diff --git a/CHANGELOG.md b/CHANGELOG.md
index cf474927e..5d582e20a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -36,6 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1381](https://github.com/nf-core/sarek/pull/1381) - Swap NGSCheckMate bed file for GATK.GRCh37 to one without the `chr` prefix
 - [#1383](https://github.com/nf-core/sarek/pull/1383) - Fix `--three_prime_clip_r{1,2}` parameter documentation
 - [#1390](https://github.com/nf-core/sarek/pull/1390) - Fix badges in README
+- [#1400](https://github.com/nf-core/sarek/pull/1400) - Fixed input channel for ASSESS_SIGNIFICANCE module, updated makegraph to makegraph2.
 - [#1403](https://github.com/nf-core/sarek/pull/1403) - Fix intervals usage with dot in chromosome names
 
 ### Removed
diff --git a/README.md b/README.md
index a5e6e8948..e922c7c32 100644
--- a/README.md
+++ b/README.md
@@ -152,6 +152,7 @@ We thank the following people for their extensive assistance in the development
 - [Malin Larsson](https://github.com/malinlarsson)
 - [Marcel Martin](https://github.com/marcelm)
 - [Nick Smith](https://github.com/nickhsmith)
+- [Nicolas Schcolnicov](https://github.com/nschcolnicov)
 - [Nilesh Tawari](https://github.com/nilesh-tawari)
 - [Olga Botvinnik](https://github.com/olgabot)
 - [Oskar Wacker](https://github.com/WackerO)
diff --git a/conf/modules/controlfreec.config b/conf/modules/controlfreec.config
index 8ed3920c4..b6fa043d0 100644
--- a/conf/modules/controlfreec.config
+++ b/conf/modules/controlfreec.config
@@ -50,8 +50,7 @@ process {
         ]
     }
 
-    withName: 'MAKEGRAPH' {
-        ext.args   = { "${params.cf_ploidy}" }
+    withName: 'MAKEGRAPH2' {
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
diff --git a/modules.json b/modules.json
index 995c350b5..555c3fb73 100644
--- a/modules.json
+++ b/modules.json
@@ -107,11 +107,10 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
-                    "controlfreec/makegraph": {
+                    "controlfreec/makegraph2": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff"
+                        "git_sha": "a7bae48d8bccfae99e3b862fa07bbd50a8df6b82",
+                        "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
diff --git a/modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff b/modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff
deleted file mode 100644
index 13f4208a0..000000000
--- a/modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff
+++ /dev/null
@@ -1,23 +0,0 @@
-Changes in module 'nf-core/controlfreec/makegraph'
---- modules/nf-core/controlfreec/makegraph/main.nf
-+++ modules/nf-core/controlfreec/makegraph/main.nf
-@@ -8,7 +8,7 @@
-         'biocontainers/control-freec:11.6b--hdbdd923_0' }"
- 
-     input:
--    tuple val(meta), path(ratio), path(baf), val(ploidy)
-+    tuple val(meta), path(ratio), path(baf)
- 
-     output:
-     tuple val(meta), path("*_BAF.png")       , emit: png_baf
-@@ -25,7 +25,7 @@
-     def prefix = task.ext.prefix ?: "${meta.id}"
-     def baf = baf ?: ""
-     """
--    cat \$(which makeGraph.R) | R --slave --args ${ploidy} ${args} ${ratio} ${baf}
-+    cat \$(which makeGraph.R) | R --slave --args ${args} ${ratio} ${baf}
- 
-     mv *_BAF.txt.png ${prefix}_BAF.png
-     mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png
-
-************************************************************
diff --git a/modules/nf-core/controlfreec/makegraph/environment.yml b/modules/nf-core/controlfreec/makegraph2/environment.yml
similarity index 76%
rename from modules/nf-core/controlfreec/makegraph/environment.yml
rename to modules/nf-core/controlfreec/makegraph2/environment.yml
index 897eadf3b..720c2e950 100644
--- a/modules/nf-core/controlfreec/makegraph/environment.yml
+++ b/modules/nf-core/controlfreec/makegraph2/environment.yml
@@ -1,4 +1,4 @@
-name: controlfreec_makegraph
+name: controlfreec_makegraph2
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph2/main.nf
similarity index 72%
rename from modules/nf-core/controlfreec/makegraph/main.nf
rename to modules/nf-core/controlfreec/makegraph2/main.nf
index 8d489f71f..a85589d6f 100644
--- a/modules/nf-core/controlfreec/makegraph/main.nf
+++ b/modules/nf-core/controlfreec/makegraph2/main.nf
@@ -1,10 +1,10 @@
-process CONTROLFREEC_MAKEGRAPH {
+process CONTROLFREEC_MAKEGRAPH2 {
     tag "$meta.id"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' :
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0':
         'biocontainers/control-freec:11.6b--hdbdd923_0' }"
 
     input:
@@ -24,8 +24,9 @@ process CONTROLFREEC_MAKEGRAPH {
     def args = task.ext.args ?: ""
     def prefix = task.ext.prefix ?: "${meta.id}"
     def baf = baf ?: ""
+    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
-    cat \$(which makeGraph.R) | R --slave --args ${args} ${ratio} ${baf}
+    cat \$(which makeGraph2.0.R) | R --slave --args ${args} ${ratio} ${baf}
 
     mv *_BAF.txt.png ${prefix}_BAF.png
     mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png
@@ -33,12 +34,13 @@ process CONTROLFREEC_MAKEGRAPH {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+        controlfreec: $VERSION
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}_BAF.png
     touch ${prefix}_ratio.log2.png
@@ -46,7 +48,7 @@ process CONTROLFREEC_MAKEGRAPH {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+        controlfreec: $VERSION
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/controlfreec/makegraph/meta.yml b/modules/nf-core/controlfreec/makegraph2/meta.yml
similarity index 89%
rename from modules/nf-core/controlfreec/makegraph/meta.yml
rename to modules/nf-core/controlfreec/makegraph2/meta.yml
index 6f91db38a..1325da4a8 100644
--- a/modules/nf-core/controlfreec/makegraph/meta.yml
+++ b/modules/nf-core/controlfreec/makegraph2/meta.yml
@@ -1,4 +1,4 @@
-name: controlfreec_makegraph
+name: controlfreec_makegraph2
 description: Plot Freec output
 keywords:
   - cna
@@ -14,6 +14,7 @@ tools:
       tool_dev_url: https://github.com/BoevaLab/FREEC/
       doi: "10.1093/bioinformatics/btq635"
       licence: ["GPL >=2"]
+
 input:
   # Only when we have meta
   - meta:
@@ -29,9 +30,7 @@ input:
       type: file
       description: .BAF file generated by FREEC
       pattern: "*.BAF"
-  - ploidy:
-      type: integer
-      description: Ploidy value for which graph should be created
+
 output:
   - meta:
       type: map
@@ -54,7 +53,6 @@ output:
       type: file
       description: Image of ratio plot
       pattern: "*_ratio.png"
+
 authors:
   - "@FriederikeHanssen"
-maintainers:
-  - "@FriederikeHanssen"
diff --git a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
index a2e7e17cf..3be4da8e4 100644
--- a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
@@ -8,7 +8,7 @@ include { CONTROLFREEC_FREEC              as FREEC_SOMATIC       } from '../../.
 include { CONTROLFREEC_ASSESSSIGNIFICANCE as ASSESS_SIGNIFICANCE } from '../../../modules/nf-core/controlfreec/assesssignificance/main'
 include { CONTROLFREEC_FREEC2BED          as FREEC2BED           } from '../../../modules/nf-core/controlfreec/freec2bed/main'
 include { CONTROLFREEC_FREEC2CIRCOS       as FREEC2CIRCOS        } from '../../../modules/nf-core/controlfreec/freec2circos/main'
-include { CONTROLFREEC_MAKEGRAPH          as MAKEGRAPH           } from '../../../modules/nf-core/controlfreec/makegraph/main'
+include { CONTROLFREEC_MAKEGRAPH2         as MAKEGRAPH2           } from '../../../modules/nf-core/controlfreec/makegraph2/main'
 
 workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
     take:
@@ -27,16 +27,39 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
 
     FREEC_SOMATIC(controlfreec_input, fasta, fasta_fai, [], dbsnp, dbsnp_tbi, chr_files, mappability, intervals_bed, [])
 
-    ASSESS_SIGNIFICANCE(FREEC_SOMATIC.out.CNV.join(FREEC_SOMATIC.out.ratio, failOnDuplicate: true, failOnMismatch: true))
+    //Filter the files that come out of freec somatic as ASSESS_SIGNIFICANCE only takes one cnv and one ratio file
+    //Creates empty channel if file is missing
+    cnv_files = FREEC_SOMATIC.out.CNV
+    .map{ meta, cnv ->
+        def tumor_file = cnv instanceof List ? cnv.find { it.toString().endsWith("gz_CNVs") } : cnv //only find if its a list, else it returns only the filename without the path
+        if (!tumor_file){
+            error("CNVs tumor file not found for sample $meta.id")
+        }
+        [meta,tumor_file]
+    }
+
+    ratio_files = FREEC_SOMATIC.out.ratio
+    .map{ meta, ratio ->
+        def tumor_file = ratio instanceof List ? ratio.find { it.toString().endsWith("gz_ratio.txt") } : ratio //same here as cnv
+        if (!tumor_file){
+            error("Ratio tumor file not found for sample $meta.id")
+        }
+        [meta,tumor_file]
+    }
+
+    //Join the pairs
+    assess_significance_input = cnv_files.join(ratio_files, failOnDuplicate: true, failOnMismatch: true)
+
+    ASSESS_SIGNIFICANCE(assess_significance_input)
     FREEC2BED(FREEC_SOMATIC.out.ratio)
     FREEC2CIRCOS(FREEC_SOMATIC.out.ratio)
-    MAKEGRAPH(FREEC_SOMATIC.out.ratio.join(FREEC_SOMATIC.out.BAF, failOnDuplicate: true, failOnMismatch: true))
+    MAKEGRAPH2(FREEC_SOMATIC.out.ratio.join(FREEC_SOMATIC.out.BAF, failOnDuplicate: true, failOnMismatch: true))
 
     ch_versions = ch_versions.mix(FREEC_SOMATIC.out.versions)
     ch_versions = ch_versions.mix(ASSESS_SIGNIFICANCE.out.versions)
     ch_versions = ch_versions.mix(FREEC2BED.out.versions)
     ch_versions = ch_versions.mix(FREEC2CIRCOS.out.versions)
-    ch_versions = ch_versions.mix(MAKEGRAPH.out.versions)
+    ch_versions = ch_versions.mix(MAKEGRAPH2.out.versions)
 
     emit:
     versions = ch_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 993faf127..e7178cbaa 100644
--- a/subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf
@@ -8,7 +8,7 @@ include { CONTROLFREEC_FREEC as FREEC_TUMORONLY                  } from '../../.
 include { CONTROLFREEC_ASSESSSIGNIFICANCE as ASSESS_SIGNIFICANCE } from '../../../modules/nf-core/controlfreec/assesssignificance/main'
 include { CONTROLFREEC_FREEC2BED as FREEC2BED                    } from '../../../modules/nf-core/controlfreec/freec2bed/main'
 include { CONTROLFREEC_FREEC2CIRCOS as FREEC2CIRCOS              } from '../../../modules/nf-core/controlfreec/freec2circos/main'
-include { CONTROLFREEC_MAKEGRAPH as MAKEGRAPH                    } from '../../../modules/nf-core/controlfreec/makegraph/main'
+include { CONTROLFREEC_MAKEGRAPH2 as MAKEGRAPH2                  } from '../../../modules/nf-core/controlfreec/makegraph2/main'
 
 workflow BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC {
     take:
@@ -30,13 +30,13 @@ 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))
+    MAKEGRAPH2(FREEC_TUMORONLY.out.ratio.join(FREEC_TUMORONLY.out.BAF, failOnDuplicate: true, failOnMismatch: true))
 
     ch_versions = ch_versions.mix(FREEC_TUMORONLY.out.versions)
     ch_versions = ch_versions.mix(ASSESS_SIGNIFICANCE.out.versions)
     ch_versions = ch_versions.mix(FREEC2BED.out.versions)
     ch_versions = ch_versions.mix(FREEC2CIRCOS.out.versions)
-    ch_versions = ch_versions.mix(MAKEGRAPH.out.versions)
+    ch_versions = ch_versions.mix(MAKEGRAPH2.out.versions)
 
     emit:
     versions = ch_versions
diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml
index 3664978be..0c3c05c55 100644
--- a/tests/config/pytesttags.yml
+++ b/tests/config/pytesttags.yml
@@ -248,7 +248,7 @@ controlfreec:
   - modules/nf-core/controlfreec/freec/**
   - modules/nf-core/controlfreec/freec2bed/**
   - modules/nf-core/controlfreec/freec2circos/**
-  - modules/nf-core/controlfreec/makegraph/**
+  - modules/nf-core/controlfreec/makegraph2/**
   - modules/nf-core/samtools/mpileup/**
   - subworkflows/local/bam_variant_calling_mpileup/**
   - subworkflows/local/bam_variant_calling_somatic_all/**