From c98150b9e1a8ead0f4d4d7685b5350c61e18caa9 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 13 Apr 2021 11:05:18 +0200
Subject: [PATCH] fastp: add accel_1splus protocol trimming with a switch
---
src/nf_modules/fastp/main.nf | 87 +++++++++++++++++++++++++++++++++++-
1 file changed, 86 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf
index 267b7d86..fa61ab6b 100644
--- a/src/nf_modules/fastp/main.nf
+++ b/src/nf_modules/fastp/main.nf
@@ -1,11 +1,34 @@
version = "0.20.1"
container_url = "lbmc/fastp:${version}"
+params.fastp_protocol = ""
params.fastp = ""
params.fastp_pairedend = ""
params.fastp_singleend = ""
-process fastp {
+workflow fastp {
+ take:
+ fastq
+
+ main:
+ switch(params.fastp_protocol) {
+ case "accel_1splus":
+ fastp_accel_1splus(fastq)
+ fastp_accel_1splus.out.fastq.set{res_fastq}
+ fastp_accel_1splus.out.report.set{res_report}
+ break;
+ default:
+ fastp_default(fastq)
+ fastp_default.out.fastq.set{res_fastq}
+ fastp_default.out.report.set{res_report}
+ break;
+ }
+ emit:
+ fastq = res_fastq
+ report = res_report
+}
+
+process fastp_default {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$pair_id"
@@ -50,6 +73,68 @@ ${params.fastp} \
"""
}
+process fastp_accel_1splus {
+ container = "${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} \
+--disable_quality_filtering \
+--disable_length_filtering \
+--disable_trim_poly_g \
+--stdout \
+--in1 ${reads[0]} \
+--in2 ${reads[1]} \
+--out1 ${pair_id}_R1_trim.fastq.gz \
+--out2 ${pair_id}_R2_trim.fastq.gz | \
+fastp --thread ${task.cpus} \
+--stdin \
+--trim_front1=10 \
+--trim_tail1=10 \
+--trim_tail2=10 \
+--qualified_quality_phred 20 \
+--disable_length_filtering \
+--detect_adapter_for_pe \
+${params.fastp} \
+--html ${pair_id}.html \
+--json ${pair_id}_fastp.json \
+--report_title ${pair_id}
+"""
+else
+"""
+fastp --thread ${task.cpus} \
+--disable_quality_filtering \
+--disable_length_filtering \
+--disable_trim_poly_g \
+--stdout \
+--in1 ${reads[0]} \
+--out1 ${pair_id}_R1_trim.fastq.gz \
+fastp --thread ${task.cpus} \
+--stdin \
+--trim_front1=10 \
+--trim_tail1=10 \
+--qualified_quality_phred 20 \
+--disable_length_filtering \
+--detect_adapter_for_pe \
+${params.fastp} \
+--html ${pair_id}.html \
+--json ${pair_id}_fastp.json \
+--report_title ${pair_id}
+"""
+}
+
process fastp_pairedend {
container = "${container_url}"
label "big_mem_multi_cpus"
--
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