From 9cc57a97ae354cdf4f92dfa98977fc07f2603f43 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 18 Feb 2021 15:47:08 +0100
Subject: [PATCH] fastp: add json output for multiqc

---
 src/nf_modules/fastp/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf
index c69412e4..273ae3d3 100644
--- a/src/nf_modules/fastp/main.nf
+++ b/src/nf_modules/fastp/main.nf
@@ -25,6 +25,7 @@ fastp --thread ${task.cpus} \
 --out1 ${pair_id}_R1_trim.fastq.gz \
 --out2 ${pair_id}_R2_trim.fastq.gz \
 --html ${pair_id}.html \
+--json ${pair_id}.json \
 --report_title ${pair_id}
 """
 }
@@ -50,6 +51,7 @@ fastp --thread ${task.cpus} \
 --in1 ${reads} \
 --out1 ${pair_id}_trim.fastq.gz \
 --html ${pair_id}.html \
+--json ${pair_id}.json \
 --report_title ${pair_id}
 """
 }
-- 
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