[ADD] reduced xrefs

DessimozLab · Dec 18, 2024 · 241ae58 · 241ae58
1 parent b79b75e
commit 241ae58
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Showing 3 changed files with 27 additions and 2 deletions.
diff --git a/modules/local/xref_fetch/main.nf b/modules/local/xref_fetch/main.nf
@@ -135,3 +135,25 @@ process COMBINE_ALL_XREFS {
             --xrefs $xref_dbs \\
         """
 }
+
+process BUILD_REDUCED_XREFS {
+    label "process_low"
+    container "dessimozlab/omabuild:nf-latest"
+    tag "Building a reduced set of xrefs for lookup and search"
+
+    input:
+        path db
+        path xref_db
+
+    output:
+        path("reduced-xrefs-db.h5"), emit: red_xref_db_h5
+
+    script:
+        """
+        oma-build -vv reduced-xrefs \\
+            --out reduced-xrefs-db.h5 \\
+            --xrefs $xref_dbs \\
+            --db $db \\
+            --nr-procs ${task.cpus}
+        """
+}
diff --git a/subworkflows/local/xrefs/main.nf b/subworkflows/local/xrefs/main.nf
@@ -22,9 +22,11 @@ workflow GENERATE_XREFS {
                      db_h5, 
                      seqidx_h5,
                      source_xref_h5)
+        BUILD_REDUCED_XREFS(db_h5, MAP_XREFS_WF.out.xref_db)
 
 
     emit:
         taxmap  = PREPARE_XREFS.out.taxmap
         xref_db = MAP_XREFS_WF.out.xref_db
+        red_xref_db = BUILD_REDUCED_XREFS.out.red_xref_db_h5
 }
diff --git a/workflows/oma_browser_build.nf b/workflows/oma_browser_build.nf
@@ -35,7 +35,7 @@ workflow OMA_BROWSER_BUILD {
             DOMAINS(IMPORT_HDF5.out.db_h5, domains, cath_names, pfam_names)
             domains_h5 = DOMAINS.out.domains_h5
         } else {
-            domains_h5 = null
+            domains_h5 = Channel.empty()
         }
         CACHE_BUILDER(IMPORT_HDF5.out.db_h5)
         GEN_BROWSER_AUX_FILES(IMPORT_HDF5.out.db_h5)
@@ -60,7 +60,8 @@ workflow OMA_BROWSER_BUILD {
              domains_h5,
              GENERATE_XREFS.out.xref_db,
              GO_IMPORT.out.go_h5,
-             CACHE_BUILDER.out.cache_h5)
+             CACHE_BUILDER.out.cache_h5,
+             GENERATE_XREFS.out.red_xref_db)
         h5_dbs_to_combine.view()
         COMBINE_HDF(h5_dbs_to_combine.collect())