diff --git a/CHANGELOG.md b/CHANGELOG.md
index a59a636aef..2e11b9b308 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -59,6 +59,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#941](https://github.com/nf-core/sarek/pull/941) - Fix json validation for `tools`, `skip_tools` and `use_gatk_spark` [#892](https://github.com/nf-core/sarek/issues/892)
 - [#954](https://github.com/nf-core/sarek/pull/954) - Fix missing annotation keys with `snpeff` and `ensemblvep` for `hg19`
 - [#957](https://github.com/nf-core/sarek/pull/957) - Add `failOnDuplicate` and `failOnMismatch` options to all `join()` operator where it was possible
+- [#980](https://github.com/nf-core/sarek/pull/941) - Fix allowing multiple ploidy values for plotting of controlfreec output ([#808](https://github.com/nf-core/sarek/issues/808))
 - [#982](https://github.com/nf-core/sarek/pull/982) - Remove usage of exit statements, using `Nextflow.error` instead
 - [#985](https://github.com/nf-core/sarek/pull/985) - Cache correctly identifies when it needs to be updated
 - [#988](https://github.com/nf-core/sarek/pull/988) - Updated ascat module to fix seed for reproducibility
diff --git a/conf/modules/controlfreec.config b/conf/modules/controlfreec.config
index 3945756957..c853241204 100644
--- a/conf/modules/controlfreec.config
+++ b/conf/modules/controlfreec.config
@@ -51,7 +51,6 @@ process {
     }
 
     withName: 'MAKEGRAPH' {
-        ext.args = { "${params.cf_ploidy}" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf
index 293cf1feaa..91231ad8c7 100644
--- a/modules/nf-core/controlfreec/makegraph/main.nf
+++ b/modules/nf-core/controlfreec/makegraph/main.nf
@@ -8,7 +8,7 @@ process CONTROLFREEC_MAKEGRAPH {
         'biocontainers/control-freec:11.6--h1b792b2_1' }"
 
     input:
-    tuple val(meta), path(ratio), path(baf)
+    tuple val(meta), path(ratio), path(baf), val(ploidy)
 
     output:
     tuple val(meta), path("*_BAF.png")       , emit: png_baf
@@ -25,7 +25,7 @@ process CONTROLFREEC_MAKEGRAPH {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def baf = baf ?: ""
     """
-    cat \$(which makeGraph.R) | R --slave --args ${args} ${ratio} ${baf}
+    cat \$(which makeGraph.R) | R --slave --args ${ploidy} ${args} ${ratio} ${baf}
 
     mv *_BAF.txt.png ${prefix}_BAF.png
     mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png
diff --git a/subworkflows/local/bam_variant_calling_somatic_all/main.nf b/subworkflows/local/bam_variant_calling_somatic_all/main.nf
index 0644a5cbb4..d2834eb500 100644
--- a/subworkflows/local/bam_variant_calling_somatic_all/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_all/main.nf
@@ -92,6 +92,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
         mpileup_pair = mpileup_normal.cross(mpileup_tumor).map{ normal, tumor -> [ normal[0], normal[1], tumor[1], [], [], [], [] ] }
 
         length_file = cf_chrom_len ?: fasta_fai
+        ploidy = params.cf_ploidy && !params.cf_ploidy.toString().contains(",") ? [params.cf_ploidy] : params.cf_ploidy.split(',')
 
         BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC(
             mpileup_pair,
@@ -101,7 +102,8 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
             dbsnp_tbi,
             chr_files,
             mappability,
-            intervals_bed_combined
+            intervals_bed_combined,
+            ploidy
         )
 
         versions = versions.mix(MPILEUP_NORMAL.out.versions)
diff --git a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
index 93b91e605a..9ca08da3a1 100644
--- a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
@@ -14,6 +14,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
     chr_files                // channel: [mandatory]
     mappability              // channel: [mandatory]
     intervals_bed            // channel: [optional]  Contains a bed file of all intervals combined provided with the cram input(s). Should be empty for WGS
+    ploidy                   // channel: [mandatory] list of ploidy values
 
     main:
 
@@ -24,7 +25,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
     ASSESS_SIGNIFICANCE(FREEC_SOMATIC.out.CNV.join(FREEC_SOMATIC.out.ratio, failOnDuplicate: true, failOnMismatch: true))
     FREEC2BED(FREEC_SOMATIC.out.ratio)
     FREEC2CIRCOS(FREEC_SOMATIC.out.ratio)
-    MAKEGRAPH(FREEC_SOMATIC.out.ratio.join(FREEC_SOMATIC.out.BAF, failOnDuplicate: true, failOnMismatch: true))
+    MAKEGRAPH(FREEC_SOMATIC.out.ratio.join(FREEC_SOMATIC.out.BAF, failOnDuplicate: true, failOnMismatch: true).combine(ploidy))
 
     ch_versions = ch_versions.mix(FREEC_SOMATIC.out.versions)
     ch_versions = ch_versions.mix(ASSESS_SIGNIFICANCE.out.versions)
diff --git a/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
index 8507899366..99c59d7edf 100644
--- a/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
+++ b/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
@@ -60,6 +60,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
     // CONTROLFREEC (depends on MPILEUP)
     if (tools.split(',').contains('controlfreec')) {
         length_file = cf_chrom_len ?: fasta_fai
+        ploidy = params.cf_ploidy && !params.cf_ploidy.toString().contains(",") ? [params.cf_ploidy] : params.cf_ploidy.split(',')
 
         BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC(
             // Remap channel to match module/subworkflow
@@ -70,7 +71,8 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
             dbsnp_tbi,
             chr_files,
             mappability,
-            intervals_bed_combined
+            intervals_bed_combined,
+            ploidy
         )
 
         versions = versions.mix(BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC.out.versions)
diff --git a/subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf
index 42e0b0567c..07bbf9364d 100644
--- a/subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf
@@ -14,6 +14,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC {
     chr_files                // channel: [mandatory]
     mappability              // channel: [mandatory]
     intervals_bed            // channel: [optional]  Contains a bed file of all intervals combined provided with the cram input(s). Should be empty for WGS
+    ploidy                   // channel: [mandatory] list of ploidy values
 
     main:
 
@@ -24,7 +25,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC {
     ASSESS_SIGNIFICANCE(FREEC_TUMORONLY.out.CNV.join(FREEC_TUMORONLY.out.ratio, failOnDuplicate: true, failOnMismatch: true))
     FREEC2BED(FREEC_TUMORONLY.out.ratio)
     FREEC2CIRCOS(FREEC_TUMORONLY.out.ratio)
-    MAKEGRAPH(FREEC_TUMORONLY.out.ratio.join(FREEC_TUMORONLY.out.BAF, failOnDuplicate: true, failOnMismatch: true))
+    MAKEGRAPH(FREEC_TUMORONLY.out.ratio.join(FREEC_TUMORONLY.out.BAF, failOnDuplicate: true, failOnMismatch: true).combine(ploidy))
 
     ch_versions = ch_versions.mix(FREEC_TUMORONLY.out.versions)
     ch_versions = ch_versions.mix(ASSESS_SIGNIFICANCE.out.versions)