From 62775173f695b6f41ac8de476cfcd635ab6d5da3 Mon Sep 17 00:00:00 2001
From: tcezard <tcezard@ebi.ac.uk>
Date: Mon, 2 Dec 2024 14:43:44 +0000
Subject: [PATCH] Ensure that out of memory error in minimap2 are resported as
 out of memory error

---
 variant_to_realignment.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/variant_to_realignment.nf b/variant_to_realignment.nf
index 4d45acb..1c1042d 100755
--- a/variant_to_realignment.nf
+++ b/variant_to_realignment.nf
@@ -173,6 +173,7 @@ process alignWithMinimap {
     }
     if (flanklength < 500)
         """
+        set -o pipefail
         # Options used by the 'sr' preset with some modifications:
         # -O6,16 instead of -O12,32 --> reduce indel cost
         # -B5 instead of -B10 --> reduce mismatch cost
@@ -188,6 +189,7 @@ process alignWithMinimap {
         """
     else
         """
+        set -o pipefail
         minimap2 $index_size -k19 -w19 -A2 -B5 -O6,16 --end-bonus 20 -E3,1 -s200 -z200 -N50 --min-occ-floor=100 \
                  --secondary=yes -N 2 -y \
                  -a genome.fa ${reads} | \