From 1bba35ce803772f1590f8542859193fe382ff539 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Fri, 22 Aug 2025 14:59:10 +0100
Subject: [PATCH] Busco module update (stop ignoring errors)

---
 modules.json                                 | 2 +-
 modules/nf-core/busco/busco/busco-busco.diff | 6 +++---
 modules/nf-core/busco/busco/main.nf          | 6 ++++++
 3 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/modules.json b/modules.json
index 17b2e3b4..a2111293 100644
--- a/modules.json
+++ b/modules.json
@@ -13,7 +13,7 @@
                     },
                     "busco/busco": {
                         "branch": "master",
-                        "git_sha": "de5b67889ef5f53d6996fb4dac300ed399a51212",
+                        "git_sha": "36c6c8445284e021d95ce30cdf743baef66b21aa",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/busco/busco/busco-busco.diff"
                     },
diff --git a/modules/nf-core/busco/busco/busco-busco.diff b/modules/nf-core/busco/busco/busco-busco.diff
index b0a3cbb4..92a8374b 100644
--- a/modules/nf-core/busco/busco/busco-busco.diff
+++ b/modules/nf-core/busco/busco/busco-busco.diff
@@ -1,4 +1,5 @@
 Changes in component 'nf-core/busco/busco'
+'modules/nf-core/busco/busco/environment.yml' is unchanged
 'modules/nf-core/busco/busco/meta.yml' is unchanged
 Changes in 'busco/busco/main.nf':
 --- modules/nf-core/busco/busco/main.nf
@@ -21,8 +22,7 @@ Changes in 'busco/busco/main.nf':
          './*-busco/*/auto_lineage',
          './*-busco/*/**/{miniprot,hmmer,.bbtools}_output',
 
-'modules/nf-core/busco/busco/environment.yml' is unchanged
-'modules/nf-core/busco/busco/tests/main.nf.test' is unchanged
-'modules/nf-core/busco/busco/tests/nextflow.config' is unchanged
 'modules/nf-core/busco/busco/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/busco/busco/tests/nextflow.config' is unchanged
+'modules/nf-core/busco/busco/tests/main.nf.test' is unchanged
 ************************************************************
diff --git a/modules/nf-core/busco/busco/main.nf b/modules/nf-core/busco/busco/main.nf
index 133883ea..a5ecd9cd 100644
--- a/modules/nf-core/busco/busco/main.nf
+++ b/modules/nf-core/busco/busco/main.nf
@@ -109,6 +109,12 @@ process BUSCO_BUSCO {
     mv ${prefix}-busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found."
     mv ${prefix}-busco/logs/busco.log ${prefix}-busco.log
 
+    if grep 'Run failed; check logs' ${prefix}-busco.batch_summary.txt > /dev/null
+    then
+        echo "Busco run failed"
+        exit 1
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         busco: \$( busco --version 2> /dev/null | sed 's/BUSCO //g' )