From 550390345785fe0ebb1835616f895af2bdadf122 Mon Sep 17 00:00:00 2001
From: ljmesi <37740329+ljmesi@users.noreply.github.com>
Date: Tue, 3 May 2022 09:46:04 +0200
Subject: [PATCH] Add compression for output fastq file

---
 modules/samtools/bam2fq/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/samtools/bam2fq/main.nf b/modules/samtools/bam2fq/main.nf
index 5d6aa79d..554af48b 100644
--- a/modules/samtools/bam2fq/main.nf
+++ b/modules/samtools/bam2fq/main.nf
@@ -45,7 +45,7 @@ process SAMTOOLS_BAM2FQ {
             bam2fq \\
             $args \\
             -@ $task.cpus \\
-            $inputbam >${prefix}_interleaved.fq.gz
+            $inputbam | gzip > ${prefix}_interleaved.fq.gz
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":