feat: extend datavzrd template for fusions

Author: dlaehnemann

workflow/resources/datavzrd/fusion-calls-template.datavzrd.yaml

@@ -22,7 +22,56 @@ views:
           desc: ?f"Fusion calls"
           dataset: ?f"{group}-fusions"
           render-table:
+            add-columns:
+              breakpoint 1:
+                value: function create_position(row) { return ":".join([row.chromosome_partner1, row.position_partner1]) }
+                link_to_url: f"https://www.ensembl.org/{params.species}/Gene/Summary?g={value}"
             columns:
+              feature_id_partner1:
+                label: HUGO gene name breakpoint 1
+                link_to_url: "https://www.genecards.org/cgi-bin/carddisp.pl?gene={value}"
+              exon_partner1:
+                label: exon breakpoint 1
+              site1:
+                label: site breakpoint 1
+                plot:
+                  heatmap:
+                    type: nominal
+                    color-scheme: set1
+                    aux-domain-columns: site2
+              feature_name_partner1:
+                label: ensembl ID breakpoint 1
+                display-mode: detail
+                link_to_url: f"https://www.ensembl.org/{params.species}/Gene/Summary?g={value}"
+              feature_name_partner2:
+                label: ensembl ID breakpoint 2
+                display-mode: detail
+                link_to_url: f"https://www.ensembl.org/{params.species}/Gene/Summary?g={value}"
+            add-columns:
+              breakpoint 2:
+               value: function create_position(row) { return ":".join([row.chromosome_partner2, row.position_partner2]) }
+               link_to_url: f"https://www.ensembl.org/{params.species}/Location/View?r={{value}}"
+            columns:
+              feature_id_partner2:
+                label: HUGO gene name breakpoint 2
+                link_to_url: "https://www.genecards.org/cgi-bin/carddisp.pl?gene={value}"
+              exon_partner2:
+                label: exon breakpoint 2
+              site2:
+                label: site breakpoint 2
+                plot:
+                  heatmap:
+                    type: nominal
+                    color-scheme: set1
+                    aux-domain-columns: site1
+              type:
+                  heatmap:
+                    type: nominal
+                    color-scheme: category10
+              reading_frame:
+                  heatmap:
+                    type: nominal
+                    color-scheme: dark2
               "regex('.+: allele frequency')":
                 plot: 
                   ticks:

workflow/rules/datavzrd.smk

@@ -147,6 +147,7 @@ rule datavzrd_fusion_calls:
         "logs/datavzrd_report/{batch}.{event}.log",
     params:
         groups=get_report_batch("fusions"),
+        species=lookup(within=config, dpath="ref/species"),
         samples=samples,
     wrapper:
         "v6.2.0/utils/datavzrd"