Verified Commit 8f2c8522 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

Merge branch 'elabaron/nextflow-master' into dev to get FastQC modif

from @elabaron
parents 4be336cf 49faa7f0
......@@ -2,7 +2,8 @@ FROM ubuntu:18.04
MAINTAINER Laurent Modolo
ENV FASTQC_VERSION=0.11.5
ENV PACKAGES fastqc=${FASTQC_VERSION}*
ENV PACKAGES fastqc=${FASTQC_VERSION}* \
perl
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
......
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$fastqc {
container = "fastqc:0.11.5"
}
}
}
sge {
process{
$fastqc {
beforeScript = "module purge; module load FastQC/0.11.5"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128'
}
}
}
}
/*
* fastqc :
* Imputs : fastq files
* Output : pdf files
*/
/* fastQC */
params.fastq = ""
log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
process fastqc {
tag "$fastq.baseName"
publishDir "results/fastqc/", mode: 'copy'
input:
file fastq from fastq_files
output:
file "*.htlm" into fastqc_repport
script:
"""
fastqc -o ./ --noextract -f fastq ${fastq}
"""
}
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