From 2c488dbfc63f5c1c2f53febe4345ce0ca4607c02 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 1 Jun 2018 14:15:56 +0200
Subject: [PATCH] cutadapt: add tests and config
---
src/nf_modules/cutadapt/1.14/Dockerfile | 15 ++++++++
src/nf_modules/cutadapt/1.14/docker_init.sh | 2 +
src/nf_modules/cutadapt/cutadapt.config | 37 +++++++++++++++++++
src/nf_modules/cutadapt/cutadapt.nf | 4 --
.../cutadapt/tests/adaptor_removal_paired.nf | 24 ++++++++++++
.../cutadapt/tests/adaptor_removal_single.nf | 24 ++++++++++++
src/nf_modules/cutadapt/tests/tests.sh | 19 ++++++++++
.../cutadapt/tests/trimming_paired.nf | 24 ++++++++++++
.../cutadapt/tests/trimming_single.nf | 24 ++++++++++++
9 files changed, 169 insertions(+), 4 deletions(-)
create mode 100644 src/nf_modules/cutadapt/1.14/Dockerfile
create mode 100755 src/nf_modules/cutadapt/1.14/docker_init.sh
create mode 100644 src/nf_modules/cutadapt/cutadapt.config
create mode 100644 src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf
create mode 100644 src/nf_modules/cutadapt/tests/adaptor_removal_single.nf
create mode 100644 src/nf_modules/cutadapt/tests/tests.sh
create mode 100644 src/nf_modules/cutadapt/tests/trimming_paired.nf
create mode 100644 src/nf_modules/cutadapt/tests/trimming_single.nf
diff --git a/src/nf_modules/cutadapt/1.14/Dockerfile b/src/nf_modules/cutadapt/1.14/Dockerfile
new file mode 100644
index 0000000..b8c5f54
--- /dev/null
+++ b/src/nf_modules/cutadapt/1.14/Dockerfile
@@ -0,0 +1,15 @@
+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV CUTADAPT_VERSION=1.14
+ENV PACKAGES build-essential=12.4* \
+ python3-pip=9.0.1* \
+ python3-setuptools=39.0.1* \
+ python3-dev=3.6.5* \
+ python3-wheel=0.30.0*
+
+RUN apt-get update && \
+ apt-get install -y --no-install-recommends ${PACKAGES} && \
+ apt-get clean
+
+RUN pip3 install cutadapt==${CUTADAPT_VERSION}
diff --git a/src/nf_modules/cutadapt/1.14/docker_init.sh b/src/nf_modules/cutadapt/1.14/docker_init.sh
new file mode 100755
index 0000000..5765746
--- /dev/null
+++ b/src/nf_modules/cutadapt/1.14/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/nf_modules/cutadapt/1.14 -t 'cutadapt:1.14'
diff --git a/src/nf_modules/cutadapt/cutadapt.config b/src/nf_modules/cutadapt/cutadapt.config
new file mode 100644
index 0000000..79a6478
--- /dev/null
+++ b/src/nf_modules/cutadapt/cutadapt.config
@@ -0,0 +1,37 @@
+profiles {
+ docker {
+ docker {
+ temp = 'auto'
+ enabled = true
+ }
+ process {
+ $adaptor_removal {
+ container = "cutadapt:1.14"
+ }
+ }
+ }
+ sge {
+ process{
+ $adaptor_removal {
+ beforeScript = "module purge; module load cutadapt/1.14"
+ }
+ }
+ }
+}
+
+profiles {
+ docker {
+ process {
+ $trimming {
+ container = "cutadapt:1.14"
+ }
+ }
+ }
+ sge {
+ process{
+ $trimming {
+ beforeScript = "module purge; module load cutadapt/1.14"
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/cutadapt/cutadapt.nf b/src/nf_modules/cutadapt/cutadapt.nf
index b5f69fb..3f3db6a 100644
--- a/src/nf_modules/cutadapt/cutadapt.nf
+++ b/src/nf_modules/cutadapt/cutadapt.nf
@@ -67,10 +67,6 @@ process adaptor_removal {
/* quality trimming */
-${this.params.cutadapt} -q ${this.params.quality_threshold},${this.params.quality_threshold} -o ${tagname}_trim_R1.fastq.gz -p ${tagname}_trim_R2.fastq.gz ${file[0]} ${file[1]} > ${tagname}_cutadapt_report.txt"
-
-${this.params.cutadapt} -q ${this.params.quality_threshold},${this.params.quality_threshold} -o ${tagname}_trim.fastq.gz ${file} > ${tagname}_cutadapt_report.txt
-
/*
* for paired-end data
*/
diff --git a/src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf b/src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf
new file mode 100644
index 0000000..d665d23
--- /dev/null
+++ b/src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf
@@ -0,0 +1,24 @@
+log.info "fastq files : ${params.fastq}"
+
+Channel
+ .fromFilePairs( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+
+process adaptor_removal {
+ tag "$pair_id"
+
+ input:
+ set pair_id, file(reads) from fastq_files
+
+ output:
+ file "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+
+ script:
+ """
+ cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
+ -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
+ ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+ """
+}
+
diff --git a/src/nf_modules/cutadapt/tests/adaptor_removal_single.nf b/src/nf_modules/cutadapt/tests/adaptor_removal_single.nf
new file mode 100644
index 0000000..dc889a0
--- /dev/null
+++ b/src/nf_modules/cutadapt/tests/adaptor_removal_single.nf
@@ -0,0 +1,24 @@
+log.info "fastq files : ${params.fastq}"
+
+Channel
+ .fromPath( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+
+process adaptor_removal {
+ tag "$reads.baseName"
+
+ input:
+ file reads from fastq_files
+
+ output:
+ file "*_cut.fastq.gz" into fastq_files_cut
+
+ script:
+ """
+ cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT\
+ -o ${reads.baseName}_cut.fastq.gz \
+ ${reads} > ${reads.baseName}_report.txt
+ """
+}
+
diff --git a/src/nf_modules/cutadapt/tests/tests.sh b/src/nf_modules/cutadapt/tests/tests.sh
new file mode 100644
index 0000000..9651978
--- /dev/null
+++ b/src/nf_modules/cutadapt/tests/tests.sh
@@ -0,0 +1,19 @@
+nextflow src/nf_modules/cutadapt/test/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 \
+ -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 \
+ -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 \
+ -c src/nf_modules/cutadapt/cutadapt.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
diff --git a/src/nf_modules/cutadapt/tests/trimming_paired.nf b/src/nf_modules/cutadapt/tests/trimming_paired.nf
new file mode 100644
index 0000000..d0b83e1
--- /dev/null
+++ b/src/nf_modules/cutadapt/tests/trimming_paired.nf
@@ -0,0 +1,24 @@
+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"
+
+ input:
+ set pair_id, file(reads) from fastq_files
+
+ output:
+ file "*_trim_R{1,2}.fastq.gz" into fastq_files_cut
+
+ script:
+ """
+ cutadapt -q 20,20 \
+ -o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \
+ ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+ """
+}
+
diff --git a/src/nf_modules/cutadapt/tests/trimming_single.nf b/src/nf_modules/cutadapt/tests/trimming_single.nf
new file mode 100644
index 0000000..c2dd262
--- /dev/null
+++ b/src/nf_modules/cutadapt/tests/trimming_single.nf
@@ -0,0 +1,24 @@
+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"
+
+ input:
+ file reads from fastq_files
+
+ output:
+ file "*_trim.fastq.gz" into fastq_files_cut
+
+ script:
+ """
+ cutadapt -q 20,20 \
+ -o ${reads.baseName}_trim.fastq.gz \
+ ${reads} > ${reads.baseName}_report.txt
+ """
+}
+
--
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