From 4e8c6a71387a6e00387a08bbad2a63f5cec2da7d Mon Sep 17 00:00:00 2001
From: Maarten-vd-Sande <Maarten-vd-Sande@users.noreply.github.com>
Date: Fri, 2 Feb 2024 13:06:05 +0100
Subject: [PATCH] Update get_fastq.smk

---
 seq2science/rules/get_fastq.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seq2science/rules/get_fastq.smk b/seq2science/rules/get_fastq.smk
index 65c7f5bcd..92cf146ce 100644
--- a/seq2science/rules/get_fastq.smk
+++ b/seq2science/rules/get_fastq.smk
@@ -155,7 +155,7 @@ rule sra2fastq_PE:
 
         # dump to tmp dir
         parallel-fastq-dump -s {input} -O {output.tmpdir} \
-        --threads {threads} --split-e --skip-technical --dumpbase \
+        --threads {threads} --split-3 --skip-technical --dumpbase \
         --readids --clip --read-filter pass --defline-seq '@$ac.$si.$sg/$ri' \
         --defline-qual '+' --gzip >> {log} 2>&1