diff --git a/src/docker_modules/FastQC/0.11.5/Dockerfile b/src/docker_modules/FastQC/0.11.5/Dockerfile index f7b999e418fc358eaf063989e0ff058820164a95..d8956a1507345f7177657dbb7e86ab9f52d46f12 100644 --- a/src/docker_modules/FastQC/0.11.5/Dockerfile +++ b/src/docker_modules/FastQC/0.11.5/Dockerfile @@ -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} && \ diff --git a/src/nf_modules/FastQC/fastqc.config b/src/nf_modules/FastQC/fastqc.config new file mode 100644 index 0000000000000000000000000000000000000000..db3b0270190b5e736a709774713ac3115b5fa6ba --- /dev/null +++ b/src/nf_modules/FastQC/fastqc.config @@ -0,0 +1,25 @@ +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' + } + } + } +} diff --git a/src/nf_modules/FastQC/fastqc.nf b/src/nf_modules/FastQC/fastqc.nf new file mode 100644 index 0000000000000000000000000000000000000000..abe18a49fbf4f17e2ff2a538bc20f34bf0796c51 --- /dev/null +++ b/src/nf_modules/FastQC/fastqc.nf @@ -0,0 +1,33 @@ +/* +* 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} +""" +} + +