diff --git a/modules.json b/modules.json
index e0a92fa6..0f435238 100644
--- a/modules.json
+++ b/modules.json
@@ -449,9 +449,8 @@
                     },
                     "tiddit/cov": {
                         "branch": "master",
-                        "git_sha": "1c90a501d102b800c27697f5ef39a6e217ab1915",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/tiddit/cov/tiddit-cov.diff"
+                        "git_sha": "ae07bd3d3e229ca82bd94531648736d44367a391",
+                        "installed_by": ["modules"]
                     },
                     "tiddit/sv": {
                         "branch": "master",
@@ -475,9 +474,8 @@
                     },
                     "vcf2cytosure": {
                         "branch": "master",
-                        "git_sha": "2dba354d7c0a43a1e6d6ce26f408b4936d4ed619",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/vcf2cytosure/vcf2cytosure.diff"
+                        "git_sha": "8694793954175ddd3001ddfbc0e36782a674d8a7",
+                        "installed_by": ["modules"]
                     },
                     "vcfanno": {
                         "branch": "master",
diff --git a/modules/nf-core/tiddit/cov/environment.yml b/modules/nf-core/tiddit/cov/environment.yml
new file mode 100644
index 00000000..6b024492
--- /dev/null
+++ b/modules/nf-core/tiddit/cov/environment.yml
@@ -0,0 +1,7 @@
+name: tiddit_cov
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::tiddit=3.6.1
diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf
index e8cafaa5..20d4720e 100644
--- a/modules/nf-core/tiddit/cov/main.nf
+++ b/modules/nf-core/tiddit/cov/main.nf
@@ -2,7 +2,7 @@ process TIDDIT_COV {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::tiddit=3.6.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/tiddit:3.6.1--py38h24c8ff8_0' :
         'biocontainers/tiddit:3.6.1--py38h24c8ff8_0' }"
diff --git a/modules/nf-core/tiddit/cov/meta.yml b/modules/nf-core/tiddit/cov/meta.yml
index 9cc586a9..c28546cc 100644
--- a/modules/nf-core/tiddit/cov/meta.yml
+++ b/modules/nf-core/tiddit/cov/meta.yml
@@ -12,7 +12,6 @@ tools:
       documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md
       doi: "10.12688/f1000research.11168.1"
       licence: ["GPL v3"]
-
 input:
   - meta:
       type: map
@@ -34,7 +33,6 @@ input:
         Reference genome file. Only needed when passing in CRAM instead of BAM.
         If not using CRAM, please pass an empty file instead.
       pattern: "*.fasta"
-
 output:
   - meta:
       type: map
@@ -43,7 +41,7 @@ output:
         e.g. [ id:'test', single_end:false ]
   - cov:
       type: file
-      description: The coverage of different regions. Optional.
+      description: The coverage of different regions in bed format. Optional.
       pattern: "*.bed"
   - wig:
       type: file
@@ -56,3 +54,6 @@ output:
 authors:
   - "@projectoriented"
   - "@ramprasadn"
+maintainers:
+  - "@projectoriented"
+  - "@ramprasadn"
diff --git a/modules/nf-core/tiddit/cov/tests/main.nf.test b/modules/nf-core/tiddit/cov/tests/main.nf.test
new file mode 100644
index 00000000..72746648
--- /dev/null
+++ b/modules/nf-core/tiddit/cov/tests/main.nf.test
@@ -0,0 +1,160 @@
+nextflow_process {
+
+    name "Test Process TIDDIT_COV"
+    script "../main.nf"
+    process "TIDDIT_COV"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tiddit"
+    tag "tiddit/cov"
+
+    test("homo_sapiens - cram - bed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
+                ]
+
+                input[1] = [
+                    [:],  // meta map
+                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.cov).match("cov") },
+                { assert process.out.cov[0][1] ==~ ".*/test.bed" },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - bam - bed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+                ]
+                input[1] = [ [:], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.cov).match("cov") },
+                { assert process.out.cov[0][1] ==~ ".*/test.bed" },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - cram - wig") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
+                ]
+
+                input[1] = [
+                    [:],  // meta map
+                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.wig).match("wig") },
+                { assert process.out.wig[0][1] ==~ ".*/test.wig" },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - bam - wig") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+                ]
+
+                input[1] = [ [:], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.wig).match("wig") },
+                { assert process.out.wig[0][1] ==~ ".*/test.wig" },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+
+    test("homo_sapiens - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
+                ]
+
+                input[1] = [
+                    [:],  // meta map
+                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.cov).match("cov - stub") },
+                { assert process.out.cov[0][1] ==~ ".*/test.bed" },
+                { assert snapshot(process.out.wig).match("wig - stub") },
+                { assert process.out.wig[0][1] ==~ ".*/test.wig" },
+                { assert snapshot(process.out.versions).match("versions - stub") }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/tiddit/cov/tests/main.nf.test.snap b/modules/nf-core/tiddit/cov/tests/main.nf.test.snap
new file mode 100644
index 00000000..dcd24edc
--- /dev/null
+++ b/modules/nf-core/tiddit/cov/tests/main.nf.test.snap
@@ -0,0 +1,74 @@
+{
+    "wig": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.wig:md5,7c46b6ef30574acdce0ad854f40126ae"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-22T11:24:06.649602"
+    },
+    "wig - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-22T11:30:00.831686"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a"
+            ]
+        ],
+        "timestamp": "2023-12-22T11:23:58.227251"
+    },
+    "cov": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bed:md5,caf0742f2d4a6f713ceb85268dd48c14"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-22T11:23:58.220115"
+    },
+    "versions - stub": {
+        "content": [
+            [
+                "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a"
+            ]
+        ],
+        "timestamp": "2023-12-22T11:30:00.834854"
+    },
+    "cov - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-22T11:30:00.826974"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tiddit/cov/tests/nextflow.config b/modules/nf-core/tiddit/cov/tests/nextflow.config
new file mode 100644
index 00000000..f83bd699
--- /dev/null
+++ b/modules/nf-core/tiddit/cov/tests/nextflow.config
@@ -0,0 +1,8 @@
+process {
+
+
+    withName: TIDDIT_COV {
+        ext.args = '-w'
+    }
+
+}
diff --git a/modules/nf-core/tiddit/cov/tests/tags.yml b/modules/nf-core/tiddit/cov/tests/tags.yml
new file mode 100644
index 00000000..d5831f1d
--- /dev/null
+++ b/modules/nf-core/tiddit/cov/tests/tags.yml
@@ -0,0 +1,2 @@
+tiddit/cov:
+  - "modules/nf-core/tiddit/cov/**"
diff --git a/modules/nf-core/tiddit/cov/tiddit-cov.diff b/modules/nf-core/tiddit/cov/tiddit-cov.diff
deleted file mode 100644
index acf8216f..00000000
--- a/modules/nf-core/tiddit/cov/tiddit-cov.diff
+++ /dev/null
@@ -1,26 +0,0 @@
-Changes in module 'nf-core/tiddit/cov'
---- modules/nf-core/tiddit/cov/meta.yml
-+++ modules/nf-core/tiddit/cov/meta.yml
-@@ -44,7 +44,7 @@
-   - cov:
-       type: file
-       description: The coverage of different regions. Optional.
--      pattern: "*.tab"
-+      pattern: "*.bed"
-   - wig:
-       type: file
-       description: The coverage of different regions in WIG format. Optional.
-
---- modules/nf-core/tiddit/cov/main.nf
-+++ modules/nf-core/tiddit/cov/main.nf
-@@ -41,7 +41,7 @@
-     def prefix = task.ext.prefix ?: "${meta.id}"
-     """
-     touch ${prefix}.wig
--    touch ${prefix}.tab
-+    touch ${prefix}.bed
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
-
-************************************************************
diff --git a/modules/nf-core/vcf2cytosure/environment.yml b/modules/nf-core/vcf2cytosure/environment.yml
index 30e0542f..d4bf9959 100644
--- a/modules/nf-core/vcf2cytosure/environment.yml
+++ b/modules/nf-core/vcf2cytosure/environment.yml
@@ -1,3 +1,4 @@
+name: vcf2cytosure
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/vcf2cytosure/meta.yml b/modules/nf-core/vcf2cytosure/meta.yml
index 39badd4c..2430f1ae 100644
--- a/modules/nf-core/vcf2cytosure/meta.yml
+++ b/modules/nf-core/vcf2cytosure/meta.yml
@@ -13,7 +13,7 @@ tools:
       homepage: "https://github.com/NBISweden/vcf2cytosure"
       documentation: "https://github.com/NBISweden/vcf2cytosure"
       tool_dev_url: "https://github.com/NBISweden/vcf2cytosure"
-      licence: "['MIT']"
+      licence: ["MIT"]
 
 input:
   - meta:
@@ -53,7 +53,7 @@ input:
         VCF file with SNVs to calculate probe coverage,
         not compatible with coverage_bed
         pattern: "*.{vcf,vcf.gz}"
-  - blacklilst_bed:
+  - blacklist_bed:
       type: file
       description: Bed file with regions to exclude
       pattern: "*.bed"
diff --git a/modules/nf-core/vcf2cytosure/tests/main.nf.test b/modules/nf-core/vcf2cytosure/tests/main.nf.test
new file mode 100644
index 00000000..d017cb0e
--- /dev/null
+++ b/modules/nf-core/vcf2cytosure/tests/main.nf.test
@@ -0,0 +1,73 @@
+nextflow_process {
+
+    name "Test Process VCF2CYTOSURE"
+    script "../main.nf"
+    process "VCF2CYTOSURE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vcf2cytosure"
+
+    test("homo sapiens - vcf - bed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [ file(params.test_data['homo_sapiens']['illumina']['na24385_chr22_sv_vcf'], checkIfExists: true) ]
+                ]
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    [ file(params.test_data['homo_sapiens']['illumina']['na24385_chr22_coverage'], checkIfExists: true) ]
+                ]
+                input[2] = [ [:], [] ]
+                input[3] = [ [:], [] ]
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.cgh).match("cgh") },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("homo sapiens - vcf - bed - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [ file(params.test_data['homo_sapiens']['illumina']['na24385_chr22_sv_vcf'], checkIfExists: true) ]
+                ]
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    [ file(params.test_data['homo_sapiens']['illumina']['na24385_chr22_coverage'], checkIfExists: true) ]
+                ]
+                input[2] = [ [:], [] ]
+                input[3] = [ [:], [] ]
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.cgh).match("cgh - stub") },
+                { assert snapshot(process.out.versions).match("versions - stub") }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/vcf2cytosure/tests/main.nf.test.snap b/modules/nf-core/vcf2cytosure/tests/main.nf.test.snap
new file mode 100644
index 00000000..0a0fae29
--- /dev/null
+++ b/modules/nf-core/vcf2cytosure/tests/main.nf.test.snap
@@ -0,0 +1,44 @@
+{
+    "cgh": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.cgh:md5,fc3f1ffac5b797881d992994d5d56550"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-21T18:33:25.202806"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,a1850e66d57cee0b98adb056c1dc3ebb"
+            ]
+        ],
+        "timestamp": "2023-12-21T18:33:25.205826"
+    },
+    "cgh - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.cgh:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-21T18:38:06.660655"
+    },
+    "versions - stub": {
+        "content": [
+            [
+                "versions.yml:md5,a1850e66d57cee0b98adb056c1dc3ebb"
+            ]
+        ],
+        "timestamp": "2023-12-21T18:38:06.663571"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/vcf2cytosure/tests/tags.yml b/modules/nf-core/vcf2cytosure/tests/tags.yml
new file mode 100644
index 00000000..88ff6038
--- /dev/null
+++ b/modules/nf-core/vcf2cytosure/tests/tags.yml
@@ -0,0 +1,2 @@
+vcf2cytosure:
+  - "modules/nf-core/vcf2cytosure/**"
diff --git a/modules/nf-core/vcf2cytosure/vcf2cytosure.diff b/modules/nf-core/vcf2cytosure/vcf2cytosure.diff
deleted file mode 100644
index f80980da..00000000
--- a/modules/nf-core/vcf2cytosure/vcf2cytosure.diff
+++ /dev/null
@@ -1,23 +0,0 @@
-Changes in module 'nf-core/vcf2cytosure'
---- modules/nf-core/vcf2cytosure/main.nf
-+++ modules/nf-core/vcf2cytosure/main.nf
-@@ -12,7 +12,7 @@
-     tuple val(meta2), path(coverage_bed)
-     tuple val(meta3), path(cns)
-     tuple val(meta4), path(snv_vcf)
--    path blacklist_bed
-+    path(blacklist_bed)
- 
-     output:
-     tuple val(meta), path("*.cgh"), emit: cgh
-@@ -56,7 +56,7 @@
-     def prefix = task.ext.prefix ?: "${meta.id}"
- 
-     """
--    touch ${prefix}.xml
-+    touch ${prefix}.cgh
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
-
-************************************************************