From 8ef138b4761eced5dc13c166c11582528d514e4f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 13 Apr 2021 11:50:34 +0200
Subject: [PATCH] fastp: add --interleaved_in for 2nd fastp for accel_s1plus
---
src/nf_modules/fastp/main.nf | 1 +
1 file changed, 1 insertion(+)
diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf
index 5997fdf1..da328807 100644
--- a/src/nf_modules/fastp/main.nf
+++ b/src/nf_modules/fastp/main.nf
@@ -101,6 +101,7 @@ fastp --thread ${task.cpus} \
--out2 ${pair_id}_R2_trim.fastq.gz | \
fastp --thread ${task.cpus} \
--stdin \
+ --interleaved_in \
--trim_front1=10 \
--trim_front2=10 \
--qualified_quality_phred 20 \
--
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