From 720b19773d559c39fee79e5d93b612941e4a4e4a Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Mar 2021 15:43:43 +0100
Subject: [PATCH] fastp: test paired_end & single_end process
---
src/nf_modules/fastp/main.nf | 42 ++++++++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)
diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf
index 8b264375..82f8d880 100644
--- a/src/nf_modules/fastp/main.nf
+++ b/src/nf_modules/fastp/main.nf
@@ -1,6 +1,48 @@
version = "0.20.1"
container_url = "lbmc/fastp:${version}"
+process fastp {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$pair_id"
+ publishDir "results/QC/fastp/", mode: 'copy', pattern: "*.html"
+
+ input:
+ tuple val(pair_id), path(reads)
+
+ output:
+ tuple val(pair_id), path("*.fastq.gz"), emit: fastq
+ tuple val(pair_id), path("*.html"), emit: html
+ tuple val(pair_id), path("*.json"), emit: report
+
+ script:
+if (reads instanceof List)
+"""
+fastp --thread ${task.cpus} \
+--qualified_quality_phred 20 \
+--disable_length_filtering \
+--detect_adapter_for_pe \
+--in1 ${reads[0]} \
+--in2 ${reads[1]} \
+--out1 ${pair_id}_R1_trim.fastq.gz \
+--out2 ${pair_id}_R2_trim.fastq.gz \
+--html ${pair_id}.html \
+--json ${pair_id}_fastp.json \
+--report_title ${pair_id}
+"""
+else
+"""
+fastp --thread ${task.cpus} \
+--qualified_quality_phred 20 \
+--disable_length_filtering \
+--detect_adapter_for_pe \
+--in1 ${reads} \
+--out1 ${pair_id}_trim.fastq.gz \
+--html ${pair_id}.html \
+--json ${pair_id}_fastp.json \
+--report_title ${pair_id}
+"""
+}
process fastp_pairedend {
container = "${container_url}"
--
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