diff --git a/conf/modules.config b/conf/modules.config
index f378b3f9..8cbcb4e9 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -57,10 +57,23 @@ process {
         ]
     }
 
+    withName: COUNT_READS {
+        publishDir       = [
+            [
+                path: { "${params.outdir}/count_reads/${meta.id}" },
+                mode: params.publish_dir_mode,
+            ]
+        ]
+    }
 
-
-
-
+    withName: COUNT_READS_AFTER_TRIMMING {
+        publishDir       = [
+            [
+                path: { "${params.outdir}/count_reads_after_trimming/${meta.id}" },
+                mode: params.publish_dir_mode,
+            ]
+        ]
+    }
 
     withName: FASTQC {
         ext.args = '--quiet'
diff --git a/modules/local/count_reads.nf b/modules/local/count_reads.nf
new file mode 100644
index 00000000..89352212
--- /dev/null
+++ b/modules/local/count_reads.nf
@@ -0,0 +1,39 @@
+process COUNT_READS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'nfcore/dualrnaseq:dev' :
+        'nfcore/dualrnaseq:dev' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path('*.txt'), emit: read_counts
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    if (reads instanceof Path || reads.size() == 1) {
+        // Code to process a single file
+        """
+        count_1=\$((\$(zcat ${reads[0]} | wc -l) / 4))
+        echo "${reads[0].baseName}\t\$count_1" > ${reads[0].baseName}_counts.txt
+        """
+    } else if (reads instanceof Path || reads.size() == 2) {
+        // Code to process two files
+        """
+        count_1=\$((\$(zcat ${reads[0]} | wc -l) / 4))
+        count_2=\$((\$(zcat ${reads[1]} | wc -l) / 4))
+        echo "${reads[0].baseName}\t\$count_1" > ${reads[0].baseName}_counts.txt
+        echo "${reads[1].baseName}\t\$count_2" > ${reads[1].baseName}_counts.txt
+        """
+    } else {
+        """
+        echo "Error: Input 'reads' should contain either one or two files."
+        exit 1
+        """
+    }
+}
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 9ae58381..76a42dd8 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -2,10 +2,10 @@ process FASTQC {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::fastqc=0.11.9"
+    conda "bioconda::fastqc=0.12.1--hdfd78af_0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
-        'quay.io/biocontainers/fastqc:0.11.9--0' }"
+        'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' :
+        'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/workflows/dualrnaseq.nf b/workflows/dualrnaseq.nf
index 727ac560..51459580 100644
--- a/workflows/dualrnaseq.nf
+++ b/workflows/dualrnaseq.nf
@@ -72,11 +72,13 @@ include { SALMON_ALIGNMENT_BASED } from '../subworkflows/local/salmon_alignment_
 //
 // MODULE: Installed directly from nf-core/modules
 //
-include { FASTQC                            } from '../modules/nf-core/fastqc/main'
-include { FASTQC as FASTQC_AFTER_TRIMMING   } from '../modules/nf-core/fastqc/main'
-include { CUTADAPT                          } from '../modules/nf-core/cutadapt/main'
-include { MULTIQC                           } from '../modules/nf-core/multiqc/main'
-include { CUSTOM_DUMPSOFTWAREVERSIONS       } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { COUNT_READS                                        } from '../modules/local/count_reads'
+include { COUNT_READS as COUNT_READS_AFTER_TRIMMING          } from '../modules/local/count_reads'
+include { FASTQC                                             } from '../modules/nf-core/fastqc/main'
+include { FASTQC as FASTQC_AFTER_TRIMMING                    } from '../modules/nf-core/fastqc/main'
+include { CUTADAPT                                           } from '../modules/nf-core/cutadapt/main'
+include { MULTIQC                                            } from '../modules/nf-core/multiqc/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS                        } from '../modules/nf-core/custom/dumpsoftwareversions/main'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -99,12 +101,17 @@ workflow DUALRNASEQ {
     )
     ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
 
+    COUNT_READS (
+        INPUT_CHECK.out.reads
+    )
+
+    ch_count_reads_merged = Channel.fromPath( "${params.outdir}/count_reads/*" ).collectFile(name: 'count_reads_merged.txt').view()
+
     if (!(params.skip_tools && params.skip_tools.split(',').contains('fastqc'))) {
             FASTQC(INPUT_CHECK.out.reads)
             ch_versions = ch_versions.mix(FASTQC.out.versions.first())
     }
 
-    ch_reads = INPUT_CHECK.out.reads
     if (!(params.skip_tools && params.skip_tools.split(',').contains('cutadapt'))) {
             CUTADAPT(INPUT_CHECK.out.reads)
             ch_reads = CUTADAPT.out.reads
@@ -114,6 +121,8 @@ workflow DUALRNASEQ {
     if (!(params.skip_tools && (params.skip_tools.split(',').contains('fastqc') || params.skip_tools.split(',').contains('cutadapt')))) {
             FASTQC_AFTER_TRIMMING(ch_reads)
             ch_versions = ch_versions.mix(FASTQC_AFTER_TRIMMING.out.versions.first())
+            COUNT_READS_AFTER_TRIMMING (INPUT_CHECK.out.reads)
+            ch_count_reads_merged = Channel.fromPath( "${params.outdir}/count_reads/*" ).collectFile(name: 'count_reads_after_trimming_merged.txt').view()
     }