From 86a16ba60f367b6ad9fef1bc5e0b3389693fcabe Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 1 Jun 2018 14:39:08 +0200
Subject: [PATCH] UrQt: add tests, nf and config
---
src/nf_modules/UrQt/tests/tests.sh | 9 +++
src/nf_modules/UrQt/tests/trimming_paired.nf | 25 +++++++
src/nf_modules/UrQt/tests/trimming_single.nf | 28 ++++++++
src/nf_modules/UrQt/urqt.config | 16 +++++
src/nf_modules/UrQt/urqt.nf | 71 ++++++++++++++++++++
src/nf_modules/cutadapt/tests/tests.sh | 8 +--
6 files changed, 153 insertions(+), 4 deletions(-)
create mode 100644 src/nf_modules/UrQt/tests/tests.sh
create mode 100644 src/nf_modules/UrQt/tests/trimming_paired.nf
create mode 100644 src/nf_modules/UrQt/tests/trimming_single.nf
create mode 100644 src/nf_modules/UrQt/urqt.config
create mode 100644 src/nf_modules/UrQt/urqt.nf
diff --git a/src/nf_modules/UrQt/tests/tests.sh b/src/nf_modules/UrQt/tests/tests.sh
new file mode 100644
index 0000000..49099e2
--- /dev/null
+++ b/src/nf_modules/UrQt/tests/tests.sh
@@ -0,0 +1,9 @@
+nextflow src/nf_modules/UrQt/tests/trimming_paired.nf \
+ -c src/nf_modules/UrQt/UrQt.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+
+nextflow src/nf_modules/UrQt/tests/trimming_single.nf \
+ -c src/nf_modules/UrQt/UrQt.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
diff --git a/src/nf_modules/UrQt/tests/trimming_paired.nf b/src/nf_modules/UrQt/tests/trimming_paired.nf
new file mode 100644
index 0000000..4c289c0
--- /dev/null
+++ b/src/nf_modules/UrQt/tests/trimming_paired.nf
@@ -0,0 +1,25 @@
+log.info "fastq files : ${params.fastq}"
+
+Channel
+ .fromFilePairs( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+
+process trimming {
+ tag "$pair_id"
+ cpus 4
+
+ input:
+ set pair_id, file(reads) from fastq_files
+
+ output:
+ file "*_trim_R{1,2}.fastq.gz" into fastq_files_cut
+
+ 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 \
+> ${pair_id}_trimming_report.txt
+"""
+}
diff --git a/src/nf_modules/UrQt/tests/trimming_single.nf b/src/nf_modules/UrQt/tests/trimming_single.nf
new file mode 100644
index 0000000..3160f3b
--- /dev/null
+++ b/src/nf_modules/UrQt/tests/trimming_single.nf
@@ -0,0 +1,28 @@
+params.fastq = "$baseDir/data/fastq/*.fastq"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+ .fromPath( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+
+process trimming {
+ tag "$reads.baseName"
+ cpus 4
+
+ input:
+ file reads from fastq_files
+
+ output:
+ file "*_trim.fastq.gz" into fastq_files_trim
+
+ script:
+ """
+ UrQt --t 20 --m ${task.cpus} --gz \
+ --in ${reads} \
+ --out ${reads.baseName}_trim.fastq.gz \
+ > ${reads.baseName}_trimming_report.txt
+ """
+}
+
diff --git a/src/nf_modules/UrQt/urqt.config b/src/nf_modules/UrQt/urqt.config
new file mode 100644
index 0000000..0309d09
--- /dev/null
+++ b/src/nf_modules/UrQt/urqt.config
@@ -0,0 +1,16 @@
+profiles {
+ docker {
+ process {
+ $trimming {
+ container = "urqt:d62c1f8"
+ }
+ }
+ }
+ sge {
+ process{
+ $trimming {
+ beforeScript = "module purge; module load UrQt/d62c1f8"
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/UrQt/urqt.nf b/src/nf_modules/UrQt/urqt.nf
new file mode 100644
index 0000000..4c0d07c
--- /dev/null
+++ b/src/nf_modules/UrQt/urqt.nf
@@ -0,0 +1,71 @@
+/*
+* urqt :
+* Imputs : fastq files
+* Output : fastq files
+*/
+/* quality trimming */
+
+/*
+* for paired-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+ .fromFilePairs( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+
+process trimming {
+ tag "$pair_id"
+ cpus 4
+
+ input:
+ set pair_id, file(reads) from fastq_files
+
+ output:
+ file "*_trim_R{1,2}.fastq.gz" into fastq_files_cut
+
+ 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 \
+> ${pair_id}_trimming_report.txt
+"""
+}
+
+/*
+* for single-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*.fastq"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+ .fromPath( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+
+process trimming {
+ tag "$reads.baseName"
+ cpus 4
+
+ input:
+ file reads from fastq_files
+
+ output:
+ file "*_trim.fastq.gz" into fastq_files_trim
+
+ script:
+"""
+UrQt --t 20 --m ${task.cpus} --gz \
+--in ${reads} \
+--out ${reads.baseName}_trim.fastq.gz \
+> ${reads.baseName}_trimming_report.txt
+"""
+}
+
diff --git a/src/nf_modules/cutadapt/tests/tests.sh b/src/nf_modules/cutadapt/tests/tests.sh
index 9651978..a684410 100644
--- a/src/nf_modules/cutadapt/tests/tests.sh
+++ b/src/nf_modules/cutadapt/tests/tests.sh
@@ -1,19 +1,19 @@
-nextflow src/nf_modules/cutadapt/test/adaptor_removal_paired.nf \
+nextflow src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf \
-c src/nf_modules/cutadapt/cutadapt.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-nextflow src/nf_modules/cutadapt/test/adaptor_removal_single.nf \
+nextflow src/nf_modules/cutadapt/tests/adaptor_removal_single.nf \
-c src/nf_modules/cutadapt/cutadapt.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-nextflow src/nf_modules/cutadapt/test/trimming_paired.nf \
+nextflow src/nf_modules/cutadapt/tests/trimming_paired.nf \
-c src/nf_modules/cutadapt/cutadapt.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-nextflow src/nf_modules/cutadapt/test/trimming_single.nf \
+nextflow src/nf_modules/cutadapt/tests/trimming_single.nf \
-c src/nf_modules/cutadapt/cutadapt.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
--
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