[FIX] adding lots of missing files...

subworkflows/local/xrefs/map/main.nf

@@ -0,0 +1,34 @@
+#!/usr/bin/env nextflow
+
+include { MAP_XREFS; COLLECT_XREFS; COMBINE_ALL_XREFS } from "./../../../../modules/local/xref_fetch"
+
+
+
+workflow MAP_XREFS_WF {
+    take:
+        xref
+        tax_map
+        db
+        seq_idx_db
+        source_xref_db
+
+    main:
+        map_xref_params = xref
+           .combine(tax_map)
+           .combine(db)
+           .combine(seq_idx_db)
+           .combine(source_xref_db) 
+        MAP_XREFS(map_xref_params)
+        grouped_by_source = MAP_XREFS.out.matched_xrefs
+            .groupTuple()
+            .map { source, map_resList, format, xrefList -> [source, map_resList, format[0], xrefList.flatten()] }
+        COLLECT_XREFS(grouped_by_source)
+        xref_dbs_list = COLLECT_XREFS.out.xref_by_source_h5
+            .map{ source, h5db -> h5db}
+            .mix(source_xref_db)
+            .collect()
+        COMBINE_ALL_XREFS(xref_dbs_list)
+    emit:
+        xref_db = COMBINE_ALL_XREFS.out.xref_db_h5
+}
+