From 8e1543d2fb5ccfa48147145b799c198472f46683 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 15 Apr 2021 17:23:59 +0200
Subject: [PATCH] fastp: fix accel_s1plus protocol
---
src/nf_modules/fastp/main.nf | 12 +++++++-----
1 file changed, 7 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf
index 428da793..b0b31c62 100644
--- a/src/nf_modules/fastp/main.nf
+++ b/src/nf_modules/fastp/main.nf
@@ -111,18 +111,19 @@ process fastp_accel_1splus {
--detect_adapter_for_pe \
--stdout \
--in1 ${reads[0]} \
- --in2 ${reads[1]} \
- --out1 ${file_prefix}_R1_trim.fastq.gz \
- --out2 ${file_prefix}_R2_trim.fastq.gz | \
+ --in2 ${reads[1]} 2> /dev/null | \
fastp --thread ${task.cpus} \
--stdin \
--interleaved_in \
--trim_front1=10 \
--trim_front2=10 \
+ --disable_adapter_trimming \
--qualified_quality_phred 20 \
--disable_length_filtering \
--detect_adapter_for_pe \
${params.fastp} \
+ --out1 ${file_prefix}_R1_trim.fastq.gz \
+ --out2 ${file_prefix}_R2_trim.fastq.gz \
--html ${file_prefix}.html \
--json ${file_prefix}_fastp.json \
--report_title ${file_prefix}
@@ -135,15 +136,16 @@ process fastp_accel_1splus {
--disable_trim_poly_g \
--detect_adapter_for_pe \
--stdout \
- --in1 ${reads[0]} \
- --out1 ${file_prefix}_R1_trim.fastq.gz \
+ --in1 ${reads[0]} 2> /dev/null | \
fastp --thread ${task.cpus} \
+ --disable_adapter_trimming \
--stdin \
--trim_front1=10 \
--qualified_quality_phred 20 \
--disable_length_filtering \
--detect_adapter_for_pe \
${params.fastp} \
+ --out1 ${file_prefix}_trim.fastq.gz \
--html ${file_prefix}.html \
--json ${file_prefix}_fastp.json \
--report_title ${file_prefix}
--
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