Adding channel operator to include sample IDs.

plugins/nf-iridanext/src/main/nextflow/iridanext/IDParser.groovy

@@ -0,0 +1,36 @@
+package nextflow.iridanext
+
+import groovyx.gpars.dataflow.DataflowWriteChannel
+import groovyx.gpars.dataflow.DataflowReadChannel
+import nextflow.Channel
+import nextflow.extension.CH
+import nextflow.extension.DataflowHelper
+import nextflow.Session
+import nextflow.plugin.extension.Operator
+import nextflow.plugin.extension.PluginExtensionPoint
+import nextflow.iridanext.IridaNextJSONOutput
+
+
+class IDParser extends PluginExtensionPoint {
+
+    @Override
+    void init(Session session) {}
+
+    @Operator
+    DataflowWriteChannel parseSamplesheet( DataflowReadChannel source ) {
+        final target = CH.createBy(source)
+
+        final next = { it ->
+            IridaNextJSONOutput.addId("samples", it[0].id)
+            target.bind(it)
+        }
+
+        final done = {
+            target.bind(Channel.STOP)
+        }
+
+        DataflowHelper.subscribeImpl(source, [onNext: next, onComplete: done])
+        return target
+    }
+
+}

plugins/nf-iridanext/src/main/nextflow/iridanext/IridaNextJSONOutput.groovy

@@ -39,7 +39,7 @@ import groovy.util.logging.Slf4j
 class IridaNextJSONOutput {
     private Map files = ["global": [], "samples": [:]]
     private Map metadata = ["samples": [:]]
-    private Map<String,Set<String>> scopeIds = ["samples": [] as Set<String>]
+    private static Map<String,Set<String>> scopeIds = ["samples": [] as Set<String>]
     private Path relativizePath
     private Boolean shouldRelativize
     private Schema jsonSchema
@@ -99,7 +99,7 @@ class IridaNextJSONOutput {
         }
     }
 
-    public void addId(String scope, String id) {
+    public static void addId(String scope, String id) {
         log.trace "Adding scope=${scope} id=${id}"
         scopeIds[scope].add(id)
     }

plugins/nf-iridanext/src/resources/META-INF/extensions.idx

@@ -1 +1,2 @@
-nextflow.iridanext.IridaNextObserverFactory
+nextflow.iridanext.IridaNextObserverFactory
+nextflow.iridanext.IDParser