 exe_ver: scout/demo/exe_ver.yaml
 reference_info: scout/demo/reference_info.yaml
 

scout/models/case/case_loading_models.py

@@ -58,6 +58,7 @@
     "RNAfusion_inspector_research",
     "RNAfusion_report",
     "RNAfusion_report_research",
+    "rna_delivery_report",
 ]
 
 VCF_FILE_PATH_CHECKS = FILE_TYPE_MAP.keys()
@@ -431,6 +432,7 @@ class CaseLoader(BaseModel):
     RNAfusion_inspector_research: Optional[str] = None
     RNAfusion_report: Optional[str] = None
     RNAfusion_report_research: Optional[str] = None
+    rna_delivery_report: Optional[str] = None
     smn_tsv: Optional[str] = None
     sv_rank_model_version: Optional[str] = None
     synopsis: Optional[Union[List[str], str]] = None

scout/server/app.py

@@ -2,6 +2,7 @@
 
 import logging
 import os
+import re
 from datetime import timedelta
 from typing import Dict, Union
 from urllib.parse import parse_qsl, unquote, urlsplit
@@ -253,6 +254,14 @@ def cosmic_prefix(cosmicId):
             return "COSM" + str(cosmicId)
         return cosmicId
 
+    @app.template_filter()
+    def upper_na(string):
+        """
+        Uppercase ocurences of "dna" and "rna" for nice display.
+        """
+
+        return re.sub(r"[Dd][Nn][Aa]", r"DNA", re.sub(r"[Rr][Nn][Aa]", r"RNA", string))
+
     @app.template_filter()
     def count_cursor(pymongo_cursor):
         """Count number of returned documents (deprecated pymongo.cursor.count())"""

scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html

@@ -121,11 +121,6 @@
     </div>
     {% endif %}
 
-    <!-- Custom case reports as in constants.CUSTOM_CASE_REPORTS -->
-    {% for _, report_data in report_types.items() %}
-      {{ custom_case_report(institute, case, report_data) }}
-    {% endfor %}
-
     <!-- Delivery reports for old analyses -->
     {% if case.analyses %}
       {% for analysis in case.analyses %}
@@ -134,6 +129,11 @@
         {% endif %}
       {% endfor %}
     {% endif %}
+
+    <!-- Custom case reports as in constants.CUSTOM_CASE_REPORTS -->
+    {% for _, report_data in report_types.items() %}
+      {{ custom_case_report(institute, case, report_data) }}
+    {% endfor %}
 </div>
 <!-- end reports macro -->
 {% endmacro %}
@@ -144,7 +144,7 @@
     <div href="#" class="bg-dark list-group-item text-white">
       <div class="d-flex flex-row bd-highlight mt-1">
         <div>
-          <span class="menu-collapsed">{{report_key|replace("_"," ")|title}}</span>
+          <span class="menu-collapsed">{{report_key|replace("_"," ")|title|upper_na}}</span>
         </div>
         {% if case.get(report_key) is existing %}
           <div>