change boxplot to violin plot

assets/multiqc_config_global.yml

@@ -1,3 +1,6 @@
+export_plots: true
+data_format: 'csv'
+
 report_comment: >
   This report has been generated by the <a href="https://github.com/scilus/nf-pediatric/" target="_blank">nf-pediatric</a>
   analysis pipeline.
@@ -6,6 +9,7 @@ report_section_order:
   software_versions:
     order: -500
   "nf-pediatric-summary":
+    title: "nf-pediatric Workflow Summary"
     order: -600
   "subcortical_volumes":
     order: -700
@@ -28,6 +32,9 @@ report_section_order:
   "nf-pediatric-methods-description":
     order: -900
 
+run_modules:
+  - custom_content
+
 custom_data:
   sc_values:
     file_format: "csv"
@@ -37,13 +44,12 @@ custom_data:
       following tractography. If you selected the connectomics profile, this count will reflect the number of streamline following filtering with COMMIT. You can use this value to
       perform a sanity check on the quality of the tractography and flags potential outliers. Subjects with too low or too high streamline counts may have had some issues during
       processing or filtering. Refer to the individual subject reports for more details (found in the subject's output directory).
-    plot_type: "boxplot"
-    data_format: "long"
+    plot_type: "violin"
+    data_format: "wide"
     pconfig:
       id: "sc_values_plot"
       title: "SC Values Distribution"
       ylab: "SC Value"
-      colors: "#00ff8c"
 
   dice_values:
     file_format: "csv"
@@ -54,13 +60,12 @@ custom_data:
       covers the white matter found in the tracking mask. A DICE score of 1 indicates a perfect overlap, meaning a perfect coverage of the white matter, while a lower DICE score indicates
       a lower coverage. Usually, a DICE score above 0.8 is considered acceptable. Subjects with lower DICE score may have had some issues during processing or filtering. Refer to the
       individual subject reports for more details (found in the subject's output directory).
-    plot_type: "boxplot"
-    #data_format: "long"
+    plot_type: "violin"
+    data_format: "wide"
     pconfig:
       id: "dice_values_plot"
       title: "Dice Scores Distribution"
       ylab: "Dice Score"
-      colors: "#00BFFF"
 
   subcortical_volumes:
     file_format: "tsv"
@@ -70,13 +75,12 @@ custom_data:
       The subcortical parcellations volumes are useful to assess the volume of the subcortical structures and can be used to detect potential abnormalities. Subjects with either too low or
       too high subcortical volumes may have had some issues during segmentation resulting in a bad segmentation quality. As a recommendation, outliers should be visually inspected to confirm
       the quality of the segmentation. Refer to the individual subject reports for more details (found in the subject's output directory).
-    plot_type: "boxplot"
-    data_format: "long"
+    plot_type: "violin"
+    data_format: "wide"
     pconfig:
       id: "subcortical_volume_plot"
       title: "Subcortical Volumes Distribution"
       ylab: "Subcortical Volume"
-      colors: "#00BFFF"
 
   cortical_volume_lh:
     file_format: "tsv"
@@ -86,13 +90,12 @@ custom_data:
       FastSurfer pipeline. The cortical parcellations volumes are useful to assess the volume of the cortical structures and can be used to detect potential abnormalities. Subjects with
       either too low or too high cortical volumes may have had some issues during segmentation resulting in a bad segmentation quality. As a recommendation, outliers should be visually inspected
       to confirm the quality of the segmentation. Refer to the individual subject reports for more details (found in the subject's output directory).
-    plot_type: "boxplot"
-    data_format: "long"
+    plot_type: "violin"
+    data_format: "wide"
     pconfig:
       id: "cortical_volume_lh_plot"
       title: "Cortical Volumes (Left Hemisphere) Distribution"
       ylab: "Cortical Volume"
-      colors: "#00BFFF"
 
   cortical_volume_rh:
     file_format: "tsv"
@@ -102,13 +105,12 @@ custom_data:
       FastSurfer pipeline. The cortical parcellations volumes are useful to assess the volume of the cortical structures and can be used to detect potential abnormalities. Subjects with
       either too low or too high cortical volumes may have had some issues during segmentation resulting in a bad segmentation quality. As a recommendation, outliers should be visually inspected
       to confirm the quality of the segmentation. Refer to the individual subject reports for more details (found in the subject's output directory).
-    plot_type: "boxplot"
-    data_format: "long"
+    plot_type: "violin"
+    data_format: "wide"
     pconfig:
       id: "cortical_volume_rh_plot"
       title: "Cortical Volumes (Right Hemisphere) Distribution"
       ylab: "Cortical Volume"
-      colors: "#00BFFF"
 
   cortical_thickness_lh:
     file_format: "tsv"
@@ -118,13 +120,12 @@ custom_data:
       FastSurfer pipeline. The cortical parcellations thickness are useful to assess the thickness of the cortical structures and can be used to detect potential abnormalities. Subjects with
       either too low or too high cortical thickness may have had some issues during segmentation resulting in a bad segmentation quality. As a recommendation, outliers should be visually inspected
       to confirm the quality of the segmentation. Refer to the individual subject reports for more details (found in the subject's output directory).
-    plot_type: "boxplot"
-    data_format: "long"
+    plot_type: "violin"
+    data_format: "wide"
     pconfig:
       id: "cortical_thickness_lh_plot"
       title: "Cortical Thickness (Left Hemisphere) Distribution"
       ylab: "Cortical Thickness"
-      colors: "#00BFFF"
 
   cortical_thickness_rh:
     file_format: "tsv"
@@ -134,13 +135,12 @@ custom_data:
       FastSurfer pipeline. The cortical parcellations thickness are useful to assess the thickness of the cortical structures and can be used to detect potential abnormalities. Subjects with
       either too low or too high cortical thickness may have had some issues during segmentation resulting in a bad segmentation quality. As a recommendation, outliers should be visually inspected
       to confirm the quality of the segmentation. Refer to the individual subject reports for more details (found in the subject's output directory).
-    plot_type: "boxplot"
-    data_format: "long"
+    plot_type: "violin"
+    data_format: "wide"
     pconfig:
       id: "cortical_thickness_rh_plot"
       title: "Cortical Thickness (Right Hemisphere) Distribution"
       ylab: "Cortical Thickness"
-      colors: "#00BFFF"
 
   cortical_surface_area_lh:
     file_format: "tsv"
@@ -150,13 +150,12 @@ custom_data:
       FastSurfer pipeline. The cortical parcellations surface area are useful to assess the surface area of the cortical structures and can be used to detect potential abnormalities. Subjects with
       either too low or too high cortical surface area may have had some issues during segmentation resulting in a bad segmentation quality. As a recommendation, outliers should be visually inspected
       to confirm the quality of the segmentation. Refer to the individual subject reports for more details (found in the subject's output directory).
-    plot_type: "boxplot"
-    data_format: "long"
+    plot_type: "violin"
+    data_format: "wide"
     pconfig:
       id: "cortical_surface_area_lh_plot"
       title: "Cortical Surface Area (Left Hemisphere) Distribution"
       ylab: "Cortical Surface Area"
-      colors: "#00BFFF"
 
   cortical_surface_area_rh:
     file_format: "tsv"
@@ -166,13 +165,12 @@ custom_data:
       FastSurfer pipeline. The cortical parcellations surface area are useful to assess the surface area of the cortical structures and can be used to detect potential abnormalities. Subjects with
       either too low or too high cortical surface area may have had some issues during segmentation resulting in a bad segmentation quality. As a recommendation, outliers should be visually inspected
       to confirm the quality of the segmentation. Refer to the individual subject reports for more details (found in the subject's output directory).
-    plot_type: "boxplot"
-    data_format: "long"
+    plot_type: "violin"
+    data_format: "wide"
     pconfig:
       id: "cortical_surface_area_rh_plot"
       title: "Cortical Surface Area (Right Hemisphere) Distribution"
       ylab: "Cortical Surface Area"
-      colors: "#00BFFF"
 
 sp:
   sc_values: