setup for annotated kegg map viewer

Author: aw-watson

workflows/Nextflow/modules/runAnnotation/runAnnotation.nf

@@ -159,6 +159,11 @@ process keggPlots {
         path: "${settings["annotationOutDir"]}",
         mode: 'copy'
     )
+    publishDir(
+        path: "${settings["keggViewerDir"]}"
+        mode: 'symlink'
+        pattern: "kegg_map/*"
+    )
 
     input:
     path gff

workflows/Nextflow/nextflow.config

@@ -118,6 +118,7 @@ params {
         evalue = null
         gcode = null
         keggView = false
+        keggViewerDir = "${projectDir}/../../../database/opaver_web/data/kegg_map"
     }
 
     binning {

workflows/Nextflow/templates/module_params.tmpl

@@ -85,6 +85,7 @@
         evalue = <% if(typeof evalue !== 'undefined') { %><%= evalue %><% } else { %>0.000000001<%} %>
         gcode = <% if(typeof gcode !== 'undefined') { %><%= gcode %><% } else { %>11<%} %>
         keggView =  <% if(typeof keggView !== 'undefined') { %><%= keggView %><% } else { %>false<%} %>
+        keggViewerDir = "<%=keggViewerDir %>"
     }
 
     binning {