[ADD] MultiQC process #7

workflows/.MD5SUM

@@ -6,3 +6,4 @@
 b0acb10858b49469a5b2a5a9280eef6f  fastqc.sif
 e01183981649840b399144a52b08f05a  bowtie.sif
 c0f12b882505a739f902ce5deb9f713c  DESeq2.sif
+93da993f77b444147804f484edbc9dda  multiqc.sif

workflows/main.nf

@@ -11,6 +11,7 @@ include { downloadfastq } from './process/downloadfastq.nf'
 include { fastqc as fastqcBT } from './process/fastqc.nf'
 include { fastqc as fastqcAT } from './process/fastqc.nf'
 include { trimgalore } from './process/trimgalore.nf'
+include { multiqc } from './process/multiqc.nf'
 include { mapping } from './process/bowtie.nf'
 include { indexingG } from './process/bowtie.nf'
 include { featureCounts } from './process/featurecounts.nf'
@@ -42,6 +43,9 @@ workflow {
     // Run FastQC on each trimmed FASTQ file
     fastqcAT(trimmedFASTQ.map { file -> [file.getSimpleName(), file] })
 
+    // Run MultiQC to generate a summary report
+    multiqc(fastqcBT.out.zip.collect(),fastqcAT.out.zip.collect())
+
     if(params.refg ==~ /^http.*/){
         genome = downloadREF("reference.fasta",params.refg)
     }

workflows/process/multiqc.nf

@@ -0,0 +1,20 @@
+process multiqc {
+
+        label 'lowCPU'
+
+        container ''
+
+        publishDir "${params.outputDir}/multiqc", mode: 'symlink', pattern: "multiqc_report.html"
+
+        input:
+        path(fastqcBT)
+        path(fastqcAT)
+
+        output:
+        path("multiqc_report.html"), emit: report
+
+        script:
+        """
+        multiqc ./
+        """   
+}

workflows/workflow.sh

@@ -6,15 +6,16 @@ CONFIG=./config/nextflow.config
 DOWNLOAD=true
 REF="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=CP000253.1&rettype=fasta"
 GFF=""
-IMAGES_NAMES=('ubuntu.sif' 'sratoolkit.sif' 'fastqc.sif' 'trimgalore.sif' 'bowtie.sif' 'samtools.sif' 'featurecounts.sif' 'DESeq2.sif')
+IMAGES_NAMES=('ubuntu.sif' 'sratoolkit.sif' 'fastqc.sif' 'trimgalore.sif' 'bowtie.sif' 'samtools.sif' 'featurecounts.sif' 'DESeq2.sif' 'multiqc.sif')
 IMAGES_PATH=("https://storage.googleapis.com/rrnaseq/ubuntu.sif" "https://storage.googleapis.com/rrnaseq/sratoolkit.sif" \
             "https://storage.googleapis.com/rrnaseq/fastqc.sif" "https://storage.googleapis.com/rrnaseq/trimgalore.sif" \
             "https://storage.googleapis.com/rrnaseq/bowtie.sif" "https://storage.googleapis.com/rrnaseq/samtools.sif" \
-            "https://storage.googleapis.com/rrnaseq/featurecounts.sif" "https://storage.googleapis.com/rrnaseq/DESeq2.sif")
+            "https://storage.googleapis.com/rrnaseq/featurecounts.sif" "https://storage.googleapis.com/rrnaseq/DESeq2.sif" \
+            "https://storage.googleapis.com/rrnaseq/multiqc.sif")
 BUCKET="https://storage.googleapis.com/rrnaseq/"
 MD5SUM_FILE=".MD5SUM"
 PROCESS_FILES=("main.nf" "tools.nf" "downloadfastq.nf" "fastqc.nf" "trimgalore.nf" \
-            "bowtie.nf" "samtools.nf" "featurecounts.nf" "deseq2.nf")
+            "bowtie.nf" "samtools.nf" "featurecounts.nf" "deseq2.nf" "multiqc.nf")
 PROCESS_DIR="process"
 CONFIG_FILE="nextflow.config"
 NEXTFLOW_DEV_VERSION="24.10"