Add Cirro config

Author: dltamayo

.cirro/process-form.json

@@ -50,8 +50,31 @@
                 "description": "p_depth (GLIPH2)",
                 "title": "p_depth",
                 "type": "string"
+            },
+            "samplechart_x_col": {
+                "default": "timepoint",
+                "description": "Metadata column for x axis of sample-level plots for Sample workflow notebook",
+                "title": "Sample plot X axis column",
+                "type": "string"
+            },
+            "samplechart_color_col": {
+                "default": "origin",
+                "description": "Metadata column for legend color of sample-level plots for Sample workflow notebook",
+                "title": "Sample plot X axis column",
+                "type": "string"
+            },
+            "vgene_subject_col": {
+                "default": "subject_id",
+                "description": "Metadata column for grouping of samples for V gene plots for Sample workflow notebook",
+                "title": "V gene plot subject column",
+                "type": "string"
+            },
+            "vgene_x_cols": {
+                "default": "timepoint,origin",
+                "description": "Comma-separated list of metadata columns for x axis of V gene plot (eg. timepoint,origin or timepoint)",
+                "title": "V gene plot X axis columns",
+                "type": "string"
             }
-            
         }
     },
     "ui": {}

.cirro/process-input.json

@@ -9,5 +9,9 @@
     "local_min_OVE": "$.params.dataset.paramJson.local_min_OVE",
     "local_min_pvalue": "$.params.dataset.paramJson.local_min_pvalue",
     "outdir": "$.params.dataset.s3|/data/",
-    "p_depth": "$.params.dataset.paramJson.p_depth"
+    "p_depth": "$.params.dataset.paramJson.p_depth",
+    "samplechart_x_col": "$.params.dataset.paramJson.samplechart_x_col",
+    "samplechart_color_col": "$.params.dataset.paramJson.samplechart_color_col",
+    "vgene_subject_col": "$.params.dataset.paramJson.vgene_subject_col",
+    "vgene_x_cols": "$.params.dataset.paramJson.vgene_x_cols"
 }

nextflow.config

@@ -30,7 +30,7 @@ params {
     samplechart_x_col = 'timepoint'
     samplechart_color_col = 'origin'
     vgene_subject_col = 'subject_id'
-    vgene_x_cols = 'timepoint,origin'
+    vgene_x_cols = 'origin,timepoint'
 
     // GIANA parameters
     threshold = 7.0