From ca4d10188b35e5da04defb9fb665989ec50ea962 Mon Sep 17 00:00:00 2001
From: Adam Rosenbaum <adam.rosenbaum@regionvasterbotten.se>
Date: Fri, 29 Nov 2024 19:26:40 +0100
Subject: [PATCH] fix custom samtools view module

---
 modules/local/samtools/fastq_longread/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/samtools/fastq_longread/main.nf b/modules/local/samtools/fastq_longread/main.nf
index c6013b70..e2ec25c5 100644
--- a/modules/local/samtools/fastq_longread/main.nf
+++ b/modules/local/samtools/fastq_longread/main.nf
@@ -28,8 +28,8 @@ process SAMTOOLS_LONGREAD_FASTQ {
         $args \\
         --threads ${task.cpus-1} \\
         -0 ${prefix}_other.fastq.gz \\
-        $input \\
-        $output
+        $output \\
+        $input
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":