syntax fix and project code isolation testing

aw-watson · aw-watson · commit 5768fc66be4a · 2025-11-05T19:12:20.000Z
diff --git a/workflows/Nextflow/modules/runAnnotation/runAnnotation.nf b/workflows/Nextflow/modules/runAnnotation/runAnnotation.nf
@@ -160,8 +160,8 @@ process keggPlots {
         mode: 'copy'
     )
     publishDir(
-        path: "${settings["keggViewerDir"]}"
-        mode: 'copy'
+        path: "${settings["keggViewerDir"]}",
+        mode: 'copy',
         pattern: "kegg_map/*"
     )
 
diff --git a/workflows/Nextflow/templates/module_params.tmpl b/workflows/Nextflow/templates/module_params.tmpl
@@ -86,6 +86,7 @@
         gcode = <% if(typeof gcode !== 'undefined') { %><%= gcode %><% } else { %>11<%} %>
         keggView =  <% if(typeof keggView !== 'undefined') { %><%= keggView %><% } else { %>false<%} %>
         keggViewerDir = "<%=keggViewerDir %>"
+        dataCode = "<%= nextflowOutDir %>".split("/")[-2]
     }
 
     binning {

Original file line number	Diff line number	Diff line change
`@@ -160,8 +160,8 @@ process keggPlots {`
`160`	`160`	`mode: 'copy'`
`161`	`161`	`)`
`162`	`162`	`publishDir(`
`163`		`- path: "${settings["keggViewerDir"]}"`
`164`		`- mode: 'copy'`
	`163`	`+ path: "${settings["keggViewerDir"]}",`
	`164`	`+ mode: 'copy',`
`165`	`165`	`pattern: "kegg_map/*"`
`166`	`166`	`)`
`167`	`167`
Original file line number	Diff line number	Diff line change
`@@ -86,6 +86,7 @@`
`86`	`86`	`gcode = <% if(typeof gcode !== 'undefined') { %><%= gcode %><% } else { %>11<%} %>`
`87`	`87`	`keggView = <% if(typeof keggView !== 'undefined') { %><%= keggView %><% } else { %>false<%} %>`
`88`	`88`	`keggViewerDir = "<%=keggViewerDir %>"`
	`89`	`+ dataCode = "<%= nextflowOutDir %>".split("/")[-2]`
`89`	`90`	`}`
`90`	`91`
`91`	`92`	`binning {`