From 05d38fb74e50352a2bc49f5d2abd9f6a3610c2f7 Mon Sep 17 00:00:00 2001
From: jvfe <jvfecav@gmail.com>
Date: Wed, 18 Oct 2023 10:05:09 -0300
Subject: [PATCH] refactor: Use names.dmp in kaiju2table

---
 modules/nf-core/kaiju/kaiju2table/kaiju-kaiju2table.diff | 9 +++++++++
 modules/nf-core/kaiju/kaiju2table/main.nf                | 2 +-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/kaiju/kaiju2table/kaiju-kaiju2table.diff b/modules/nf-core/kaiju/kaiju2table/kaiju-kaiju2table.diff
index 5451f6a..a2a0899 100644
--- a/modules/nf-core/kaiju/kaiju2table/kaiju-kaiju2table.diff
+++ b/modules/nf-core/kaiju/kaiju2table/kaiju-kaiju2table.diff
@@ -10,5 +10,14 @@ Changes in module 'nf-core/kaiju/kaiju2table'
  
      input:
      tuple val(meta), path(results)
+@@ -24,7 +24,7 @@
+     def prefix = task.ext.prefix ?: "${meta.id}"
+     """
+     dbnodes=`find -L ${db} -name "*nodes.dmp"`
+-    dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
++    dbname=`find -L ${db} -name "*names.dmp"`
+     kaiju2table   $args \\
+         -t \$dbnodes \\
+         -n \$dbname \\
 
 ************************************************************
diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf
index 52bd643..42223b1 100644
--- a/modules/nf-core/kaiju/kaiju2table/main.nf
+++ b/modules/nf-core/kaiju/kaiju2table/main.nf
@@ -24,7 +24,7 @@ process KAIJU_KAIJU2TABLE {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     dbnodes=`find -L ${db} -name "*nodes.dmp"`
-    dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
+    dbname=`find -L ${db} -name "*names.dmp"`
     kaiju2table   $args \\
         -t \$dbnodes \\
         -n \$dbname \\