diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7786c82606..2f1290849a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,11 +17,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#1232](https://github.com/nf-core/sarek/pull/1232) - Fix Zenodo IDs in manifest
 - [#1236](https://github.com/nf-core/sarek/pull/1236) - Fix annotation cache folder verification when no annotation
+- [#1241](https://github.com/nf-core/sarek/pull/1241) - Fix axis text of controlfreec plots closing [#921](https://github.com/nf-core/sarek/issues/921)
 
 ### Dependencies
 
-| Dependency | Old version | New version |
-| ---------- | ----------- | ----------- |
+| Dependency    | Old version | New version |
+| ------------- | ----------- | ----------- |
+| Control-FREEC | 11.6        | 11.6b       |
 
 ## [3.3.0](https://github.com/nf-core/sarek/releases/tag/3.3.0) - Rapaselet
 
diff --git a/modules.json b/modules.json
index 0ebe620919..cb6912f552 100644
--- a/modules.json
+++ b/modules.json
@@ -77,28 +77,29 @@
                     },
                     "controlfreec/assesssignificance": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "053564d29a20d45323547973c4023914923823df",
                         "installed_by": ["modules"]
                     },
                     "controlfreec/freec": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "053564d29a20d45323547973c4023914923823df",
                         "installed_by": ["modules"]
                     },
                     "controlfreec/freec2bed": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "053564d29a20d45323547973c4023914923823df",
                         "installed_by": ["modules"]
                     },
                     "controlfreec/freec2circos": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "053564d29a20d45323547973c4023914923823df",
                         "installed_by": ["modules"]
                     },
                     "controlfreec/makegraph": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "053564d29a20d45323547973c4023914923823df",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff"
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf
index c6d81edc3a..5019780964 100644
--- a/modules/nf-core/controlfreec/assesssignificance/main.nf
+++ b/modules/nf-core/controlfreec/assesssignificance/main.nf
@@ -2,10 +2,10 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::control-freec=11.6"
+    conda "bioconda::control-freec=11.6b"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
-        'biocontainers/control-freec:11.6--h1b792b2_1' }"
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
+        'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
 
     input:
     tuple val(meta), path(cnvs), path(ratio)
diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf
index da368a524c..7ba83353c9 100644
--- a/modules/nf-core/controlfreec/freec/main.nf
+++ b/modules/nf-core/controlfreec/freec/main.nf
@@ -2,10 +2,10 @@ process CONTROLFREEC_FREEC {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::control-freec=11.6"
+    conda "bioconda::control-freec=11.6b"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
-        'biocontainers/control-freec:11.6--h1b792b2_1' }"
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
+        'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
 
     input:
     tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor)
diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf
index 8218ce8691..31c35e1d8a 100644
--- a/modules/nf-core/controlfreec/freec2bed/main.nf
+++ b/modules/nf-core/controlfreec/freec2bed/main.nf
@@ -2,10 +2,10 @@ process CONTROLFREEC_FREEC2BED {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::control-freec=11.6"
+    conda "bioconda::control-freec=11.6b"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
-        'biocontainers/control-freec:11.6--h1b792b2_1' }"
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
+        'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
 
     input:
     tuple val(meta), path(ratio)
diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf
index f6b440f447..f0a1fb445a 100644
--- a/modules/nf-core/controlfreec/freec2circos/main.nf
+++ b/modules/nf-core/controlfreec/freec2circos/main.nf
@@ -2,10 +2,10 @@ process CONTROLFREEC_FREEC2CIRCOS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::control-freec=11.6"
+    conda "bioconda::control-freec=11.6b"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
-        'biocontainers/control-freec:11.6--h1b792b2_1' }"
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
+        'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
 
     input:
     tuple val(meta), path(ratio)
diff --git a/modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff b/modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff
new file mode 100644
index 0000000000..a78c18fa32
--- /dev/null
+++ b/modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff
@@ -0,0 +1,23 @@
+Changes in module 'nf-core/controlfreec/makegraph'
+--- modules/nf-core/controlfreec/makegraph/main.nf
++++ modules/nf-core/controlfreec/makegraph/main.nf
+@@ -7,7 +7,7 @@
+         'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
+         '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
+@@ -24,7 +24,7 @@
+     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 ${prefix}_ratio.log2.png
+
+************************************************************
diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf
index 293cf1feaa..f9978bf952 100644
--- a/modules/nf-core/controlfreec/makegraph/main.nf
+++ b/modules/nf-core/controlfreec/makegraph/main.nf
@@ -2,11 +2,10 @@ process CONTROLFREEC_MAKEGRAPH {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::control-freec=11.6"
+    conda "bioconda::control-freec=11.6b"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
-        'biocontainers/control-freec:11.6--h1b792b2_1' }"
-
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
+        'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
     input:
     tuple val(meta), path(ratio), path(baf)
 
diff --git a/modules/nf-core/controlfreec/makegraph/meta.yml b/modules/nf-core/controlfreec/makegraph/meta.yml
index a207ec8c8f..7b97dcf9bc 100644
--- a/modules/nf-core/controlfreec/makegraph/meta.yml
+++ b/modules/nf-core/controlfreec/makegraph/meta.yml
@@ -30,6 +30,9 @@ 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: