refactor: Change of the canonical function (#337)

* Exchange of the canonical function, heatmap to boolean spell * Exchange in the canonical function * refactor: Changes in the mane_plus_clinical function and updated Datavzrd version The mane_plus_clinical function changed to a spell and the rules for Datavzrd are Changed to use a newer Datavzrd version * refactor: Usage of updated Datavzrd Version The rules for Datavzrd are modified to use a newer Datavzrd version * refactor: Changes in the canonical ans mane_plus_clinical function Visualization via spells instead of heatmaps --------- Co-authored-by: Felix Mölder <felix.moelder@uk-essen.de>
snakemake-workflows · Nov 25, 2024 · 762781e · 762781e
1 parent aa583d3
commit 762781e
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diff --git a/workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml b/workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml
@@ -304,25 +304,19 @@ views:
           canonical:
             optional: true
             display-mode: detail
-            plot:
-              heatmap:
-                scale: "ordinal"
-                domain: ["", "True"]
-                range:
-                  - white
-                  - black
-                custom-content: ?empty_content
+            spell:
+              url: v1.1.3/logic/boolean
+              with:
+                true_value: "True"
+                false_value: ""
           mane_plus_clinical:
             optional: true
             display-mode: detail
-            plot:
-              heatmap:
-                scale: "ordinal"
-                domain: ["", "True"]
-                range:
-                  - white
-                  - black
-                custom-content: ?empty_content
+            spell:
+              url: v1.1.3/logic/boolean
+              with:
+                true_value: "True"
+                false_value: ""
           ?for alias in params.samples.loc[params.samples["group"] == group, "alias"]:
             '?f"{alias}: short observations"':
               optional: true
@@ -481,25 +475,19 @@ views:
           canonical:
             optional: true
             display-mode: detail
-            plot:
-              heatmap:
-                scale: "ordinal"
-                domain: ["", "True"]
-                range:
-                  - white
-                  - black
-                custom-content: ?empty_content
+            spell:
+              url: v1.1.3/logic/boolean
+              with:
+                true_value: "True"
+                false_value: ""
           mane_plus_clinical:
             optional: true
             display-mode: detail
-            plot:
-              heatmap:
-                scale: "ordinal"
-                domain: ["", "True"]
-                range:
-                  - white
-                  - black
-                custom-content: ?empty_content
+            spell:
+              url: v1.1.3/logic/boolean
+              with:
+                true_value: "True"
+                false_value: ""
           ?for alias in params.samples.loc[params.samples["group"] == group, "alias"]:
             '?f"{alias}: short observations"':
               optional: true

diff --git a/workflow/rules/datavzrd.smk b/workflow/rules/datavzrd.smk
@@ -104,7 +104,7 @@ rule datavzrd_variants_calls:
             dpath="calling/fdr-control/events/{event}/desc", within=config
         ),
     wrapper:
-        "v4.6.0/utils/datavzrd"
+        "v5.1.0/utils/datavzrd"
 
 
 rule datavzrd_fusion_calls:
@@ -142,7 +142,7 @@ rule datavzrd_fusion_calls:
         groups=get_report_batch("fusions"),
         samples=samples,
     wrapper:
-        "v4.6.0/utils/datavzrd"
+        "v5.1.0/utils/datavzrd"
 
 
 rule bedtools_merge:
@@ -196,4 +196,4 @@ rule datavzrd_coverage:
     params:
         samples=lambda wc: get_group_samples(wc.group),
     wrapper:
-        "v4.6.0/utils/datavzrd"
+        "v5.1.0/utils/datavzrd"