diff --git a/modules.json b/modules.json
index 94fd5c8b..c71a0499 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "cellranger/count": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkgtf": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkref": {
@@ -22,12 +22,12 @@
                     },
                     "cellrangerarc/count": {
                         "branch": "master",
-                        "git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["modules"]
                     },
                     "cellrangerarc/mkgtf": {
                         "branch": "master",
-                        "git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["modules"]
                     },
                     "cellrangerarc/mkref": {
@@ -42,12 +42,12 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "617777a807a1770f73deb38c80004bac06807eef",
+                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
                         "installed_by": ["modules"]
                     },
                     "gffread": {
                         "branch": "master",
-                        "git_sha": "b8858b10356b87db4325341872816f9672541b7b",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
@@ -67,12 +67,12 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
+                        "git_sha": "9e71d8519dfbfc328c078bba14d4bd4c99e39a94",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "d87a6e2156c2099c09280fa70776eaf0a824817a",
+                        "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
                         "installed_by": ["modules"]
                     },
                     "universc": {
diff --git a/modules/nf-core/cellranger/count/meta.yml b/modules/nf-core/cellranger/count/meta.yml
index a672180e..c1f4259a 100644
--- a/modules/nf-core/cellranger/count/meta.yml
+++ b/modules/nf-core/cellranger/count/meta.yml
@@ -45,7 +45,7 @@ output:
       pattern: "versions.yml"
 authors:
   - "@ggabernet"
-  - "@Emiller88"
+  - "@edmundmiller"
 maintainers:
   - "@ggabernet"
-  - "@Emiller88"
+  - "@edmundmiller"
diff --git a/modules/nf-core/cellranger/count/templates/cellranger_count.py b/modules/nf-core/cellranger/count/templates/cellranger_count.py
index 4bfb9f4f..1527ba76 100644
--- a/modules/nf-core/cellranger/count/templates/cellranger_count.py
+++ b/modules/nf-core/cellranger/count/templates/cellranger_count.py
@@ -34,11 +34,11 @@ def chunk_iter(seq, size):
 # Match R1 in the filename, but only if it is followed by a non-digit or non-character
 # match "file_R1.fastq.gz", "file.R1_000.fastq.gz", etc. but
 # do not match "SRR12345", "file_INFIXR12", etc
-filename_pattern = r"([^a-zA-Z0-9])R1([^a-zA-Z0-9])"
+filename_pattern =  r'([^a-zA-Z0-9])R1([^a-zA-Z0-9])'
 
 for i, (r1, r2) in enumerate(chunk_iter(fastqs, 2)):
     # double escapes are required because nextflow processes this python 'template'
-    if re.sub(filename_pattern, r"\\1R2\\2", r1.name) != r2.name:
+    if re.sub(filename_pattern, r'\\1R2\\2', r1.name) != r2.name:
         raise AssertionError(
             dedent(
                 f"""\
diff --git a/modules/nf-core/cellranger/mkgtf/meta.yml b/modules/nf-core/cellranger/mkgtf/meta.yml
index 7ec0e0a3..a01e2830 100644
--- a/modules/nf-core/cellranger/mkgtf/meta.yml
+++ b/modules/nf-core/cellranger/mkgtf/meta.yml
@@ -27,7 +27,7 @@ output:
       pattern: "versions.yml"
 authors:
   - "@ggabernet"
-  - "@Emiller88"
+  - "@edmundmiller"
 maintainers:
   - "@ggabernet"
-  - "@Emiller88"
+  - "@edmundmiller"
diff --git a/modules/nf-core/cellrangerarc/count/meta.yml b/modules/nf-core/cellrangerarc/count/meta.yml
index 919de4dc..8bc73c6f 100644
--- a/modules/nf-core/cellrangerarc/count/meta.yml
+++ b/modules/nf-core/cellrangerarc/count/meta.yml
@@ -36,5 +36,5 @@ output:
       pattern: "versions.yml"
 authors:
   - "@ggabernet"
-  - "@Emiller88"
+  - "@edmundmiller"
   - "@heylf"
diff --git a/modules/nf-core/cellrangerarc/mkgtf/meta.yml b/modules/nf-core/cellrangerarc/mkgtf/meta.yml
index 923c3e18..5fadc3ef 100644
--- a/modules/nf-core/cellrangerarc/mkgtf/meta.yml
+++ b/modules/nf-core/cellrangerarc/mkgtf/meta.yml
@@ -28,5 +28,5 @@ output:
       pattern: "versions.yml"
 authors:
   - "@ggabernet"
-  - "@Emiller88"
+  - "@edmundmiller"
   - "@heylf"
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index acbcbe02..70edae4d 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -33,7 +33,7 @@ nextflow_process {
             { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
             { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
 
-            { assert snapshot(process.out.versions).match("versions") }
+            { assert snapshot(process.out.versions).match("fastqc_versions_single") }
             )
         }
     }
@@ -42,7 +42,6 @@ nextflow_process {
 
         when {
             process {
-<<<<<<< HEAD
                 """
                 input[0] = Channel.of([
                     [id: 'test', single_end: false], // meta map
@@ -50,17 +49,6 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
                 ])
                 """
-=======
-            """
-            input[0] = [
-                        [id: 'test', single_end: false], // meta map
-                        [
-                            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-                        ]
-            ]
-            """
->>>>>>> dev
             }
         }
 
@@ -75,7 +63,7 @@ nextflow_process {
             { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
             { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
 
-            { assert snapshot(process.out.versions).match("versions") }
+            { assert snapshot(process.out.versions).match("fastqc_versions_paired") }
             )
         }
     }
@@ -84,19 +72,11 @@ nextflow_process {
 
         when {
             process {
-<<<<<<< HEAD
                 """
                 input[0] = Channel.of([
                     [id: 'test', single_end: false], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
                 ])
-=======
-            """
-            input[0] = [
-                        [id: 'test', single_end: false], // meta map
-                        file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true)
-            ]
->>>>>>> dev
             """
             }
         }
@@ -109,7 +89,7 @@ nextflow_process {
             { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
             { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
 
-            { assert snapshot(process.out.versions).match("versions") }
+            { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") }
             )
         }
     }
@@ -118,21 +98,12 @@ nextflow_process {
 
         when {
             process {
-<<<<<<< HEAD
                 """
                 input[0] = Channel.of([
                     [id: 'test', single_end: false], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
                 ])
                 """
-=======
-            """
-            input[0] = [
-                        [id: 'test', single_end: false], // meta map
-                        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-            ]
-            """
->>>>>>> dev
             }
         }
 
@@ -144,7 +115,7 @@ nextflow_process {
             { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
             { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
 
-            { assert snapshot(process.out.versions).match("versions") }
+            { assert snapshot(process.out.versions).match("fastqc_versions_bam") }
             )
         }
     }
@@ -153,7 +124,6 @@ nextflow_process {
 
         when {
             process {
-<<<<<<< HEAD
                 """
                 input[0] = Channel.of([
                     [id: 'test', single_end: false], // meta map
@@ -163,19 +133,6 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
                 ])
                 """
-=======
-            """
-            input[0] = [
-                        [id: 'test', single_end: false], // meta map
-                        [
-                            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true)
-                        ]
-            ]
-            """
->>>>>>> dev
             }
         }
 
@@ -196,7 +153,7 @@ nextflow_process {
             { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
             { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
 
-            { assert snapshot(process.out.versions).match("versions") }
+            { assert snapshot(process.out.versions).match("fastqc_versions_multiple") }
             )
         }
     }
@@ -205,21 +162,12 @@ nextflow_process {
 
         when {
             process {
-<<<<<<< HEAD
                 """
                 input[0] = Channel.of([
                     [ id:'mysample', single_end:true ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                 ])
                 """
-=======
-            """
-            input[0] = [
-                        [ id:'mysample', single_end:true ], // meta map
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-            ]
-            """
->>>>>>> dev
             }
         }
 
@@ -231,7 +179,7 @@ nextflow_process {
             { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
             { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
 
-            { assert snapshot(process.out.versions).match("versions") }
+            { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") }
             )
         }
     }
@@ -243,19 +191,10 @@ nextflow_process {
         when {
             process {
                 """
-<<<<<<< HEAD
                 input[0] = Channel.of([
                     [ id: 'test', single_end:true ],
                     [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
                 ])
-=======
-                input[0] = [
-                            [ id: 'test', single_end:true ],
-                            [
-                                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-                            ]
-                ]
->>>>>>> dev
                 """
             }
         }
@@ -265,7 +204,7 @@ nextflow_process {
             { assert process.success },
             { assert snapshot(process.out.html.collect { file(it[1]).getName() } +
                                 process.out.zip.collect { file(it[1]).getName() } +
-                                process.out.versions ).match() }
+                                process.out.versions ).match("fastqc_stub") }
             )
         }
     }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index 5d624bb8..86f7c311 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,5 +1,17 @@
 {
-    "sarscov2 single-end [fastq] - stub": {
+    "fastqc_versions_interleaved": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:40:07.293713"
+    },
+    "fastqc_stub": {
         "content": [
             [
                 "test.html",
@@ -7,14 +19,70 @@
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
-        "timestamp": "2024-01-17T18:40:57.254299"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:31:01.425198"
+    },
+    "fastqc_versions_multiple": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:40:55.797907"
+    },
+    "fastqc_versions_bam": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:40:26.795862"
+    },
+    "fastqc_versions_single": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:39:27.043675"
+    },
+    "fastqc_versions_paired": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:39:47.584191"
     },
-    "versions": {
+    "fastqc_versions_custom_prefix": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
-        "timestamp": "2024-01-17T18:36:50.033627"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:41:14.576531"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/gffread/meta.yml b/modules/nf-core/gffread/meta.yml
index 27ac3105..d38cbcda 100644
--- a/modules/nf-core/gffread/meta.yml
+++ b/modules/nf-core/gffread/meta.yml
@@ -31,6 +31,6 @@ output:
       description: File containing software versions
       pattern: "versions.yml"
 authors:
-  - "@emiller88"
+  - "@edmundmiller"
 maintainers:
-  - "@emiller88"
+  - "@edmundmiller"
diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test
index c4dfbdf4..bdbc96ae 100644
--- a/modules/nf-core/gffread/tests/main.nf.test
+++ b/modules/nf-core/gffread/tests/main.nf.test
@@ -25,10 +25,12 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-            { assert snapshot(process.out).match() },
-            { assert process.out.gtf != null },
-            { assert process.out.gffread_gff == [] }
+                { assert process.success },
+                { assert snapshot(
+                    process.out.gtf,
+                    process.out.versions
+                ).match() },
+                { assert process.out.gffread_gff == [] }
             )
         }
 
@@ -49,10 +51,12 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-            { assert snapshot(process.out).match() },
-            { assert process.out.gtf == [] },
-            { assert process.out.gffread_gff != null },
+                { assert process.success },
+                { assert snapshot(
+                    process.out.gffread_gff,
+                    process.out.versions
+                ).match() },
+                { assert process.out.gtf == [] },
             )
         }
 
diff --git a/modules/nf-core/gffread/tests/main.nf.test.snap b/modules/nf-core/gffread/tests/main.nf.test.snap
index 1f1342e1..00a11a40 100644
--- a/modules/nf-core/gffread/tests/main.nf.test.snap
+++ b/modules/nf-core/gffread/tests/main.nf.test.snap
@@ -1,52 +1,24 @@
 {
     "sarscov2-gff3-gtf": {
         "content": [
-            {
-                "0": [
-                    "genome.gtf:md5,2394072d7d31530dfd590c4a117bf6e3"
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6"
-                ],
-                "gffread_gff": [
-                    
-                ],
-                "gtf": [
-                    "genome.gtf:md5,2394072d7d31530dfd590c4a117bf6e3"
-                ],
-                "versions": [
-                    "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6"
-                ]
-            }
+            [
+                "genome.gtf:md5,2394072d7d31530dfd590c4a117bf6e3"
+            ],
+            [
+                "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6"
+            ]
         ],
-        "timestamp": "2023-11-29T15:39:30.006985"
+        "timestamp": "2024-01-23T20:00:32.688779117"
     },
     "sarscov2-gff3-gff3": {
         "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    "genome.gffread.gff3:md5,a7d40d99dcddac23ac673c473279ea2d"
-                ],
-                "2": [
-                    "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6"
-                ],
-                "gffread_gff": [
-                    "genome.gffread.gff3:md5,a7d40d99dcddac23ac673c473279ea2d"
-                ],
-                "gtf": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6"
-                ]
-            }
+            [
+                "genome.gffread.gff3:md5,a7d40d99dcddac23ac673c473279ea2d"
+            ],
+            [
+                "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6"
+            ]
         ],
-        "timestamp": "2023-11-29T15:39:34.636061"
+        "timestamp": "2024-01-23T20:07:11.457356625"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index d0438eda..f1c4242e 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -3,6 +3,7 @@ nextflow_process {
     name "Test Process MULTIQC"
     script "../main.nf"
     process "MULTIQC"
+
     tag "modules"
     tag "modules_nfcore"
     tag "multiqc"
@@ -12,7 +13,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)])
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
                 input[1] = []
                 input[2] = []
                 input[3] = []
@@ -25,7 +26,7 @@ nextflow_process {
                 { assert process.success },
                 { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
                 { assert process.out.data[0] ==~ ".*/multiqc_data" },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out.versions).match("multiqc_versions_single") }
             )
         }
 
@@ -36,7 +37,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)])
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
                 input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
                 input[2] = []
                 input[3] = []
@@ -49,7 +50,7 @@ nextflow_process {
                 { assert process.success },
                 { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
                 { assert process.out.data[0] ==~ ".*/multiqc_data" },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out.versions).match("multiqc_versions_config") }
             )
         }
     }
@@ -61,7 +62,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)])
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
                 input[1] = []
                 input[2] = []
                 input[3] = []
@@ -75,7 +76,7 @@ nextflow_process {
                 { assert snapshot(process.out.report.collect { file(it).getName() } +
                                 process.out.data.collect { file(it).getName() } +
                                 process.out.plots.collect { file(it).getName() } +
-                                process.out.versions ).match() }
+                                process.out.versions ).match("multiqc_stub") }
             )
         }
 
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index d37e7304..549ba79c 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -1,13 +1,17 @@
 {
-    "versions": {
+    "multiqc_versions_single": {
         "content": [
             [
                 "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d"
             ]
         ],
-        "timestamp": "2024-01-09T23:02:49.911994"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:43:40.529579"
     },
-    "sarscov2 single-end [fastqc] - stub": {
+    "multiqc_stub": {
         "content": [
             [
                 "multiqc_report.html",
@@ -16,6 +20,22 @@
                 "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d"
             ]
         ],
-        "timestamp": "2024-01-09T23:03:14.524346"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:45:09.605359"
+    },
+    "multiqc_versions_config": {
+        "content": [
+            [
+                "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-01-31T17:44:53.535994"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml
index 93e4476a..791f255e 100644
--- a/modules/nf-core/star/genomegenerate/environment.yml
+++ b/modules/nf-core/star/genomegenerate/environment.yml
@@ -1,11 +1,10 @@
 name: star_genomegenerate
-
 channels:
   - conda-forge
   - bioconda
   - defaults
-
 dependencies:
   - bioconda::samtools=1.18
+  - bioconda::htslib=1.18
   - bioconda::star=2.7.10a
   - conda-forge::gawk=5.1.0
diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test
index af0c9421..c17c8ba4 100644
--- a/modules/nf-core/star/genomegenerate/tests/main.nf.test
+++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test
@@ -8,18 +8,18 @@ nextflow_process {
     tag "star"
     tag "star/genomegenerate"
 
-    test("homo_sapiens") {
+    test("fasta_gtf") {
 
         when {
             process {
                 """
                 input[0] = Channel.of([
                     [ id:'test_fasta' ],
-                    [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
                 ])
                 input[1] = Channel.of([
                     [ id:'test_gtf' ],
-                    [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
                 ])
                 """
             }
@@ -28,14 +28,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_with_gtf") },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_index") },
+                { assert snapshot(process.out.versions).match("fasta_gtf_versions") }
             )
         }
-
     }
 
-    test("homo_sapiens-stub") {
+    test("fasta_gtf_stub") {
 
         options '-stub'
 
@@ -44,11 +43,11 @@ nextflow_process {
                 """
                 input[0] = Channel.of([
                     [ id:'test_fasta' ],
-                    [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
                 ])
                 input[1] = Channel.of([
                     [ id:'test_gtf' ],
-                    [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
                 ])
                 """
             }
@@ -57,21 +56,20 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_with_gtf") },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_stub_index") },
+                { assert snapshot(process.out.versions).match("fasta_gtf_stub_versions") }
             )
         }
-
     }
 
-    test("homo_sapiens-without_gtf") {
+    test("fasta") {
 
         when {
             process {
                 """
                 input[0] = Channel.of([
                     [ id:'test_fasta' ],
-                    [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
                 ])
                 input[1] = Channel.of([ [], [] ])
                 """
@@ -81,14 +79,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_without_gtf") },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_index") },
+                { assert snapshot(process.out.versions).match("fasta_versions") }
             )
         }
 
     }
 
-    test("homo_sapiens-without_gtf-stub") {
+    test("fasta_stub") {
 
         options '-stub'
 
@@ -97,7 +95,7 @@ nextflow_process {
                 """
                 input[0] = Channel.of([
                     [ id:'test_fasta' ],
-                    [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
                 ])
                 input[1] = Channel.of([ [], [] ])
                 """
@@ -107,11 +105,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_without_gtf") },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_stub_index") },
+                { assert snapshot(process.out.versions).match("fasta_stub_versions") }
             )
         }
 
     }
 
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap
index 9de08c74..5653d6e6 100644
--- a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap
+++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap
@@ -1,22 +1,90 @@
 {
-    "versions": {
+    "fasta_gtf_versions": {
         "content": [
             [
                 "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
             ]
         ],
-        "timestamp": "2023-12-19T11:05:51.741109"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:54:31.798555"
     },
-    "index_with_gtf": {
+    "fasta_stub_versions": {
+        "content": [
+            [
+                "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:55:07.521209"
+    },
+    "fasta_gtf_stub_index": {
+        "content": [
+            "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:54:46.478098"
+    },
+    "fasta_gtf_stub_versions": {
+        "content": [
+            [
+                "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:54:46.491657"
+    },
+    "fasta_index": {
+        "content": [
+            "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:54:57.552329"
+    },
+    "fasta_versions": {
+        "content": [
+            [
+                "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:54:57.560541"
+    },
+    "fasta_gtf_index": {
         "content": [
             "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]"
         ],
-        "timestamp": "2023-12-19T11:38:14.551548"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:54:31.786814"
     },
-    "index_without_gtf": {
+    "fasta_stub_index": {
         "content": [
             "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]"
         ],
-        "timestamp": "2023-12-19T11:38:22.382905"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-01T15:55:07.517472"
     }
 }
\ No newline at end of file