initial add of viz WDL

.dockstore.yml

@@ -374,3 +374,9 @@ workflows:
     primaryDescriptorPath: /pipes/WDL/workflows/bam_to_qiime.wdl
     testParameterFiles:
       - empty.json
+
+  - name: create_enterics_qc_viz
+    subclass: WDL
+    primaryDescriptorPath: /pipes/WDL/workflows/create_enterics_qc_viz.wdl
+    testParameterFiles:
+      - empty.json

pipes/WDL/workflows/create_enterics_qc_viz.wdl

@@ -0,0 +1,71 @@
+version 1.0
+
+workflow CreateEntericsWCViz {
+
+    parameter_meta {
+        sample_ids: {description: "selected rows of data from data table which will be used for plotting"}
+        input_table_name: {description: "name of the Terra data table - root entity type - from where input data is selected"}
+        workspace_name: {description: "name of Terra workspace where data lives"}
+        workspace_project: {description: "name of Terra project associated with Terra workspace"}
+        grouping_column_name: {description: "name of column to be used for grouping/coloring - ex. gambit_predicted_taxon (organism)"}
+        output_filename: {description: "name of output file containing visualizations"}
+    }
+
+    input {
+
+        Array[String]   sample_ids
+        String          input_table_name
+        String          workspace_name
+        String          workspace_project
+
+        String?         grouping_column_name
+        String?         output_filename
+    }
+
+    call create_viz {
+        input:
+            sample_ids              =   sample_ids,
+            workspace_name          =   workspace_name,
+            workspace_project       =   workspace_project,
+            input_table_name        =   input_table_name,
+            grouping_column_name    =   grouping_column_name,
+            output_filename         =   output_filename
+    }
+
+    output {
+        File    viz_pdf     =   create_viz.vizualizations
+        File    color_chart =   create_viz.color_chart
+    }
+}
+
+task create_viz {
+    input {
+        Array[String]   sample_ids
+        String          workspace_name
+        String          workspace_project
+        String          input_table_name
+
+        String          grouping_column_name    = "gambit_predicted_taxon"
+        String          output_filename         = "QC_vizualizations.pdf"
+
+        String  docker                          =   "broadinstitute/horsefish:pgs_visualizations"        
+    }
+
+    command {
+        python3 /scripts/create_visualizations.py -s ~{sep=' ' sample_ids} \
+                                                  -t ~{input_table_name} \
+                                                  -w ~{workspace_name} \
+                                                  -p ~{workspace_project} \
+                                                  ~{"-g" + grouping_column_name} \
+                                                  ~{"-o" + output_filename}
+    }
+
+    runtime {
+        docker: docker
+    }
+
+    output {
+        File vizualizations = "~{output_filename}"
+        File color_chart    = "Colorized_Scores.xlsx"
+    }
+}