From 46d97f5bed4ff29ca6d08b8f06d5f38200055a48 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Fri, 4 Dec 2020 11:20:44 +0100
Subject: [PATCH] Added --ignore-overlaps to disable read-pair overlap
 detection.

---
 main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/main.nf b/main.nf
index e6ccf689..9be3611f 100644
--- a/main.nf
+++ b/main.nf
@@ -1287,6 +1287,7 @@ process SAMTOOLS_MPILEUP {
     """
     samtools mpileup \\
         --count-orphans \\
+        --ignore-overlaps \\
         --no-BAQ \\
         --max-depth $params.mpileup_depth \\
         --fasta-ref $fasta \\