diff --git a/conf/modules/cnvkit.config b/conf/modules/cnvkit.config
index 93b06518b5..f77c6ef446 100644
--- a/conf/modules/cnvkit.config
+++ b/conf/modules/cnvkit.config
@@ -28,7 +28,7 @@ process {
 
     withName: 'CNVKIT_REFERENCE' {
         ext.prefix       = "cnvkit"
-        ext.when         = { params.tools && params.tools.split(',').contains('cnvkit') }
+        ext.when         = { params.tools && params.tools.split(',').contains('cnvkit') && !params.cnvkit_reference }
         publishDir       = [
             enabled: params.save_reference,
             mode: params.publish_dir_mode,
diff --git a/nextflow.config b/nextflow.config
index dd886f8262..bf074101ca 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -63,6 +63,7 @@ params {
     cf_minqual                  = 0     // ControlFreec default values
     cf_window                   = null  // by default we are not using this in Control-FREEC
     cf_chrom_len                = null  // by default we are using the fasta_fai. This can be used to circumvent this issue until there is a better option available upstream: https://github.com/nf-core/sarek/issues/670
+    cnvkit_reference            = null  // by default the reference is build from the fasta file
     ignore_soft_clipped_bases   = false // no --dont-use-soft-clipped-bases for GATK Mutect2
     wes                         = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers
     joint_germline              = false // g.vcf & joint germline calling are not run by default if HaplotypeCaller is selected
diff --git a/nextflow_schema.json b/nextflow_schema.json
index bd50522344..64c319f511 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -278,7 +278,7 @@
                 },
                 "cf_chrom_len": {
                     "type": "string",
-                    "default": null,
+                    "default": "None",
                     "fa_icon": "fas fa-ruler-horizontal",
                     "description": "Specify a custom chromosome length file.",
                     "help_text": "Control-FREEC requires a file containing all chromosome lenghts. By default the fasta.fai is used. If the fasta.fai file contains chromosomes not present in the intervals, it fails (see: https://github.com/BoevaLab/FREEC/issues/106).\n\nIn this case, a custom chromosome length can be specified. It must be of the same format as the fai, but only contain the relevant chromosomes.\n\n\n\n",
@@ -338,6 +338,12 @@
                     "help_text": "Details, see [ControlFREEC manual](http://boevalab.inf.ethz.ch/FREEC/tutorial.html).",
                     "hidden": true
                 },
+                "cnvkit_reference": {
+                    "type": "string",
+                    "default": null,
+                    "fa_icon": "fas fa-file",
+                    "help_text": "https://cnvkit.readthedocs.io/en/stable/pipeline.html?highlight=reference.cnn#batch"
+                },
                 "pon": {
                     "type": "string",
                     "fa_icon": "fas fa-file",
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index ca91a47231..682f4aaf91 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -18,6 +18,7 @@ def checkPathParamList = [
     params.bwa,
     params.bwamem2,
     params.cf_chrom_len,
+    params.cnvkit_reference,
     params.chr_dir,
     params.dbnsfp,
     params.dbnsfp_tbi,
@@ -372,7 +373,8 @@ workflow SAREK {
 
      // Antitarget based reference for CNVKit
     PREPARE_REFERENCE_CNVKIT(fasta, intervals_bed_combined)
-    cnvkit_reference            = params.tools && params.tools.split(',').contains('cnvkit') ? PREPARE_REFERENCE_CNVKIT.out.cnvkit_reference : Channel.empty()
+    cnvkit_reference            = params.tools && params.tools.split(',').contains('cnvkit') ? (params.cnvkit_reference ? Channel.fromPath(params.cnvkit_reference).collect() : PREPARE_REFERENCE_CNVKIT.out.cnvkit_reference) : Channel.empty()
+
     ch_versions = ch_versions.mix(PREPARE_REFERENCE_CNVKIT.out.versions)
 
     // PREPROCESSING