Dev - Adding FastQC to the pipeline, with integration into MultiQC

docs/output.md

@@ -12,6 +12,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   - [:warning: Please read this documentation on the nf-core website: https://nf-co.re/scrnaseq/output](#warning-please-read-this-documentation-on-the-nf-core-website-httpsnf-corescrnaseqoutput)
   - [Introduction](#introduction)
   - [Pipeline overview](#pipeline-overview)
+  - [FastQC](#fastqc)
   - [Kallisto & Bustools Results](#kallisto--bustools-results)
   - [STARsolo](#starsolo)
   - [Salmon Alevin & AlevinQC](#salmon-alevin--alevinqc)
@@ -20,6 +21,19 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   - [MultiQC](#multiqc)
   - [Pipeline information](#pipeline-information)
 
+## FastQC
+
+See [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc) for details about FastQC.
+
+The pipeline analyzes the raw data and generates for each file a FastQC report. All report are collected in MultiQC.
+
+**Output directory: `results/fastqc`**
+
+- `.html`
+  - Contains the FastQC report.
+- `.zip`
+  - Contains additional information, such as individual plots, and FastQC raw data.
+
 ## Kallisto & Bustools Results
 
 See [Kallisto](https://pachterlab.github.io/kallisto/about) for details about Kallisto and [Bustools](https://bustools.github.io/) for more information on BusTools.

modules/local/multiqc.nf

@@ -1,30 +1,39 @@
 process MULTIQC {
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::multiqc=1.10.1" : null)
+    conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.10.1--py_0' :
-        'quay.io/biocontainers/multiqc:1.10.1--py_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
 
     input:
-    path 'multiqc_config.yaml'
-    path multiqc_custom_config
-    path software_versions
+    path ch_multiqc_config
+    path ch_multiqc_custom_config
+    path software_versions_yaml
     path workflow_summary
+    path ('fastqc/*')
     path ("STAR/*")
     path ("salmon_alevin/*")
 
     output:
-    path "*multiqc_report.html"     , emit: report
-    path "*_data"                   , emit: data
-    path "*variants_metrics_mqc.csv", optional:true, emit: csv_variants
-    path "*assembly_metrics_mqc.csv", optional:true, emit: csv_assembly
-    path "*_plots"                  , optional:true, emit: plots
+    path "*multiqc_report.html", emit: report
+    path "*_data"              , emit: data
+    path "*_plots"             , optional:true, emit: plots
+    path "versions.yml"        , emit: versions
 
     script:
-    def custom_config = params.multiqc_config ? "--config $multiqc_custom_config" : ''
     def args = task.ext.args ?: ''
+    def custom_config = params.multiqc_config ? "--config $multiqc_custom_config" : ''
     """
-    multiqc -f $args $custom_config .
+    multiqc \\
+        -f \\
+        $args \\
+        $custom_config \\
+        .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
     """
 }

nextflow.config

@@ -48,7 +48,8 @@ params {
     igenomes_base              = 's3://ngi-igenomes/igenomes'
     igenomes_ignore            = false
 
-    // MultiQC options
+    // QC and MultiQC options
+    skip_fastqc                = false
     multiqc_config             = null
     multiqc_title              = null
     max_multiqc_email_size     = '25.MB'

nextflow_schema.json

@@ -373,6 +373,10 @@
                     "hidden": true,
                     "fa_icon": "fas fa-bacon"
                 },
+                "skip_fastqc": {
+                    "type": "boolean",
+                    "description": "Skip the FastQC reporting feature in the pipeline."
+                },                
                 "skip_multiqc": {
                     "type": "boolean",
                     "description": "Skip the MultiQC reporting feature in the pipeline."

subworkflows/local/fastqc.nf

@@ -0,0 +1,45 @@
+//
+// Check input samplesheet and get read channels
+//
+
+//TODO --> add skip_fastqc to params
+
+include { FASTQC } from '../../modules/nf-core/modules/fastqc/main'
+
+workflow FASTQC_CHECK {
+  take:
+  ch_fastq
+
+  main:
+  ch_fastq
+      .map { ch -> [ ch[0], ch[1] ] }
+      .set { ch_fastq }
+
+  /*
+   * FastQ QC using FASTQC
+   */
+  fastqc_zip     = Channel.empty()
+  fastqc_html    = Channel.empty()
+  fastqc_multiqc = Channel.empty()
+  fastqc_version = Channel.empty()
+
+  FASTQC ( ch_fastq )
+  fastqc_zip     = FASTQC.out.zip
+  fastqc_html    = FASTQC.out.html
+
+  fastqc_zip
+      .map { it -> [ it[1] ] }
+      .set { fastqc_zip_only }
+  fastqc_html
+      .map { it -> [ it[1] ] }
+      .set { fastqc_html_only }
+
+  fastqc_multiqc = fastqc_multiqc.mix( fastqc_zip_only, fastqc_html_only )
+  fastqc_version = FASTQC.out.versions
+
+  emit:
+  fastqc_zip
+  fastqc_html
+  fastqc_version
+  fastqc_multiqc
+}

workflows/scrnaseq.nf

@@ -36,6 +36,7 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
 //
 include { INPUT_CHECK       } from '../subworkflows/local/input_check'
+include { FASTQC_CHECK } from '../subworkflows/local/fastqc'
 include { KALLISTO_BUSTOOLS } from '../subworkflows/local/kallisto_bustools'
 include { SCRNASEQ_ALEVIN   } from '../subworkflows/local/alevin'
 include { STARSOLO          } from '../subworkflows/local/starsolo'
@@ -105,6 +106,14 @@ workflow SCRNASEQ {
 
     ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
 
+    // Run FastQC
+    ch_multiqc_fastqc = Channel.empty()
+    if (!params.skip_fastqc){
+      FASTQC_CHECK ( ch_fastq )
+      ch_versions = ch_versions.mix(FASTQC_CHECK.out.fastqc_version.first().ifEmpty(null))
+      ch_multiqc_fastqc    = FASTQC_CHECK.out.fastqc_multiqc.ifEmpty([])
+    }
+
     // Run kallisto bustools pipeline
     if (params.aligner == "kallisto") {
         KALLISTO_BUSTOOLS(
@@ -169,15 +178,17 @@ workflow SCRNASEQ {
     )
 
     if (!params.skip_multiqc) {
+
         ch_workflow_summary = Channel.value(
             WorkflowScrnaseq.paramsSummaryMultiqc(workflow, summary_params)
         ).collectFile(name: 'workflow_summary_mqc.yaml')
 
         MULTIQC(
             ch_multiqc_config,
-            ch_multiqc_custom_config,
+            ch_multiqc_custom_config.collect().ifEmpty([]),
             CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect(),
             ch_workflow_summary,
+            ch_multiqc_fastqc.collect{it[0]}.ifEmpty([]),
             ch_multiqc_alevin,
             ch_multiqc_star
         )