From aefdae4d7bb824301bb1bf01780079f9b8d7487b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 20 Jan 2021 17:22:21 +0100
Subject: [PATCH] nf_modules: add urqt for DSL2
---
src/nf_modules/cutadapt/main.nf | 2 +-
src/nf_modules/urqt/main.nf | 49 +++++++++++++++++++++++++++++++++
2 files changed, 50 insertions(+), 1 deletion(-)
create mode 100644 src/nf_modules/urqt/main.nf
diff --git a/src/nf_modules/cutadapt/main.nf b/src/nf_modules/cutadapt/main.nf
index 74c37be0..0859ea92 100644
--- a/src/nf_modules/cutadapt/main.nf
+++ b/src/nf_modules/cutadapt/main.nf
@@ -6,7 +6,7 @@ adapter_5_prim = "CTCTTCCGATCT"
trim_quality = "20"
-process adaptor_removal_paired {
+process adaptor_removal_pairedend {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$pair_id"
diff --git a/src/nf_modules/urqt/main.nf b/src/nf_modules/urqt/main.nf
new file mode 100644
index 00000000..48a1a3ec
--- /dev/null
+++ b/src/nf_modules/urqt/main.nf
@@ -0,0 +1,49 @@
+version = "d62c1f8"
+container_url = "lbmc/urqt:${version}"
+
+trim_quality = "20"
+
+process trimming_pairedend {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "${reads}"
+ publishDir "results/fastq/trimming/", mode: 'copy'
+
+ input:
+ tuple val(pair_id), path(reads)
+
+ output:
+ tuple val(pair_id), path("*_trim_R{1,2}.fastq.gz"), emit: fastq
+ path "*_report.txt", emit: report
+
+ script:
+"""
+UrQt --t 20 --m ${task.cpus} --gz \
+ --in ${reads[0]} --inpair ${reads[1]} \
+ --out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
+ > ${pair_id}_trimming_report.txt
+"""
+}
+
+process trimming_singleend {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+ publishDir "results/fastq/trimming/", mode: 'copy'
+
+ input:
+ tuple val(file_id), path(reads)
+
+ output:
+ tuple val(file_id), path("*_trim.fastq.gz"), emit: fastq
+ path "*_report.txt", emit: report
+
+ script:
+"""
+UrQt --t 20 --m ${task.cpus} --gz \
+ --in ${reads} \
+ --out ${file_id}_trim.fastq.gz \
+ > ${file_id}_trimming_report.txt
+"""
+}
+
--
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