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

from @elabaron

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} && \

src/nf_modules/FastQC/fastqc.config

+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'
+      }
+    }
+  }
+}

src/nf_modules/FastQC/fastqc.nf

+/*
+* 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}
+"""
+}
+
+