FastQC: update nf structure

src/nf_modules/FastQC/fastqc.nf

-/*
-* fastqc :
-* Imputs : fastq files
-* Output : pdf files
-*/
-
-/*                      fastQC                                     */
-
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { fastq_files }
-
-process fastqc_fastq {
-  tag "$file_id"
-  publishDir "results/fastq/fastqc/", mode: 'copy'
-  cpus = 1
-
-  input:
-  set file_id, file(reads) from fastq_files
-
-  output:
-    file "*.{zip,html}" into fastqc_report
-
-  script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
-"""
-}
-
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$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_report
-
-  script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
-${reads[0]} ${reads[1]}
-"""
-}
-

src/nf_modules/FastQC/fastqc_single.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $fastqc_fastq {
+        container = "fastqc:0.11.5"
+      }
+    }
+  }
+  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'
+      }
+    }
+  }
+}

src/nf_modules/FastQC/tests/tests.sh → src/nf_modules/FastQC/tests.sh

-nextflow src/nf_modules/FastQC/tests/fastqc_paired.nf \
-  -c src/nf_modules/FastQC/fastqc.config \
+nextflow src/nf_modules/FastQC/fastqc_paired.nf \
+  -c src/nf_modules/FastQC/fastqc_paired.config \
   -profile docker \
   --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
 
-nextflow src/nf_modules/FastQC/tests/fastqc_single.nf \
-  -c src/nf_modules/FastQC/fastqc.config \
+nextflow src/nf_modules/FastQC/fastqc_single.nf \
+  -c src/nf_modules/FastQC/fastqc_single.config \
   -profile docker \
   --fastq "data/tiny_dataset/fastq/tiny_S.fastq"