From a366ef20575c1446452e545534a33c939bfd208b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 25 Jul 2018 17:36:35 +0200
Subject: [PATCH] MultiQC: add nf, test, and fix Dockerfile
---
src/docker_modules/MultiQC/1.0/Dockerfile | 8 +++-
src/nf_modules/MultiQC/multiqc.config | 38 ++++++++++++++++
src/nf_modules/MultiQC/multiqc.nf | 25 +++++++++++
.../MultiQC/tests/multiqc_paired.nf | 43 +++++++++++++++++++
.../MultiQC/tests/multiqc_single.nf | 43 +++++++++++++++++++
src/nf_modules/MultiQC/tests/tests.sh | 9 ++++
6 files changed, 165 insertions(+), 1 deletion(-)
create mode 100644 src/nf_modules/MultiQC/multiqc.config
create mode 100644 src/nf_modules/MultiQC/multiqc.nf
create mode 100644 src/nf_modules/MultiQC/tests/multiqc_paired.nf
create mode 100644 src/nf_modules/MultiQC/tests/multiqc_single.nf
create mode 100755 src/nf_modules/MultiQC/tests/tests.sh
diff --git a/src/docker_modules/MultiQC/1.0/Dockerfile b/src/docker_modules/MultiQC/1.0/Dockerfile
index 09b218a..d351f1c 100644
--- a/src/docker_modules/MultiQC/1.0/Dockerfile
+++ b/src/docker_modules/MultiQC/1.0/Dockerfile
@@ -6,10 +6,16 @@ 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*
+ python3-wheel=0.30.0* \
+ locales
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
+RUN locale-gen en_US.UTF-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+
RUN pip3 install multiqc==${MULTIQC_VERSION}
+
diff --git a/src/nf_modules/MultiQC/multiqc.config b/src/nf_modules/MultiQC/multiqc.config
new file mode 100644
index 0000000..c1bda95
--- /dev/null
+++ b/src/nf_modules/MultiQC/multiqc.config
@@ -0,0 +1,38 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $fastqc_fastq {
+ container = "fastqc:0.11.5"
+ }
+ $multiqc {
+ container = "multiqc:1.0"
+ }
+ }
+ }
+ sge {
+ process{
+ $fastqc_fastq {
+ beforeScript = "module purge; module load FastQC/0.11.5"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ $multiqc {
+ beforeScript = "module purge; module load FastQC/1.0"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/MultiQC/multiqc.nf b/src/nf_modules/MultiQC/multiqc.nf
new file mode 100644
index 0000000..eae20b5
--- /dev/null
+++ b/src/nf_modules/MultiQC/multiqc.nf
@@ -0,0 +1,25 @@
+/*
+* multiqc :
+* Imputs : report files
+* Output : multiqc report
+*/
+
+/* MultiQC */
+
+process multiqc {
+ tag "$repport.baseName"
+ publishDir "results/fastq/multiqc/", mode: 'copy'
+ cpus = 1
+
+ input:
+ file repport from fastqc_repport.collect()
+
+ output:
+ file "*multiqc_*" into multiqc_report
+
+ script:
+"""
+multiqc -f .
+"""
+}
+
diff --git a/src/nf_modules/MultiQC/tests/multiqc_paired.nf b/src/nf_modules/MultiQC/tests/multiqc_paired.nf
new file mode 100644
index 0000000..7db2ea3
--- /dev/null
+++ b/src/nf_modules/MultiQC/tests/multiqc_paired.nf
@@ -0,0 +1,43 @@
+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: ${params.fastq}" }
+ .set { fastq_files }
+
+process fastqc_fastq {
+ tag "$pair_id"
+ publishDir "results/fastq/fastqc/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files
+
+ output:
+ file "*.{zip,html}" into fastqc_repport
+
+ script:
+"""
+fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
+${reads[0]} ${reads[1]}
+"""
+}
+
+process multiqc {
+ tag "$repport[0].baseName"
+ publishDir "results/fastq/multiqc/", mode: 'copy'
+ cpus = 1
+
+ input:
+ file repport from fastqc_repport.collect()
+
+ output:
+ file "*multiqc_*" into multiqc_report
+
+ script:
+"""
+multiqc -f .
+"""
+}
+
diff --git a/src/nf_modules/MultiQC/tests/multiqc_single.nf b/src/nf_modules/MultiQC/tests/multiqc_single.nf
new file mode 100644
index 0000000..30edc7b
--- /dev/null
+++ b/src/nf_modules/MultiQC/tests/multiqc_single.nf
@@ -0,0 +1,43 @@
+params.fastq = "$baseDir/data/fastq/*.fastq"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+ .fromPath( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+
+process fastqc_fastq {
+ tag "$reads.baseName"
+ publishDir "results/fastq/fastqc/", mode: 'copy'
+ cpus = 1
+
+ input:
+ file reads from fastq_files
+
+ output:
+ file "*.{zip,html}" into fastqc_repport
+
+ script:
+"""
+fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
+"""
+}
+
+process multiqc {
+ tag "$repport[0].baseName"
+ publishDir "results/fastq/multiqc/", mode: 'copy'
+ cpus = 1
+
+ input:
+ file repport from fastqc_repport.collect()
+
+ output:
+ file "*multiqc_*" into multiqc_report
+
+ script:
+"""
+multiqc -f .
+"""
+}
+
diff --git a/src/nf_modules/MultiQC/tests/tests.sh b/src/nf_modules/MultiQC/tests/tests.sh
new file mode 100755
index 0000000..8aaa83c
--- /dev/null
+++ b/src/nf_modules/MultiQC/tests/tests.sh
@@ -0,0 +1,9 @@
+nextflow src/nf_modules/MultiQC/tests/multiqc_paired.nf \
+ -c src/nf_modules/MultiQC/multiqc.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+
+nextflow src/nf_modules/MultiQC/tests/multiqc_single.nf \
+ -c src/nf_modules/MultiQC/multiqc.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_S.fastq"
--
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