[ADD] COMBINE all xrefs

DessimozLab · Oct 28, 2024 · 4f33ea6 · 4f33ea6
1 parent 2b40c50
commit 4f33ea6
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Showing 2 changed files with 27 additions and 2 deletions.
diff --git a/modules/local/xref_fetch/main.nf b/modules/local/xref_fetch/main.nf
@@ -92,4 +92,24 @@ process COLLECT_XREFS {
             --source $source \\
             --out ./xref-${source}.h5
         """
+}
+
+
+process COMBINE_ALL_XREFS {
+    label "process_single"
+    container "dessimozlab/omabuild:nf-latest"
+    tag "Collecting xrefs for $source"
+
+    input:
+        path xref_dbs
+
+    output:
+        tuple "XRef-db.h5", emit: xref_db_h5
+
+    script:
+        """
+        oma-build -vv combine-xrefs \\
+            --out "XRef-db.h5"
+            --xrefs $xref_dbs \\
+        """
 }
diff --git a/subworkflows/local/xrefs/main.nf b/subworkflows/local/xrefs/main.nf
@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 
-include { FETCH_REFSEQ; FILTER_AND_SPLIT; MAP_XREFS; COLLECT_XREFS } from "./../../../modules/local/xref_fetch"
+include { FETCH_REFSEQ; FILTER_AND_SPLIT; MAP_XREFS; COLLECT_XREFS; COMBINE_ALL_XREFS } from "./../../../modules/local/xref_fetch"
 
 workflow PREPARE_XREFS {
     take:
@@ -65,7 +65,12 @@ workflow MAP_XREFS_WF {
             .groupTuple()
             .map { source, map_resList, format, xrefList -> [source, map_resList, format, xrefList.flatten()]
         COLLECT_XREFS(grouped_by_source)
+        xref_dbs_list = COLLECT_XREFS.out.xref_by_source_h5
+            .map{ source, db -> db}
+            .mix(source_xref_db)
+            .collect()
+        COMBINE_ALL_XREFS(xref_dbs_list)
     emit:
-        xref_db = COLLECT_XREFS.out.xref_by_source_h5
+        xref_db = COMBINE_ALL_XREFS.out.xref_db_h5
 }