diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2a7922da..c0a0bcdf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -47,6 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - The split into clincial and research VCFs is now done before ranking the varaints [#485](https://github.com/nf-core/raredisease/pull/485)
 - Installed the nf-core version of ensemblvep/vep module [#482](https://github.com/nf-core/raredisease/pull/482)
 - The filenames of the ranked output VCF files have been changed. See [output.md](docs/output.md#filtering-and-ranking) for more information[#485](https://github.com/nf-core/raredisease/pull/485)
+- Patched cnvnator module so that the processes didn't have to rerun after a failed run [#503](https://github.com/nf-core/raredisease/pull/503).
 
 ### `Fixed`
 
diff --git a/modules.json b/modules.json
index e33ea340..f7eae8be 100644
--- a/modules.json
+++ b/modules.json
@@ -88,7 +88,8 @@
                     "cnvnator/cnvnator": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff"
                     },
                     "cnvnator/convert2vcf": {
                         "branch": "master",
diff --git a/modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff b/modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff
new file mode 100644
index 00000000..f06d7f6c
--- /dev/null
+++ b/modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff
@@ -0,0 +1,50 @@
+Changes in module 'nf-core/cnvnator/cnvnator'
+--- modules/nf-core/cnvnator/cnvnator/main.nf
++++ modules/nf-core/cnvnator/cnvnator/main.nf
+@@ -12,11 +12,12 @@
+     tuple val(meta2), path(root)
+     tuple val(meta3), path(fasta)
+     tuple val(meta4), path(fai)
++    val step
+ 
+     output:
+-    tuple val(output_meta), path("${prefix}.root"), emit: root
+-    tuple val(output_meta), path("${prefix}.tab") , emit: tab, optional: true
+-    path "versions.yml"                           , emit: versions
++    tuple val(output_meta), path("${output_meta.id}_${step}.root"), emit: root
++    tuple val(output_meta), path("*.tab")                         , emit: tab, optional: true
++    path "versions.yml"                                           , emit: versions
+ 
+     when:
+     task.ext.when == null || task.ext.when
+@@ -32,7 +33,11 @@
+         reference = ''
+     }
+     calls_cmd = args.contains("-call") ? "> ${prefix}.tab" : ''
++    mv_cmd    = "mv ${prefix}.root ${prefix}_${step}.root"
++    steps     = ["his", "stat", "partition", "call"]
++    cp_cmd    = steps.contains(step) ? "cp ${root} ${prefix}.root" :""
+     """
++    $cp_cmd
+     cnvnator \\
+         -root ${prefix}.root \\
+         $args \\
+@@ -40,6 +45,7 @@
+         $input_cmd \\
+         $calls_cmd
+ 
++    $mv_cmd 
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+         CNVnator: \$(echo \$(cnvnator 2>&1 | sed -n '3p' | sed 's/CNVnator v//'))
+@@ -52,7 +58,7 @@
+     output_meta   = bam             ? meta                : meta2
+     def calls_cmd = args.contains("-call") ? "touch ${prefix}.tab" : ''
+     """
+-    touch ${prefix}.root
++    touch ${prefix}_${step}.root
+     $calls_cmd
+ 
+     cat <<-END_VERSIONS > versions.yml
+
+************************************************************
diff --git a/modules/nf-core/cnvnator/cnvnator/main.nf b/modules/nf-core/cnvnator/cnvnator/main.nf
index 07393639..66427cd1 100644
--- a/modules/nf-core/cnvnator/cnvnator/main.nf
+++ b/modules/nf-core/cnvnator/cnvnator/main.nf
@@ -12,11 +12,12 @@ process CNVNATOR_CNVNATOR {
     tuple val(meta2), path(root)
     tuple val(meta3), path(fasta)
     tuple val(meta4), path(fai)
+    val step
 
     output:
-    tuple val(output_meta), path("${prefix}.root"), emit: root
-    tuple val(output_meta), path("${prefix}.tab") , emit: tab, optional: true
-    path "versions.yml"                           , emit: versions
+    tuple val(output_meta), path("${output_meta.id}_${step}.root"), emit: root
+    tuple val(output_meta), path("*.tab")                         , emit: tab, optional: true
+    path "versions.yml"                                           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,7 +33,11 @@ process CNVNATOR_CNVNATOR {
         reference = ''
     }
     calls_cmd = args.contains("-call") ? "> ${prefix}.tab" : ''
+    mv_cmd    = "mv ${prefix}.root ${prefix}_${step}.root"
+    steps     = ["his", "stat", "partition", "call"]
+    cp_cmd    = steps.contains(step) ? "cp ${root} ${prefix}.root" :""
     """
+    $cp_cmd
     cnvnator \\
         -root ${prefix}.root \\
         $args \\
@@ -40,6 +45,7 @@ process CNVNATOR_CNVNATOR {
         $input_cmd \\
         $calls_cmd
 
+    $mv_cmd 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         CNVnator: \$(echo \$(cnvnator 2>&1 | sed -n '3p' | sed 's/CNVnator v//'))
@@ -52,7 +58,7 @@ process CNVNATOR_CNVNATOR {
     output_meta   = bam             ? meta                : meta2
     def calls_cmd = args.contains("-call") ? "touch ${prefix}.tab" : ''
     """
-    touch ${prefix}.root
+    touch ${prefix}_${step}.root
     $calls_cmd
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/subworkflows/local/variant_calling/call_sv_cnvnator.nf b/subworkflows/local/variant_calling/call_sv_cnvnator.nf
index 0d5c5423..995b6919 100644
--- a/subworkflows/local/variant_calling/call_sv_cnvnator.nf
+++ b/subworkflows/local/variant_calling/call_sv_cnvnator.nf
@@ -22,11 +22,11 @@ workflow CALL_SV_CNVNATOR {
     main:
         ch_versions = Channel.empty()
 
-        CNVNATOR_RD ( ch_bam_bai, [[:],[]], [[:],[]], [[:],[]] )
-        CNVNATOR_HIST ( [[:],[],[]], CNVNATOR_RD.out.root, ch_fasta, ch_fai )
-        CNVNATOR_STAT ( [[:],[],[]], CNVNATOR_HIST.out.root, [[:],[]], [[:],[]] )
-        CNVNATOR_PARTITION ( [[:],[],[]], CNVNATOR_STAT.out.root, [[:],[]], [[:],[]] )
-        CNVNATOR_CALL ( [[:],[],[]], CNVNATOR_PARTITION.out.root, [[:],[]], [[:],[]] )
+        CNVNATOR_RD ( ch_bam_bai, [[:],[]], [[:],[]], [[:],[]], "rd" )
+        CNVNATOR_HIST ( [[:],[],[]], CNVNATOR_RD.out.root, ch_fasta, ch_fai, "his" )
+        CNVNATOR_STAT ( [[:],[],[]], CNVNATOR_HIST.out.root, [[:],[]], [[:],[]], "stat" )
+        CNVNATOR_PARTITION ( [[:],[],[]], CNVNATOR_STAT.out.root, [[:],[]], [[:],[]], "partition" )
+        CNVNATOR_CALL ( [[:],[],[]], CNVNATOR_PARTITION.out.root, [[:],[]], [[:],[]], "call" )
         CNVNATOR_CONVERT2VCF (CNVNATOR_CALL.out.tab).vcf
             .collect{it[1]}
             .toList()