MultiQC: update nf structure

src/nf_modules/MultiQC/multiqc.nf

-/*
-* multiqc :
-* Imputs : report files
-* Output :  multiqc report
-*/
-
-/*                      MultiQC                                     */
-
-process multiqc {
-  tag "$report.baseName"
-  publishDir "results/fastq/multiqc/", mode: 'copy'
-  cpus = 1
-
-  input:
-    file report from fastqc_report.collect()
-
-  output:
-    file "*multiqc_*" into multiqc_report
-
-  script:
-"""
-multiqc -f .
-"""
-}
-

src/nf_modules/MultiQC/multiqc_single.config

+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'
+      }
+    }
+  }
+}

src/nf_modules/MultiQC/tests/tests.sh → src/nf_modules/MultiQC/tests.sh

-nextflow src/nf_modules/MultiQC/tests/multiqc_paired.nf \
-  -c src/nf_modules/MultiQC/multiqc.config \
+nextflow src/nf_modules/MultiQC/multiqc_paired.nf \
+  -c src/nf_modules/MultiQC/multiqc_paired.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 \
+nextflow src/nf_modules/MultiQC/multiqc_single.nf \
+  -c src/nf_modules/MultiQC/multiqc_single.config \
   -profile docker \
   --fastq "data/tiny_dataset/fastq/tiny_S.fastq"