FastQC.nf: add paired process

src/nf_modules/FastQC/fastqc.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $fastqc {
+      $fastqc_fastq {
         container = "fastqc:0.11.5"
       }
     }
   }
   sge {
     process{
-      $fastqc {
+      $fastqc_fastq {
         beforeScript = "module purge; module load FastQC/0.11.5"
         executor = "sge"
         cpus = 1

src/nf_modules/FastQC/fastqc.nf

@@ -5,7 +5,13 @@
 */
 
 /*                      fastQC                                     */
-params.fastq = ""
+
+
+/*
+* for single-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*.fastq"
 
 log.info "fastq files : ${params.fastq}"
 
@@ -14,20 +20,51 @@ Channel
   .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
   .set { fastq_files }
 
-process fastqc {
+process fastqc_fastq {
   tag "$fastq.baseName"
-  publishDir "results/fastqc/", mode: 'copy'
+  publishDir "results/fastq/fastqc/", mode: 'copy'
+  cpus = 1
 
   input:
     file fastq from fastq_files
 
   output:
-    file "*.htlm" into fastqc_repport
+    file "*.{zip,html}" into fastqc_repport
 
   script:
 """
-fastqc -o ./ --noextract -f fastq ${fastq}
+fastqc --quiet --threads ${task.cpus} --outdir -f fastq ./ ${fastq}
 """
 }
 
 
+/*
+* 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_repport
+
+  script:
+"""
+fastqc --quiet --threads ${task.cpus} --outdir -f fastq ./ \
+${fastq[0]} ${fastq[1]}
+"""
+}
+