From 56e7e85e016742183973525682173887782f18fd Mon Sep 17 00:00:00 2001
From: Adrian Altenhoff <adrian.altenhoff@inf.ethz.ch>
Date: Tue, 10 Dec 2024 15:58:27 +0100
Subject: [PATCH] bump pyoma lib

---
 containers/oma/Pipfile.lock       |  4 ++--
 modules/local/browser_aux/main.nf | 24 ++++++++++++++++++++++++
 workflows/oma_browser_build.nf    |  2 ++
 3 files changed, 28 insertions(+), 2 deletions(-)
 create mode 100644 modules/local/browser_aux/main.nf

diff --git a/containers/oma/Pipfile.lock b/containers/oma/Pipfile.lock
index b55982d..a285b4e 100644
--- a/containers/oma/Pipfile.lock
+++ b/containers/oma/Pipfile.lock
@@ -159,7 +159,7 @@
                 "sha256:ee3566f6dc3acf20e238540daf896f0af20cff531521bf41fdf5143f73e209ae",
                 "sha256:f4c1c9ad7da9eaf8d8f4515bf931a7f6548a468e7ef29b8429e31aaff2d95f4c"
             ],
-            "markers": "python_version >= '3.9'",
+            "markers": "python_version >= '3.6'",
             "version": "==1.84"
         },
         "bleach": {
@@ -2059,7 +2059,7 @@
             ],
             "git": "${LABGIT}/pyoma.git",
             "markers": "python_version >= '3.6'",
-            "ref": "a20780b3aa3e9b3a97c08b6c052ee44b5416288c"
+            "ref": "704daf9571253e8e1ede10498e8c9bf70c87611b"
         },
         "pyopa": {
             "hashes": [
diff --git a/modules/local/browser_aux/main.nf b/modules/local/browser_aux/main.nf
new file mode 100644
index 0000000..f9fcec1
--- /dev/null
+++ 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
+        """
+}
\ No newline at end of file
diff --git a/workflows/oma_browser_build.nf b/workflows/oma_browser_build.nf
index b4099ff..cdb95fa 100644
--- 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,