diff --git a/.nf-core.yml b/.nf-core.yml
deleted file mode 100644
index b78b221..0000000
--- a/.nf-core.yml
+++ /dev/null
@@ -1,3 +0,0 @@
-lint:
-    files_unchanged:
-      - docs/images/nf-core-epitopeprediction_logo_dark.png
diff --git a/CITATIONS.md b/CITATIONS.md
index b65c1c7..56daa84 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -10,7 +10,6 @@
 
 ## Pipeline tools
 
-
 * [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
     > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
diff --git a/lib/WorkflowEpitopeprediction.groovy b/lib/WorkflowEpitopeprediction.groovy
index c0b8c62..2dd09ef 100755
--- a/lib/WorkflowEpitopeprediction.groovy
+++ b/lib/WorkflowEpitopeprediction.groovy
@@ -8,12 +8,7 @@ class WorkflowEpitopeprediction {
     // Check and validate parameters
     //
     public static void initialise(params, log) {
-        //genomeExistsError(params, log)
-
-        //if (!params.fasta) {
-        //    log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
-        //    System.exit(1)
-        //}
+        // empty function...
     }
 
     //
@@ -42,18 +37,4 @@ class WorkflowEpitopeprediction {
         yaml_file_text        += "${summary_section}"
         return yaml_file_text
     }
-
-    //
-    // Exit pipeline if incorrect --genome key provided
-    //
-    //private static void genomeExistsError(params, log) {
-    //    if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-    //        log.error "=============================================================================\n" +
-    //            "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
-    //            "  Currently, the available genome keys are:\n" +
-    //            "  ${params.genomes.keySet().join(", ")}\n" +
-    //            "==================================================================================="
-    //        System.exit(1)
-    //    }
-    //}
 }
diff --git a/modules.json b/modules.json
index 80bccfc..3b7e20c 100644
--- a/modules.json
+++ b/modules.json
@@ -6,9 +6,6 @@
             "custom/dumpsoftwareversions": {
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             },
-            "fastqc": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-            },
             "multiqc": {
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             }
diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf
deleted file mode 100644
index d250eca..0000000
--- a/modules/nf-core/modules/fastqc/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-process FASTQC {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
-        'quay.io/biocontainers/fastqc:0.11.9--0' }"
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip") , emit: zip
-    path  "versions.yml"           , emit: versions
-
-    script:
-    def args = task.ext.args ?: ''
-    // Add soft-links to original FastQs for consistent naming in pipeline
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    if (meta.single_end) {
-        """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
-        fastqc $args --threads $task.cpus ${prefix}.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        END_VERSIONS
-        """
-    } else {
-        """
-        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
-        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
-        fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        END_VERSIONS
-        """
-    }
-}
diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/modules/fastqc/meta.yml
deleted file mode 100644
index b09553a..0000000
--- a/modules/nf-core/modules/fastqc/meta.yml
+++ /dev/null
@@ -1,52 +0,0 @@
-name: fastqc
-description: Run FastQC on sequenced reads
-keywords:
-    - quality control
-    - qc
-    - adapters
-    - fastq
-tools:
-    - fastqc:
-        description: |
-            FastQC gives general quality metrics about your reads.
-            It provides information about the quality score distribution
-            across your reads, the per base sequence content (%A/C/G/T).
-            You get information about adapter contamination and other
-            overrepresented sequences.
-        homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-        documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
-        licence: ['GPL-2.0-only']
-input:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - reads:
-        type: file
-        description: |
-            List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-            respectively.
-output:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - html:
-        type: file
-        description: FastQC report
-        pattern: "*_{fastqc.html}"
-    - zip:
-        type: file
-        description: FastQC report archive
-        pattern: "*_{fastqc.zip}"
-    - versions:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-authors:
-    - "@drpatelh"
-    - "@grst"
-    - "@ewels"
-    - "@FelixKrueger"