bump pyoma lib

DessimozLab · Dec 10, 2024 · 56e7e85 · 56e7e85
1 parent ca47b7f
commit 56e7e85
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Showing 3 changed files with 28 additions and 2 deletions.
diff --git a/containers/oma/Pipfile.lock b/containers/oma/Pipfile.lock
diff --git a/modules/local/browser_aux/main.nf b/modules/local/browser_aux/main.nf
@@ -0,0 +1,24 @@
+process GEN_BROWSER_AUX_FILES {
+    label "process_single"
+    container "dessimozlab/omabuild:nf-latest"
+
+    input:
+        path db
+
+    output:
+        path "genomes.json", emit: genomes_json
+        path "speciestree.*", emit: speciestree
+
+    script:
+        """
+        oma-build -vv generate-aux-files \\
+            --db $db \\
+            --out-dir ./
+        """
+
+    stub:
+        """
+        touch genomes.json
+        touch speciestree.nwk speciestree.phyloxml
+        """
+}
diff --git a/workflows/oma_browser_build.nf b/workflows/oma_browser_build.nf
@@ -8,6 +8,7 @@ include { GENERATE_XREFS } from "./../subworkflows/local/xrefs"
 include { GO_IMPORT      } from "./../modules/local/go_import"
 include { COMBINE_HDF    } from "./../modules/local/h5_combine"
 include { CACHE_BUILDER  } from "./../subworkflows/local/cache_builder"
+include { GEN_BROWSER_AUX_FILES } from "./../modules/local/browser_aux"
 
 workflow OMA_BROWSER_BUILD {
     take:
@@ -37,6 +38,7 @@ workflow OMA_BROWSER_BUILD {
             domains_h5 = null
         }
         CACHE_BUILDER(IMPORT_HDF5.out.db_h5)
+        GEN_BROWSER_AUX_FILES(IMPORT_HDF5.out.db_h5)
 
         // create crossreferences
         GENERATE_XREFS(EXTRACT_DARWIN.out.gs_file,