From f2a99c1cbfa9066da23480c6736f4640449bda90 Mon Sep 17 00:00:00 2001
From: Koustav Pal <koustavpal1988@gmail.com>
Date: Fri, 23 Feb 2024 12:21:12 +0000
Subject: [PATCH] patching samtools sort

---
 modules/nf-core/samtools/sort/main.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index 2b7753fd8..3332d000e 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -7,6 +7,8 @@ process SAMTOOLS_SORT {
         'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
         'biocontainers/samtools:1.17--h00cdaf9_0' }"
 
+    errorStrategy { task.exitStatus == 140 && task.dumpStderr().matches("\\[bam_sort_core\\] merging from \\d+\\ files and \\d+\\ in-memory blocks...") ? 'ignore' : 'terminate' }
+
     input:
     tuple val(meta), path(bam)
 
@@ -28,7 +30,7 @@ process SAMTOOLS_SORT {
         -@ $task.cpus \\
         -o ${prefix}.bam \\
         -T $prefix \\
-        $bam
+        $bam 
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":