From e8c33f9065cdf9048f85ac3d7057ce0e2155ec98 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 8 Apr 2021 17:42:54 +0200
Subject: [PATCH] fastp: add params.fastp
---
src/nf_modules/fastp/main.nf | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf
index 82f8d880..267b7d86 100644
--- a/src/nf_modules/fastp/main.nf
+++ b/src/nf_modules/fastp/main.nf
@@ -1,6 +1,10 @@
version = "0.20.1"
container_url = "lbmc/fastp:${version}"
+params.fastp = ""
+params.fastp_pairedend = ""
+params.fastp_singleend = ""
+
process fastp {
container = "${container_url}"
label "big_mem_multi_cpus"
@@ -22,6 +26,7 @@ fastp --thread ${task.cpus} \
--qualified_quality_phred 20 \
--disable_length_filtering \
--detect_adapter_for_pe \
+${params.fastp} \
--in1 ${reads[0]} \
--in2 ${reads[1]} \
--out1 ${pair_id}_R1_trim.fastq.gz \
@@ -36,6 +41,7 @@ fastp --thread ${task.cpus} \
--qualified_quality_phred 20 \
--disable_length_filtering \
--detect_adapter_for_pe \
+${params.fastp} \
--in1 ${reads} \
--out1 ${pair_id}_trim.fastq.gz \
--html ${pair_id}.html \
@@ -64,6 +70,7 @@ fastp --thread ${task.cpus} \
--qualified_quality_phred 20 \
--disable_length_filtering \
--detect_adapter_for_pe \
+${params.fastp_pairedend} \
--in1 ${reads[0]} \
--in2 ${reads[1]} \
--out1 ${pair_id}_R1_trim.fastq.gz \
@@ -94,6 +101,7 @@ fastp --thread ${task.cpus} \
--qualified_quality_phred 20 \
--disable_length_filtering \
--detect_adapter_for_pe \
+${params.fastp_singleend} \
--in1 ${reads} \
--out1 ${pair_id}_trim.fastq.gz \
--html ${pair_id}.html \
--
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