diff --git a/modules/nf-core/antismash/antismashlite/tests/main.nf.test b/modules/nf-core/antismash/antismashlite/tests/main.nf.test
index e4793eea83c..5ee21d6ded4 100644
--- a/modules/nf-core/antismash/antismashlite/tests/main.nf.test
+++ b/modules/nf-core/antismash/antismashlite/tests/main.nf.test
@@ -66,7 +66,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/bclconvert/tests/main.nf.test b/modules/nf-core/bclconvert/tests/main.nf.test
index 2779457c1d2..a4308fa3f52 100644
--- a/modules/nf-core/bclconvert/tests/main.nf.test
+++ b/modules/nf-core/bclconvert/tests/main.nf.test
@@ -15,8 +15,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id: 'test', lane:1 ],
-                    file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/bedops/convert2bed/tests/main.nf.test b/modules/nf-core/bedops/convert2bed/tests/main.nf.test
index 183f8de6c90..3f2b193a6d4 100644
--- a/modules/nf-core/bedops/convert2bed/tests/main.nf.test
+++ b/modules/nf-core/bedops/convert2bed/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
                     ]
                 """
             }
@@ -41,7 +41,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
                     ]
                 """
             }
diff --git a/modules/nf-core/bedops/gtf2bed/tests/main.nf.test b/modules/nf-core/bedops/gtf2bed/tests/main.nf.test
index 8dcc67f5760..c6f4ed22678 100644
--- a/modules/nf-core/bedops/gtf2bed/tests/main.nf.test
+++ b/modules/nf-core/bedops/gtf2bed/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [[ id:'test' ], // meta map
-                             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)
                 ]
                 """
             }
@@ -38,7 +38,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [[ id:'test' ], // meta map
-                             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)
                 ]
                 """
             }
diff --git a/modules/nf-core/biscuit/align/tests/main.nf.test b/modules/nf-core/biscuit/align/tests/main.nf.test
index e7b68171b1f..1dc3eb3faca 100644
--- a/modules/nf-core/biscuit/align/tests/main.nf.test
+++ b/modules/nf-core/biscuit/align/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
             script "../../index/main.nf"
             process {
             """
-            input[0] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+            input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
             """
         }
         }
@@ -28,7 +28,7 @@ nextflow_process {
                 """
                 input[0] = [
                             [ id:'test' ], // meta map
-                            [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
+                            [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) ]
                 ]
                 input[1] = BISCUIT_INDEX.out.index
                 """
@@ -52,8 +52,8 @@ nextflow_process {
                 """
                 input[0] = [
                             [ id:'test' ], // meta map
-                            [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
-                              file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
+                            [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true),
+                              file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) ]
                 ]
                 input[1] = BISCUIT_INDEX.out.index
                 """
diff --git a/modules/nf-core/biscuit/bsconv/tests/main.nf.test b/modules/nf-core/biscuit/bsconv/tests/main.nf.test
index d62b9411df2..1cbf306a88b 100644
--- a/modules/nf-core/biscuit/bsconv/tests/main.nf.test
+++ b/modules/nf-core/biscuit/bsconv/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
             script "../../index/main.nf"
             process {
             """
-            input[0] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+            input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
             """
             }
         }
@@ -27,8 +27,8 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [id:'test', single_end:false ], // meta map
-                            file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
                             ]
 
                 input[1] = BISCUIT_INDEX.out.index
@@ -54,8 +54,8 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [id:'test', single_end:false ], // meta map
-                            file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
                             ]
 
                 input[1] = BISCUIT_INDEX.out.index
diff --git a/modules/nf-core/checkqc/environment.yml b/modules/nf-core/checkqc/environment.yml
index 4c0fd50d3fe..e60237d5c5f 100644
--- a/modules/nf-core/checkqc/environment.yml
+++ b/modules/nf-core/checkqc/environment.yml
@@ -5,7 +5,8 @@ channels:
   - defaults
 dependencies:
   - python=3.8
+  - numpy=1.26
   - pip
   - pip: # FIXME https://github.com/nf-core/modules/issues/5814
-      - checkqc==3.8.0
-      - interop==1.2.4
+      - checkqc==4.0.3
+      - interop==1.3.2
diff --git a/modules/nf-core/checkqc/main.nf b/modules/nf-core/checkqc/main.nf
index d062a2990b9..9aacdbec5bd 100644
--- a/modules/nf-core/checkqc/main.nf
+++ b/modules/nf-core/checkqc/main.nf
@@ -2,7 +2,7 @@ process CHECKQC {
     tag "$meta.id"
     label 'process_single'
 
-    container "community.wave.seqera.io/library/python_pip_interop_checkqc:d76c912c8fadc561"
+    container "community.wave.seqera.io/library/python_numpy_pip_checkqc_interop:b5301d9801b8e66b"
 
     input:
     tuple val(meta), path(run_dir)
@@ -10,6 +10,7 @@ process CHECKQC {
 
     output:
     tuple val(meta), path("*checkqc_report.json"), emit: report
+    tuple val(meta), path("*checkqc_log.txt")    , emit: log
     path "versions.yml"                          , emit: versions
 
     when:
@@ -29,7 +30,13 @@ process CHECKQC {
         $args \
         $config \
         --json \
-        $run_dir > checkqc_report.json
+        $run_dir > checkqc_report.json 2> checkqc_log.txt || true
+
+    # Check if the output JSON file is empty
+    if [[ ! -s checkqc_report.json ]] ; then
+        echo "Error: Empty JSON files. Most likely due to missing files in run directory. See checkQC log file for errors."
+        exit 1
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/checkqc/meta.yml b/modules/nf-core/checkqc/meta.yml
index f7ae489543b..0c3d98ba916 100644
--- a/modules/nf-core/checkqc/meta.yml
+++ b/modules/nf-core/checkqc/meta.yml
@@ -34,6 +34,10 @@ output:
       type: file
       description: CheckQC report in json format
       pattern: "*checkqc_report.json"
+  - log:
+      type: file
+      description: CheckQC log in txt format
+      pattern: "*_log.txt"
 
 authors:
   - "@matrulda"
diff --git a/modules/nf-core/checkqc/tests/main.nf.test b/modules/nf-core/checkqc/tests/main.nf.test
index 751cd95327b..e9bc14faf33 100644
--- a/modules/nf-core/checkqc/tests/main.nf.test
+++ b/modules/nf-core/checkqc/tests/main.nf.test
@@ -34,7 +34,81 @@ nextflow_process {
         then {
             assertAll(
             { assert process.success },
-            { assert snapshot(process.out).match() }
+            { assert snapshot(process.out).match() },
+            { assert process.out.report },
+            { assert process.out.report.size() == 1 },
+            { assert process.out.report.get(0).get(1) ==~ ".*/checkqc_report.json" },
+            { assert path(process.out.report.get(0).get(1)).json.exit_status == 0 },
+            { assert process.out.log },
+            { assert path(process.out.log.get(0).get(1)).getText().contains("Instrument and reagent version: hiseq2500_rapidhighoutput_v4") }
+
+          )
+        }
+
+    }
+    test("homo_sapiens illumina test_miseq_noRunParameters - Log Error: no File") {
+        config "./nextflow.config"
+
+        setup {
+            run("UNTAR") {
+                script "../../untar/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([[id: 'test_no_xml'], file('https://github.com/nf-core/test-datasets/raw/demultiplex/testdata/MiSeq/220422_M11111_0222_000000000-K9H97.tar.gz', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                    input[0] = UNTAR.out.untar
+                    input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.failed }
+          )
+        }
+
+    }
+
+    test("homo_sapiens illumina test_interop_bcl2fastqstats_flowcell - QC Error") {
+
+        setup {
+            run("UNTAR") {
+                script "../../untar/main.nf"
+                process {
+                    """
+                   input[0] = Channel.of([[id: 'test_no_downgrade_errors'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/interop_bcl2fastqstats/test_flowcell_stats.tar.gz', checkIfExists: true)])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                    input[0] = UNTAR.out.untar
+                    input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() },
+            { assert process.out.report },
+            { assert process.out.report.size() == 1 },
+            { assert process.out.report.get(0).get(1) ==~ ".*/checkqc_report.json" },
+            { assert path(process.out.report.get(0).get(1)).json.exit_status == 1 },
+            { assert process.out.log },
+            { assert path(process.out.log.get(0).get(1)).getText().contains("ERROR    Fatal QC error") }
           )
         }
 
diff --git a/modules/nf-core/checkqc/tests/main.nf.test.snap b/modules/nf-core/checkqc/tests/main.nf.test.snap
index 21a2961320d..65dc20736ec 100644
--- a/modules/nf-core/checkqc/tests/main.nf.test.snap
+++ b/modules/nf-core/checkqc/tests/main.nf.test.snap
@@ -1,4 +1,53 @@
 {
+    "homo_sapiens illumina test_interop_bcl2fastqstats_flowcell - QC Error": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_no_downgrade_errors"
+                        },
+                        "checkqc_report.json:md5,c0c5655b8f09d848de97f79073b2eae0"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test_no_downgrade_errors"
+                        },
+                        "checkqc_log.txt:md5,687d57a112fda6f56755d45e5c9cd0be"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7c921c68a4de1cc3345edb1fd88444d1"
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test_no_downgrade_errors"
+                        },
+                        "checkqc_log.txt:md5,687d57a112fda6f56755d45e5c9cd0be"
+                    ]
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test_no_downgrade_errors"
+                        },
+                        "checkqc_report.json:md5,c0c5655b8f09d848de97f79073b2eae0"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7c921c68a4de1cc3345edb1fd88444d1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-29T15:12:42.632194365"
+    },
     "homo_sapiens illumina test_interop_bcl2fastqstats_flowcell - QC OK": {
         "content": [
             {
@@ -7,29 +56,45 @@
                         {
                             "id": "test"
                         },
-                        "checkqc_report.json:md5,c69cb912a8c5bf53544764bd5bd73ae5"
+                        "checkqc_report.json:md5,7e3ac9ce7163436cbd5f5420ca08ffcd"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c37381fc450f4ed00da2987430db8177"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "checkqc_log.txt:md5,3e196f53b93d614580436bc574daea45"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7c921c68a4de1cc3345edb1fd88444d1"
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "checkqc_log.txt:md5,3e196f53b93d614580436bc574daea45"
+                    ]
                 ],
                 "report": [
                     [
                         {
                             "id": "test"
                         },
-                        "checkqc_report.json:md5,c69cb912a8c5bf53544764bd5bd73ae5"
+                        "checkqc_report.json:md5,7e3ac9ce7163436cbd5f5420ca08ffcd"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c37381fc450f4ed00da2987430db8177"
+                    "versions.yml:md5,7c921c68a4de1cc3345edb1fd88444d1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.3"
         },
-        "timestamp": "2024-07-17T18:30:52.712542733"
+        "timestamp": "2024-07-29T15:12:10.423534926"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test
index 28853f4df52..0cac4c3fb0f 100644
--- a/modules/nf-core/chewbbaca/createschema/tests/main.nf.test
+++ b/modules/nf-core/chewbbaca/createschema/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
                 """
                 input[0] = [
                             [ id:'test', single_end:false ], // meta map
-                            file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
                 ]
                 input[1] = [] // ptf
                 input[2] = [] //cds
@@ -42,8 +42,8 @@ nextflow_process {
                 """
                 input[0] = [
                             [ id:'test', single_end:false ], // meta map
-                            file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 input[1] = [] // ptf
                 input[2] = [] // cds
@@ -69,8 +69,8 @@ nextflow_process {
                 """
                 input[0] = [
                             [ id:'test', single_end:false ], // meta map
-                            file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
                 ]
                 input[1] = [] // ptf
                 input[2] = [] // cds
@@ -98,8 +98,8 @@ nextflow_process {
                 """
                 input[0] = [
                             [ id:'test', single_end:false ], // meta map
-                            file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
                 ]
                 input[1] = [] // ptf
                 input[2] = [] // cds
diff --git a/modules/nf-core/cutadapt/tests/main.nf.test b/modules/nf-core/cutadapt/tests/main.nf.test
index b7ea6ef9fe7..36927bd7fbe 100644
--- a/modules/nf-core/cutadapt/tests/main.nf.test
+++ b/modules/nf-core/cutadapt/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_process {
                 input[0] = [
                     [ id: 'test', single_end:true ],
                     [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 """
@@ -47,8 +47,8 @@ nextflow_process {
                 input[0] = [
                     [ id: 'test', single_end:false ],
                     [
-                        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.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 """
diff --git a/modules/nf-core/diamond/blastp/tests/main.nf.test b/modules/nf-core/diamond/blastp/tests/main.nf.test
index 672bf050bdd..f21e926de9d 100644
--- a/modules/nf-core/diamond/blastp/tests/main.nf.test
+++ b/modules/nf-core/diamond/blastp/tests/main.nf.test
@@ -6,6 +6,7 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "diamond"
+    tag "diamond/makedb"
     tag "diamond/blastp"
 
     setup {
@@ -13,7 +14,7 @@ nextflow_process {
             script "../../makedb/main.nf"
             process {
                 """
-                input[0] = [ [id:'test2'], [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ] ]
+                input[0] = [ [id:'test2'], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ] ]
                 input[1] = []
                 input[2] = []
                 input[3] = []
@@ -30,7 +31,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [id:'test'], file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+                input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ]
                 input[1] = DIAMOND_MAKEDB.out.db
                 input[2] = 'txt'
                 input[3] = 'qseqid qlen'
@@ -41,8 +42,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.txt).match("txt") },
-                { assert process.out.versions }
+                { assert snapshot(
+                    process.out.txt,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
 
@@ -56,7 +60,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [id:'test'], file(params.test_data['sarscov2']['genome']['proteome_fasta_gz'], checkIfExists: true) ]
+                input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta.gz', checkIfExists: true) ]
                 input[1] = DIAMOND_MAKEDB.out.db
                 input[2] = 'txt'
                 input[3] = 'qseqid qlen'
@@ -67,8 +71,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.txt).match("gz_txt") },
-                { assert process.out.versions }
+                { assert snapshot(
+                    process.out.txt,
+                    process.out.versions
+                    ).match("gz_txt")
+                }
             )
         }
 
@@ -82,7 +89,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [id:'test'], file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+                input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ]
                 input[1] = DIAMOND_MAKEDB.out.db
                 input[2] = 'daa'
                 input[3] = []
@@ -94,7 +101,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert process.out.daa },
-                { assert process.out.versions }
+                { assert snapshot(process.out.versions).match() }
             )
         }
 
diff --git a/modules/nf-core/diamond/blastp/tests/main.nf.test.snap b/modules/nf-core/diamond/blastp/tests/main.nf.test.snap
index 83575bc1054..e323c8b89c1 100644
--- a/modules/nf-core/diamond/blastp/tests/main.nf.test.snap
+++ b/modules/nf-core/diamond/blastp/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "txt": {
+    "Should search for protein hits against a DIAMOND db and return a tab separated output file of hits": {
         "content": [
             [
                 [
@@ -8,9 +8,16 @@
                     },
                     "test.txt:md5,8131b1afd717f3d5f2f2417c5b562e6e"
                 ]
+            ],
+            [
+                "versions.yml:md5,57a0ebeb0a8a732c941ae0102639a9d0"
             ]
         ],
-        "timestamp": "2023-11-07T10:27:02.453987512"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-29T14:40:23.906848"
     },
     "gz_txt": {
         "content": [
@@ -21,8 +28,27 @@
                     },
                     "test.txt:md5,8131b1afd717f3d5f2f2417c5b562e6e"
                 ]
+            ],
+            [
+                "versions.yml:md5,57a0ebeb0a8a732c941ae0102639a9d0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-29T14:40:29.865487"
+    },
+    "Should search for protein hits against a DIAMOND db and return a daa format file of hits": {
+        "content": [
+            [
+                "versions.yml:md5,57a0ebeb0a8a732c941ae0102639a9d0"
             ]
         ],
-        "timestamp": "2023-11-07T09:41:13.934994026"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-29T14:40:35.362027"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/diamond/blastx/tests/main.nf.test b/modules/nf-core/diamond/blastx/tests/main.nf.test
index a367f8835ef..b8757403d73 100644
--- a/modules/nf-core/diamond/blastx/tests/main.nf.test
+++ b/modules/nf-core/diamond/blastx/tests/main.nf.test
@@ -6,6 +6,7 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "diamond"
+    tag "diamond/makedb"
     tag "diamond/blastx"
 
     setup {
@@ -13,7 +14,7 @@ nextflow_process {
             script "../../makedb/main.nf"
             process {
                 """
-                input[0] = [ [id:'test2'], [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ] ]
+                input[0] = [ [id:'test2'], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ] ]
                 input[1] = []
                 input[2] = []
                 input[3] = []
@@ -30,7 +31,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [id:'test'], file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+                input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) ]
                 input[1] = DIAMOND_MAKEDB.out.db
                 input[2] = 'tfdfdt' // Nonsense file extension to check default case.
                 input[3] = 'qseqid qlen'
@@ -41,9 +42,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.txt).match("txt") },
                 { assert path(process.out.log.get(0).get(1)).readLines().contains("11 queries aligned.") },
-                { assert process.out.versions }
+                { assert snapshot(
+                    process.out.txt,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
 
@@ -57,7 +61,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [id:'test'], file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+                input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) ]
                 input[1] = DIAMOND_MAKEDB.out.db
                 input[2] = 'daa'
                 input[3] = []
@@ -70,7 +74,7 @@ nextflow_process {
                 { assert process.success },
                 { assert process.out.daa },
                 { assert path(process.out.log.get(0).get(1)).readLines().contains("11 queries aligned.") },
-                { assert process.out.versions }
+                { assert snapshot(process.out.versions).match() }
             )
         }
 
diff --git a/modules/nf-core/diamond/blastx/tests/main.nf.test.snap b/modules/nf-core/diamond/blastx/tests/main.nf.test.snap
index 27fb0a31ead..8a128c9940c 100644
--- a/modules/nf-core/diamond/blastx/tests/main.nf.test.snap
+++ b/modules/nf-core/diamond/blastx/tests/main.nf.test.snap
@@ -1,5 +1,17 @@
 {
-    "txt": {
+    "Should search for transcriptome hits against a DIAMOND db and return the daa format output file of hits": {
+        "content": [
+            [
+                "versions.yml:md5,733d944fb173eaf1d1cdf280cd1b3b9c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-29T14:49:26.843747"
+    },
+    "Should search for transcriptome hits against a DIAMOND db and return the default tab separated output file of hits": {
         "content": [
             [
                 [
@@ -8,8 +20,15 @@
                     },
                     "test.txt:md5,33dc682dabfa44c7089abbc8fe8b84e4"
                 ]
+            ],
+            [
+                "versions.yml:md5,733d944fb173eaf1d1cdf280cd1b3b9c"
             ]
         ],
-        "timestamp": "2023-11-07T09:42:36.646074348"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-29T14:49:20.769093"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/diamond/makedb/tests/main.nf.test b/modules/nf-core/diamond/makedb/tests/main.nf.test
index e9f7df282b8..f27e142be35 100644
--- a/modules/nf-core/diamond/makedb/tests/main.nf.test
+++ b/modules/nf-core/diamond/makedb/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [id:'test'], [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ] ]
+                input[0] = [ [id:'test'], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ] ]
                 input[1] = []
                 input[2] = []
                 input[3] = []
@@ -27,8 +27,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.db).match("db") },
-                { assert process.out.versions }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -42,7 +41,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [id:'test'], [ file(params.test_data['sarscov2']['genome']['proteome_fasta_gz'], checkIfExists: true) ] ]
+                input[0] = [ [id:'test'], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta.gz', checkIfExists: true) ] ]
                 input[1] = []
                 input[2] = []
                 input[3] = []
@@ -53,8 +52,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.db).match("gz_db") },
-                { assert process.out.versions }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -68,10 +66,10 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [id:'test'], [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true)  ] ]
-                input[1] = [ file(params.test_data['sarscov2']['metagenome']['prot_accession2taxid_gz'], checkIfExists: true) ]
-                input[2] = [ file(params.test_data['sarscov2']['metagenome']['prot_nodes_dmp'], checkIfExists: true) ]
-                input[3] = [ file(params.test_data['sarscov2']['metagenome']['prot_names_dmp'], checkIfExists: true) ]
+                input[0] = [ [id:'test'], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)  ] ]
+                input[1] = [ file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/prot.accession2taxid.gz', checkIfExists: true) ]
+                input[2] = [ file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/prot_nodes.dmp', checkIfExists: true) ]
+                input[3] = [ file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/prot_names.dmp', checkIfExists: true) ]
                 """
             }
         }
@@ -79,8 +77,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.db).match("db_tax") },
-                { assert process.out.versions }
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/diamond/makedb/tests/main.nf.test.snap b/modules/nf-core/diamond/makedb/tests/main.nf.test.snap
index a8fe065cbb9..5abefce7f85 100644
--- a/modules/nf-core/diamond/makedb/tests/main.nf.test.snap
+++ b/modules/nf-core/diamond/makedb/tests/main.nf.test.snap
@@ -1,41 +1,101 @@
 {
-    "db_tax": {
+    "Should build a DIAMOND db file from a fasta file with taxonomic information": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.dmnd:md5,9d57aa88cd1766adfda8360876fc0e4f"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.dmnd:md5,9d57aa88cd1766adfda8360876fc0e4f"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,29a8cea287d2206b9a837d2750de00c4"
+                ],
+                "db": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.dmnd:md5,9d57aa88cd1766adfda8360876fc0e4f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,29a8cea287d2206b9a837d2750de00c4"
                 ]
-            ]
+            }
         ],
-        "timestamp": "2023-12-05T14:28:48.616684409"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-29T14:35:11.221381"
     },
-    "db": {
+    "Should build a DIAMOND db file from a fasta file without taxonomic information": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.dmnd:md5,6039420745dd4db6e761244498460ae1"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.dmnd:md5,6039420745dd4db6e761244498460ae1"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,29a8cea287d2206b9a837d2750de00c4"
+                ],
+                "db": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.dmnd:md5,6039420745dd4db6e761244498460ae1"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,29a8cea287d2206b9a837d2750de00c4"
                 ]
-            ]
+            }
         ],
-        "timestamp": "2023-12-05T14:22:02.696726038"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-29T14:35:00.595693"
     },
-    "gz_db": {
+    "Should build a DIAMOND db file from a zipped fasta file without taxonomic information": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.dmnd:md5,6039420745dd4db6e761244498460ae1"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.dmnd:md5,6039420745dd4db6e761244498460ae1"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,29a8cea287d2206b9a837d2750de00c4"
+                ],
+                "db": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.dmnd:md5,6039420745dd4db6e761244498460ae1"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,29a8cea287d2206b9a837d2750de00c4"
                 ]
-            ]
+            }
         ],
-        "timestamp": "2023-12-05T14:22:07.430248018"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-29T14:35:05.494933"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/fastani/tests/main.nf.test b/modules/nf-core/fastani/tests/main.nf.test
index 98c7933f4d7..a4318db49ee 100644
--- a/modules/nf-core/fastani/tests/main.nf.test
+++ b/modules/nf-core/fastani/tests/main.nf.test
@@ -14,9 +14,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
-                input[1] = file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
                 """
             }
         }
diff --git a/modules/nf-core/gt/gff3/tests/main.nf.test b/modules/nf-core/gt/gff3/tests/main.nf.test
index cb44bc8ff60..46c7da35ba7 100644
--- a/modules/nf-core/gt/gff3/tests/main.nf.test
+++ b/modules/nf-core/gt/gff3/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/gt/gff3validator/tests/main.nf.test b/modules/nf-core/gt/gff3validator/tests/main.nf.test
index 766e3e7425d..55184f84e46 100644
--- a/modules/nf-core/gt/gff3validator/tests/main.nf.test
+++ b/modules/nf-core/gt/gff3validator/tests/main.nf.test
@@ -16,13 +16,13 @@ nextflow_process {
 
         setup {
             run("GT_GFF3") {
-                script "../../../../nf-core/gt/gff3"
+                script "../../../gt/gff3"
 
                 process {
                     """
                     input[0] = [
                         [ id:'test' ],
-                        file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true)
                     ]
                     """
                 }
@@ -40,9 +40,9 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
                 { assert path(process.out.success_log[0][1]).text.contains("input is valid GFF3") },
-                { assert process.out.error_log == [] }
+                { assert process.out.error_log == [] },
+                { assert snapshot(process.out).match() },
             )
         }
 
@@ -57,7 +57,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true)
                 ]
                 """
             }
@@ -79,7 +79,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['genome']['genome_gff3'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gff3', checkIfExists: true)
                 ]
                 """
             }
@@ -88,9 +88,9 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert path(process.out.error_log[0][1]).text.contains("gt gff3validator: error:") },
                 { assert process.out.success_log == [] },
-                { assert path(process.out.error_log[0][1]).text.contains("gt gff3validator: error:") }
+                { assert snapshot(process.out).match() },
             )
         }
 
diff --git a/modules/nf-core/gt/ltrharvest/tests/main.nf.test b/modules/nf-core/gt/ltrharvest/tests/main.nf.test
index ec3ba85f83d..f9e1ce13546 100644
--- a/modules/nf-core/gt/ltrharvest/tests/main.nf.test
+++ b/modules/nf-core/gt/ltrharvest/tests/main.nf.test
@@ -21,7 +21,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test' ],
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                     ]
                     input[1] = 'dna'
                     """
@@ -40,8 +40,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -59,7 +58,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test' ],
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                     ]
                     input[1] = 'dna'
                     """
@@ -78,8 +77,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -97,7 +95,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test' ],
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                     ]
                     input[1] = 'dna'
                     """
@@ -116,8 +114,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -132,7 +129,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
@@ -141,8 +138,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -158,7 +154,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
@@ -167,8 +163,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/gt/ltrharvest/tests/main.nf.test.snap b/modules/nf-core/gt/ltrharvest/tests/main.nf.test.snap
index a2f30278257..3f48b6e60db 100644
--- a/modules/nf-core/gt/ltrharvest/tests/main.nf.test.snap
+++ b/modules/nf-core/gt/ltrharvest/tests/main.nf.test.snap
@@ -11,25 +11,25 @@
                     ]
                 ],
                 "1": [
-                    
+
                 ],
                 "2": [
-                    
+
                 ],
                 "3": [
-                    
+
                 ],
                 "4": [
                     "versions.yml:md5,8df72f2f0252e314180bde73e0bbae37"
                 ],
                 "fasta": [
-                    
+
                 ],
                 "gff3": [
-                    
+
                 ],
                 "inner_fasta": [
-                    
+
                 ],
                 "tabout": [
                     [
@@ -46,14 +46,6 @@
         ],
         "timestamp": "2024-01-16T09:42:10.114754"
     },
-    "versions": {
-        "content": [
-            [
-                "versions.yml:md5,8df72f2f0252e314180bde73e0bbae37"
-            ]
-        ],
-        "timestamp": "2024-01-17T11:12:11.954224"
-    },
     "stub": {
         "content": [
             {
@@ -66,25 +58,25 @@
                     ]
                 ],
                 "1": [
-                    
+
                 ],
                 "2": [
-                    
+
                 ],
                 "3": [
-                    
+
                 ],
                 "4": [
                     "versions.yml:md5,8df72f2f0252e314180bde73e0bbae37"
                 ],
                 "fasta": [
-                    
+
                 ],
                 "gff3": [
-                    
+
                 ],
                 "inner_fasta": [
-                    
+
                 ],
                 "tabout": [
                     [
@@ -105,7 +97,7 @@
         "content": [
             {
                 "0": [
-                    
+
                 ],
                 "1": [
                     [
@@ -159,7 +151,7 @@
                     ]
                 ],
                 "tabout": [
-                    
+
                 ],
                 "versions": [
                     "versions.yml:md5,8df72f2f0252e314180bde73e0bbae37"
@@ -172,7 +164,7 @@
         "content": [
             {
                 "0": [
-                    
+
                 ],
                 "1": [
                     [
@@ -226,7 +218,7 @@
                     ]
                 ],
                 "tabout": [
-                    
+
                 ],
                 "versions": [
                     "versions.yml:md5,8df72f2f0252e314180bde73e0bbae37"
@@ -239,7 +231,7 @@
         "content": [
             {
                 "0": [
-                    
+
                 ],
                 "1": [
                     [
@@ -293,7 +285,7 @@
                     ]
                 ],
                 "tabout": [
-                    
+
                 ],
                 "versions": [
                     "versions.yml:md5,8df72f2f0252e314180bde73e0bbae37"
@@ -302,4 +294,4 @@
         ],
         "timestamp": "2024-01-17T11:20:13.665071"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/gt/stat/tests/main.nf.test b/modules/nf-core/gt/stat/tests/main.nf.test
index d1fe2f0d734..5813b540120 100644
--- a/modules/nf-core/gt/stat/tests/main.nf.test
+++ b/modules/nf-core/gt/stat/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
                 """
                 input[0] = Channel.of(
                     "##gff-version 3" +
-                    file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true).text.toLowerCase()
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true).text.toLowerCase()
                 )
                 .collectFile(name: 'sample.gff3', newLine: true)
                 .map { file -> [ [ id:'test' ], file ] }
@@ -43,7 +43,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id: 'test' ],
-                    file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/gt/suffixerator/tests/main.nf.test b/modules/nf-core/gt/suffixerator/tests/main.nf.test
index 6a7079a912c..3f8fb5dd512 100644
--- a/modules/nf-core/gt/suffixerator/tests/main.nf.test
+++ b/modules/nf-core/gt/suffixerator/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    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] = 'dna'
                 """
@@ -28,8 +28,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -42,7 +41,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
                     ]
                 input[1] = 'protein'
                 """
@@ -52,8 +51,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -68,7 +66,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    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] = 'dna'
                 """
@@ -78,8 +76,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -94,7 +91,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    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] = 'protein'
                 """
@@ -104,8 +101,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -118,7 +114,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    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] = 'xyz'
                 """
@@ -143,7 +139,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    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] = 'xyz'
                 """
diff --git a/modules/nf-core/happy/ftxpy/tests/main.nf.test b/modules/nf-core/happy/ftxpy/tests/main.nf.test
index af7a08a3b14..12f7b225207 100644
--- a/modules/nf-core/happy/ftxpy/tests/main.nf.test
+++ b/modules/nf-core/happy/ftxpy/tests/main.nf.test
@@ -18,18 +18,18 @@ nextflow_process {
                 """
                 input[0] = [
                         [ id:'test' ], // meta map
-                        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
                         [],
                         [],
                         []
                         ]
                 input[1] = [
                         [ id:'test2' ], // meta map
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                         ]
                 input[2] = [
                         [ id:'test3' ], // meta map
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
                         ]
                 """
             }
@@ -49,18 +49,18 @@ nextflow_process {
                 """
                 input[0] = [
                         [ id:'test' ], // meta map
-                        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
                         [],
                         [],
-                        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true),
                         ]
                 input[1] = [
                         [ id:'test2' ], // meta map
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                         ]
                 input[2] = [
                         [ id:'test3' ], // meta map
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
                         ]
                 """
             }
@@ -84,18 +84,18 @@ nextflow_process {
                 """
                 input[0] = [
                         [ id:'test' ], // meta map
-                        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
                         [],
                         [],
                         []
                         ]
                 input[1] = [
                         [ id:'test2' ], // meta map
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                         ]
                 input[2] = [
                         [ id:'test3' ], // meta map
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
                         ]
                 """
             }
diff --git a/modules/nf-core/happy/prepy/tests/main.nf.test b/modules/nf-core/happy/prepy/tests/main.nf.test
index 114699777fb..ca79a7d8919 100644
--- a/modules/nf-core/happy/prepy/tests/main.nf.test
+++ b/modules/nf-core/happy/prepy/tests/main.nf.test
@@ -16,16 +16,16 @@ nextflow_process {
                 """
                 input[0] = [
                         [ id:'test' ], // meta map
-                        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
                         ]
                 input[1] = [
                         [ id:'test2' ], // meta map
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                         ]
                 input[2] = [
                         [ id:'test3' ], // meta map
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
                         ]
                 """
             }
@@ -49,16 +49,16 @@ nextflow_process {
                 """
                 input[0] = [
                         [ id:'test' ], // meta map
-                        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
                         []
                         ]
                 input[1] = [
                         [ id:'test2' ], // meta map
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                         ]
                 input[2] = [
                         [ id:'test3' ], // meta map
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
                         ]
                 """
             }
@@ -85,16 +85,16 @@ nextflow_process {
                 """
                 input[0] = [
                         [ id:'test' ], // meta map
-                        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
                         ]
                 input[1] = [
                         [ id:'test2' ], // meta map
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                         ]
                 input[2] = [
                         [ id:'test3' ], // meta map
-                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
                         ]
                 """
             }
diff --git a/modules/nf-core/kalign/align/tests/main.nf.test b/modules/nf-core/kalign/align/tests/main.nf.test
index d90ad9b094f..b359439f6c4 100644
--- a/modules/nf-core/kalign/align/tests/main.nf.test
+++ b/modules/nf-core/kalign/align/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test' ], // meta map
-                          file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+                          file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
                         ]
                 input[1] = false
                 """
@@ -26,7 +26,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - uncompressed")},
+                { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - uncompressed")}
             )
         }
     }
@@ -37,7 +37,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test' ], // meta map
-                          file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+                          file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
                         ]
                 input[1] = true
                 """
@@ -47,7 +47,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - compressed")},
+                { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - compressed")}
             )
         }
     }
diff --git a/modules/nf-core/last/dotplot/tests/main.nf.test b/modules/nf-core/last/dotplot/tests/main.nf.test
index fa5f7679c48..3ea403820d2 100644
--- a/modules/nf-core/last/dotplot/tests/main.nf.test
+++ b/modules/nf-core/last/dotplot/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_process {
                          . collectFile(name: 'dummy_annot_b.bed', newLine: true)
                          . map { [
                                    [ id:'test' ], // meta map
-                                   file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true),
+                                   file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true),
                                    it
                                  ] }
                 input[1] = channel.of('MT192765.1\t1000\t1010')
@@ -46,7 +46,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true),
                     []
                 ]
                 input[1] = [ [id: 'test'], [] ]
@@ -73,7 +73,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true),
                     []
                 ]
                 input[1] = [ [id: 'test'], [] ]
diff --git a/modules/nf-core/last/lastal/tests/main.nf.test b/modules/nf-core/last/lastal/tests/main.nf.test
index b5c073073d7..c98f07f87f7 100644
--- a/modules/nf-core/last/lastal/tests/main.nf.test
+++ b/modules/nf-core/last/lastal/tests/main.nf.test
@@ -20,7 +20,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'genome'], // meta map
-                    file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/lastdb.tar.gz', checkIfExists: true)
                 ]
                 """
                 }
@@ -32,7 +32,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'contigs', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
                     []
                 ]
                 input[1] = UNTAR.out.untar.map{ it[1] }
@@ -58,7 +58,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'genome'], // meta map
-                    file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/lastdb.tar.gz', checkIfExists: true)
                 ]
                 """
                 }
@@ -70,8 +70,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'contigs', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['contigs_genome_par'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.par', checkIfExists: true)
                 ]
                 input[1] = UNTAR.out.untar.map{ it[1] }
                 """
@@ -98,7 +98,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'genome'], // meta map
-                    file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/lastdb.tar.gz', checkIfExists: true)
                 ]
                 """
                 }
@@ -110,7 +110,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'contigs', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
                     []
                 ]
                 input[1] = UNTAR.out.untar.map{ it[1] }
diff --git a/modules/nf-core/last/lastdb/tests/main.nf.test b/modules/nf-core/last/lastdb/tests/main.nf.test
index 2e3aa2b1b25..1d5d403299a 100644
--- a/modules/nf-core/last/lastdb/tests/main.nf.test
+++ b/modules/nf-core/last/lastdb/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
@@ -39,7 +39,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                 ]
                 """
             }
@@ -62,7 +62,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/last/mafconvert/tests/main.nf.test b/modules/nf-core/last/mafconvert/tests/main.nf.test
index 112706b0779..ea21d1f62b6 100644
--- a/modules/nf-core/last/mafconvert/tests/main.nf.test
+++ b/modules/nf-core/last/mafconvert/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'contigs.genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true)
                 ]
                 input[1] = 'psl'
                 """
@@ -40,7 +40,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'contigs.genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true)
                 ]
                 input[1] = 'psl'
                 """
diff --git a/modules/nf-core/last/mafswap/tests/main.nf.test b/modules/nf-core/last/mafswap/tests/main.nf.test
index 7aa7704e598..ae4d7f0ae65 100644
--- a/modules/nf-core/last/mafswap/tests/main.nf.test
+++ b/modules/nf-core/last/mafswap/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'contigs.genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) 
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) 
                 ]
                 """
             }
@@ -39,7 +39,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'contigs.genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/last/postmask/tests/main.nf.test b/modules/nf-core/last/postmask/tests/main.nf.test
index 18cef725f52..8baf45b710f 100644
--- a/modules/nf-core/last/postmask/tests/main.nf.test
+++ b/modules/nf-core/last/postmask/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'sarscov2.contigs.genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true)
                 ]
                 """
             }
@@ -39,7 +39,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'sarscov2.contigs.genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/last/split/tests/main.nf.test b/modules/nf-core/last/split/tests/main.nf.test
index 4460d69096d..0e09941aabb 100644
--- a/modules/nf-core/last/split/tests/main.nf.test
+++ b/modules/nf-core/last/split/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'sarscov.contigs.genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true)
                 ]
                 """
             }
@@ -40,7 +40,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'sarscov.contigs.genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/last/train/tests/main.nf.test b/modules/nf-core/last/train/tests/main.nf.test
index a4168f2a9e9..8325673ae40 100644
--- a/modules/nf-core/last/train/tests/main.nf.test
+++ b/modules/nf-core/last/train/tests/main.nf.test
@@ -19,7 +19,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'genome'], // meta map
-                    file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/lastdb.tar.gz', checkIfExists: true)
                 ]
                 """
                 }
@@ -31,7 +31,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'contigs', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
                 ]
                 input[1] = UNTAR.out.untar.map{ it[1] }
                 """
@@ -56,7 +56,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'genome'], // meta map
-                    file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/lastdb.tar.gz', checkIfExists: true)
                 ]
                 """
                 }
@@ -68,7 +68,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'contigs', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
                 ]
                 input[1] = UNTAR.out.untar.map{ it[1] }
                 """
diff --git a/modules/nf-core/lima/tests/main.nf.test b/modules/nf-core/lima/tests/main.nf.test
index b2cdeb47881..bf7d22c2098 100644
--- a/modules/nf-core/lima/tests/main.nf.test
+++ b/modules/nf-core/lima/tests/main.nf.test
@@ -50,9 +50,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['pacbio']['ccs_fa'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta', checkIfExists: true),
                 ]
-                input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
+                input[1] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true) ]
                 """
             }
         }
@@ -73,9 +73,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['pacbio']['ccs_fa_gz'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz', checkIfExists: true),
                 ]
-                input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
+                input[1] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true) ]
                 """
             }
         }
@@ -96,9 +96,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['pacbio']['ccs_fq'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq', checkIfExists: true),
                 ]
-                input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
+                input[1] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true) ]
                 """
             }
         }
@@ -119,9 +119,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz', checkIfExists: true),
                 ]
-                input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
+                input[1] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true) ]
                 """
             }
         }
@@ -169,9 +169,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['pacbio']['ccs_fa'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta', checkIfExists: true),
                 ]
-                input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
+                input[1] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true) ]
                 """
             }
         }
@@ -194,9 +194,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['pacbio']['ccs_fa_gz'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz', checkIfExists: true),
                 ]
-                input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
+                input[1] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true) ]
                 """
             }
         }
@@ -219,9 +219,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['pacbio']['ccs_fq'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq', checkIfExists: true),
                 ]
-                input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
+                input[1] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true) ]
                 """
             }
         }
@@ -244,9 +244,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz', checkIfExists: true),
                 ]
-                input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ]
+                input[1] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true) ]
                 """
             }
         }
diff --git a/modules/nf-core/mapad/map/tests/main.nf.test b/modules/nf-core/mapad/map/tests/main.nf.test
index f54f46455ca..d240f231b44 100644
--- a/modules/nf-core/mapad/map/tests/main.nf.test
+++ b/modules/nf-core/mapad/map/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [id: 'test'],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -29,7 +29,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map
-                        file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
                         ])
                 input[1] = MAPAD_INDEX.out.index
                 input[2] = 0.03
diff --git a/modules/nf-core/mash/screen/tests/main.nf.test b/modules/nf-core/mash/screen/tests/main.nf.test
index f368b72cea9..6152beafbbf 100644
--- a/modules/nf-core/mash/screen/tests/main.nf.test
+++ b/modules/nf-core/mash/screen/tests/main.nf.test
@@ -19,7 +19,7 @@ nextflow_process {
                     input[0] =
                     [
                         [ id: 'sars_db' ],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                     }
@@ -32,8 +32,8 @@ nextflow_process {
                 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.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 input[1] = MASH_SKETCH.out.mash
@@ -62,7 +62,7 @@ nextflow_process {
                     input[0] =
                     [
                         [ id: 'sars_db' ],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                     }
@@ -75,8 +75,8 @@ nextflow_process {
                 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.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 input[1] = MASH_SKETCH.out.mash
diff --git a/modules/nf-core/mash/sketch/tests/main.nf.test b/modules/nf-core/mash/sketch/tests/main.nf.test
index 5b32d62187f..c73e314492d 100644
--- a/modules/nf-core/mash/sketch/tests/main.nf.test
+++ b/modules/nf-core/mash/sketch/tests/main.nf.test
@@ -17,8 +17,8 @@ nextflow_process {
                 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.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 """
@@ -44,8 +44,8 @@ nextflow_process {
                 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.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 """
diff --git a/modules/nf-core/metamaps/classify/tests/main.nf.test b/modules/nf-core/metamaps/classify/tests/main.nf.test
index 86175f4c3b4..81357bc23ce 100644
--- a/modules/nf-core/metamaps/classify/tests/main.nf.test
+++ b/modules/nf-core/metamaps/classify/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_process {
                     """
                     input[0] = [
                     [ id:'test', single_end:true ], // meta map
-                    file(params.test_data['sarscov2']['nanopore']['test2_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                     input[1] = UNTAR.out.untar.map{ it[1] }
                     """
@@ -84,7 +84,7 @@ nextflow_process {
                     """
                     input[0] = [
                     [ id:'test', single_end:true ], // meta map
-                    file(params.test_data['sarscov2']['nanopore']['test2_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                     input[1] = UNTAR.out.untar.map{ it[1] }
                     """
diff --git a/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test b/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test
index f8a101049c6..7368a3e8302 100644
--- a/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test
+++ b/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test
@@ -31,7 +31,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ], // meta map
-                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
                 ]
                 input[1] = UNTAR.out.untar.map{ it[1] }
                 """
@@ -71,7 +71,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ], // meta map
-                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
                 ]
                 input[1] = UNTAR.out.untar.map{ it[1] }
                 """
diff --git a/modules/nf-core/nanofilt/tests/main.nf.test b/modules/nf-core/nanofilt/tests/main.nf.test
index 098cb16bf7e..13be95e483e 100644
--- a/modules/nf-core/nanofilt/tests/main.nf.test
+++ b/modules/nf-core/nanofilt/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test'], // meta map
-                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
                     ]
                 input[1] = []
                 """
@@ -44,7 +44,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test'], // meta map
-                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
                     ]
                 input[1] = []
                 """
diff --git a/modules/nf-core/narfmap/align/tests/main.nf.test b/modules/nf-core/narfmap/align/tests/main.nf.test
index 367e945184f..a920339b4fe 100644
--- a/modules/nf-core/narfmap/align/tests/main.nf.test
+++ b/modules/nf-core/narfmap/align/tests/main.nf.test
@@ -9,32 +9,32 @@ nextflow_process {
     tag "narfmap/align"
     tag "narfmap/hashtable"
 
-    test("sarscov2 - fastq, hashtable, false") {
-
-        setup {
-            run("NARFMAP_HASHTABLE") {
-                script "../../hashtable/main.nf"
-                process {
-                    """
-                    input[0] = [
-                        [id:'test'],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                    ]
-                    """
-                }
+    setup {
+        run("NARFMAP_HASHTABLE") {
+            script "../../hashtable/main.nf"
+            process {
+                """
+                input[0] = [
+                    [id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
             }
         }
+    }
+
+    test("sarscov2 - fastq, hashtable, false") {
 
         when {
             process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
                 input[2] = [[:],[]]
-                input[3] = false //sort
+                input[3] = false
                 """
             }
         }
@@ -55,30 +55,16 @@ nextflow_process {
 
     test("sarscov2 - fastq, hashtable, true") {
 
-        setup {
-            run("NARFMAP_HASHTABLE") {
-                script "../../hashtable/main.nf"
-                process {
-                    """
-                    input[0] = [
-                        [id:'test'],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                    ]
-                    """
-                }
-            }
-        }
-
         when {
             process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
                 input[2] = [[:],[]]
-                input[3] = true //sort
+                input[3] = true
                 """
             }
         }
@@ -99,33 +85,19 @@ nextflow_process {
 
     test("sarscov2 - [fastq1, fastq2], hashtable, false") {
 
-        setup {
-            run("NARFMAP_HASHTABLE") {
-                script "../../hashtable/main.nf"
-                process {
-                    """
-                    input[0] = [
-                        [id:'test'],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                    ]
-                    """
-                }
-            }
-        }
-
         when {
             process {
                 """
                 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.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
                 input[2] = [[:],[]]
-                input[3] = false //sort
+                input[3] = false
                 """
             }
         }
@@ -146,33 +118,19 @@ nextflow_process {
 
     test("sarscov2 - [fastq1, fastq2], hashtable, true") {
 
-        setup {
-            run("NARFMAP_HASHTABLE") {
-                script "../../hashtable/main.nf"
-                process {
-                    """
-                    input[0] = [
-                        [id:'test'],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                    ]
-                    """
-                }
-            }
-        }
-
         when {
             process {
                 """
                 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.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
                 input[2] = [[:],[]]
-                input[3] = true //sort
+                input[3] = true
                 """
             }
         }
@@ -193,33 +151,19 @@ nextflow_process {
 
     test("homo_sapiens - [fastq1, fastq2], hashtable, true") {
 
-        setup {
-            run("NARFMAP_HASHTABLE") {
-                script "../../hashtable/main.nf"
-                process {
-                    """
-                    input[0] = [
-                        [id:'test'],
-                        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-                    ]
-                    """
-                }
-            }
-        }
-
         when {
             process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
                 input[2] = [[:],[]]
-                input[3] = true //sort
+                input[3] = true
                 """
             }
         }
@@ -241,19 +185,6 @@ nextflow_process {
     test("sarscov2 - [fastq1, fastq2], hashtable, true - stub") {
 
         options "-stub"
-        setup {
-            run("NARFMAP_HASHTABLE") {
-                script "../../hashtable/main.nf"
-                process {
-                    """
-                    input[0] = [
-                        [id:'test'],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                    ]
-                    """
-                }
-            }
-        }
 
         when {
             process {
@@ -261,13 +192,13 @@ nextflow_process {
                 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.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
                 input[2] = [[:],[]]
-                input[3] = true //sort
+                input[3] = true
                 """
             }
         }
@@ -287,30 +218,16 @@ nextflow_process {
 
     test("sarscov2 - CRAM") {
 
-        setup {
-            run("NARFMAP_HASHTABLE") {
-                script "../../hashtable/main.nf"
-                process {
-                    """
-                    input[0] = [
-                        [id:'test'],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                    ]
-                    """
-                }
-            }
-        }
-
         when {
             process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
                 input[2] = [[id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
-                input[3] = true //sort
+                input[3] = true
                 """
             }
         }
diff --git a/modules/nf-core/narfmap/align/tests/main.nf.test.snap b/modules/nf-core/narfmap/align/tests/main.nf.test.snap
index fbf14bddf34..aaaed31c86f 100644
--- a/modules/nf-core/narfmap/align/tests/main.nf.test.snap
+++ b/modules/nf-core/narfmap/align/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.bam:md5,5c407c8e621fc931af17a585526598bf"
+                    "test.bam:md5,54965e6a11a9c31b1ae3c7e896c96c32"
                 ]
             ],
             [
@@ -23,10 +23,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-07-08T12:31:24.171738358"
+        "timestamp": "2024-07-29T08:01:47.52644852"
     },
     "sarscov2 - [fastq1, fastq2], hashtable, true - stub": {
         "content": [
diff --git a/modules/nf-core/narfmap/hashtable/tests/main.nf.test b/modules/nf-core/narfmap/hashtable/tests/main.nf.test
index 2ba42803911..9e88428e3dd 100644
--- a/modules/nf-core/narfmap/hashtable/tests/main.nf.test
+++ b/modules/nf-core/narfmap/hashtable/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'test'],
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
@@ -44,7 +44,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'test'],
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/oatk/tests/main.nf.test b/modules/nf-core/oatk/tests/main.nf.test
index 7061ac7148f..88d87a7e843 100644
--- a/modules/nf-core/oatk/tests/main.nf.test
+++ b/modules/nf-core/oatk/tests/main.nf.test
@@ -19,8 +19,8 @@ nextflow_process {
             }
             process {
                     """
-                    input[0] = Channel.of([[id:"ilDeiPorc1"],file(params.test_data['deilephila_porcellus']['mito']['hifi_reads'], checkIfExists: true)])
-                    
+                    input[0] = Channel.of([[id:"ilDeiPorc1"],file(params.modules_testdata_base_path + 'genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.HiFi.reads.fa', checkIfExists: true)])
+
                     hmm = file("https://raw.githubusercontent.com/c-zhou/OatkDB/main/v20230921/insecta_mito.fam", checkIfExists: true)
                     hmm_h3f = file("https://github.com/c-zhou/OatkDB/raw/main/v20230921/insecta_mito.fam.h3f", checkIfExists: true)
                     hmm_h3i = file("https://github.com/c-zhou/OatkDB/raw/main/v20230921/insecta_mito.fam.h3i", checkIfExists: true)
@@ -29,24 +29,27 @@ nextflow_process {
                     input[1] = Channel.of([hmm, hmm_h3f, hmm_h3i, hmm_h3m, hmm_h3p])
                     input[2] = [[],[],[],[],[]]
                     """
-            } 
+            }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.mito_fasta).match("mito_fasta") },
                 { assert process.out.final_gfa.get(0).get(1) ==~ '.*utg.final.gfa' } ,
-                { assert snapshot(process.out.mito_bed).match("mito_bed") }, 
-                { assert snapshot(process.out.mito_gfa).match("mito_gfa") }, 
                 { assert process.out.initial_gfa.get(0).get(1) ==~ '.*utg.gfa' } ,
                 { assert process.out.annot_mito_txt[0][1] ==~ ".*annot_mito.txt" },
-                { assert snapshot(process.out.versions).match("versions") } 
+                { assert snapshot(
+                    process.out.mito_bed,
+                    process.out.mito_fasta,
+                    process.out.mito_gfa,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
 
     }
-    
+
     test("test_oatk_pltd") {
         tag "test_oatk_pltd"
 
@@ -57,8 +60,8 @@ nextflow_process {
             }
             process {
                     """
-                    input[0] = Channel.of([[id:"ddAraThal4"],file(params.test_data['arabidopsis_thaliana']['plastid']['hifi_reads'], checkIfExists: true)])
-                    
+                    input[0] = Channel.of([[id:"ddAraThal4"],file(params.modules_testdata_base_path + 'genomics/eukaryotes/arabidopsis_thaliana/plastid/ddAraThal4.HiFi.reads.fasta', checkIfExists: true)])
+
                     input[1] = [[],[],[],[],[]]
                     hmm = file("https://github.com/c-zhou/OatkDB/raw/main/v20230921/embryophyta_pltd.fam", checkIfExists: true)
                     hmm_h3f = file("https://github.com/c-zhou/OatkDB/raw/main/v20230921/embryophyta_pltd.fam.h3f", checkIfExists: true)
@@ -67,19 +70,22 @@ nextflow_process {
                     hmm_h3p = file("https://github.com/c-zhou/OatkDB/raw/main/v20230921/embryophyta_pltd.fam.h3p", checkIfExists: true)
                     input[2] = Channel.of([hmm, hmm_h3f, hmm_h3i, hmm_h3m, hmm_h3p])
                     """
-            } 
+            }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.pltd_fasta).match("pltd_fasta") },
                 { assert process.out.final_gfa.get(0).get(1) ==~ '.*utg.final.gfa' } ,
-                { assert snapshot(process.out.pltd_bed).match("pltd_bed") }, 
-                { assert snapshot(process.out.pltd_gfa).match("pltd_gfa") }, 
                 { assert process.out.initial_gfa.get(0).get(1) ==~ '.*utg.gfa' } ,
                 { assert process.out.annot_pltd_txt[0][1] ==~ ".*annot_pltd.txt" },
-                { assert snapshot(process.out.versions).match("versions") } 
+                { assert snapshot(
+                    process.out.pltd_bed,
+                    process.out.pltd_fasta,
+                    process.out.pltd_gfa,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
 
diff --git a/modules/nf-core/oatk/tests/main.nf.test.snap b/modules/nf-core/oatk/tests/main.nf.test.snap
index 1fc056965bf..bef3545bb47 100644
--- a/modules/nf-core/oatk/tests/main.nf.test.snap
+++ b/modules/nf-core/oatk/tests/main.nf.test.snap
@@ -1,88 +1,74 @@
 {
-    "mito_bed": {
+    "test_oatk_pltd": {
         "content": [
             [
                 [
                     {
-                        "id": "ilDeiPorc1"
+                        "id": "ddAraThal4"
                     },
-                    "ilDeiPorc1.mito.ctg.bed:md5,177c87cb89996306611f6e74dba2ff60"
+                    "ddAraThal4.pltd.ctg.bed:md5,f5925e6ec605b83547b9c72fae6f7087"
                 ]
-            ]
-        ],
-        "timestamp": "2024-01-22T11:28:03.325434126"
-    },
-    "mito_gfa": {
-        "content": [
+            ],
             [
                 [
                     {
-                        "id": "ilDeiPorc1"
+                        "id": "ddAraThal4"
                     },
-                    "ilDeiPorc1.mito.gfa:md5,88a058195aad319f57a330acea5357c5"
+                    "ddAraThal4.pltd.ctg.fasta:md5,88cf092fd935801029a26bf88f6063bf"
                 ]
-            ]
-        ],
-        "timestamp": "2024-01-22T11:28:03.334475394"
-    },
-    "versions": {
-        "content": [
-            [
-                "versions.yml:md5,bc3c4d7a42644e2c0d71422677a7d915"
-            ]
-        ],
-        "timestamp": "2024-01-22T11:28:03.361579579"
-    },
-    "mito_fasta": {
-        "content": [
+            ],
             [
                 [
                     {
-                        "id": "ilDeiPorc1"
+                        "id": "ddAraThal4"
                     },
-                    "ilDeiPorc1.mito.ctg.fasta:md5,822b20d9e8f13591cb3a7474fda97402"
+                    "ddAraThal4.pltd.gfa:md5,9749ffa1ebbf6b71fd7c9e8b410d64d4"
                 ]
+            ],
+            [
+                "versions.yml:md5,bc3c4d7a42644e2c0d71422677a7d915"
             ]
         ],
-        "timestamp": "2024-01-22T11:28:03.305999918"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T16:28:09.782502"
     },
-    "pltd_bed": {
+    "test_oatk_mito": {
         "content": [
             [
                 [
                     {
-                        "id": "ddAraThal4"
+                        "id": "ilDeiPorc1"
                     },
-                    "ddAraThal4.pltd.ctg.bed:md5,f5925e6ec605b83547b9c72fae6f7087"
+                    "ilDeiPorc1.mito.ctg.bed:md5,177c87cb89996306611f6e74dba2ff60"
                 ]
-            ]
-        ],
-        "timestamp": "2024-01-22T11:28:15.844572574"
-    },
-    "pltd_gfa": {
-        "content": [
+            ],
             [
                 [
                     {
-                        "id": "ddAraThal4"
+                        "id": "ilDeiPorc1"
                     },
-                    "ddAraThal4.pltd.gfa:md5,9749ffa1ebbf6b71fd7c9e8b410d64d4"
+                    "ilDeiPorc1.mito.ctg.fasta:md5,822b20d9e8f13591cb3a7474fda97402"
                 ]
-            ]
-        ],
-        "timestamp": "2024-01-22T11:28:15.860281161"
-    },
-    "pltd_fasta": {
-        "content": [
+            ],
             [
                 [
                     {
-                        "id": "ddAraThal4"
+                        "id": "ilDeiPorc1"
                     },
-                    "ddAraThal4.pltd.ctg.fasta:md5,88cf092fd935801029a26bf88f6063bf"
+                    "ilDeiPorc1.mito.gfa:md5,88a058195aad319f57a330acea5357c5"
                 ]
+            ],
+            [
+                "versions.yml:md5,bc3c4d7a42644e2c0d71422677a7d915"
             ]
         ],
-        "timestamp": "2024-01-22T11:28:15.81801003"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T16:27:44.199733"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/pairtools/split/tests/main.nf.test b/modules/nf-core/pairtools/split/tests/main.nf.test
index c364d0fe364..ad050dec984 100644
--- a/modules/nf-core/pairtools/split/tests/main.nf.test
+++ b/modules/nf-core/pairtools/split/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test', single_end:false ], // meta map
-                            file(params.test_data['generic']['pairtools']['mock_pairsam'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.pairsam', checkIfExists: true)
                        ]
                 """
             }
@@ -40,7 +40,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test', single_end:false ], // meta map
-                            file(params.test_data['generic']['pairtools']['mock_pairsam'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.pairsam', checkIfExists: true)
                        ]
                 """
             }
diff --git a/modules/nf-core/pear/tests/main.nf.test b/modules/nf-core/pear/tests/main.nf.test
index fffd3fd3312..31173d1cc10 100644
--- a/modules/nf-core/pear/tests/main.nf.test
+++ b/modules/nf-core/pear/tests/main.nf.test
@@ -16,8 +16,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test' ], // 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.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 """
diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
index 94713c0f965..3bbbd8cf5ca 100644
--- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
+++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
@@ -16,14 +16,14 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
                     ]
-                input[1] = [[id:'genome'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
-                input[2] = [[id:'genome'], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)]
-                input[3] = [[id:'genome'], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)]
+                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
+                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
                 """
             }
         }
@@ -55,14 +55,14 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
                     ]
-                input[1] = [[id:'genome'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
-                input[2] = [[id:'genome'], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)]
-                input[3] = [[id:'genome'], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)]
+                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
+                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
                 """
             }
         }
@@ -83,10 +83,10 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
                     ]
                 input[1] = [[:],[]]
                 input[2] = [[:],[]]
@@ -120,15 +120,15 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
                     ]
 
-                input[1] = [[id:'genome'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
-                input[2] = [[id:'genome'], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)]
-                input[3] = [[id:'genome'], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)]
+                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
+                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
                 """
             }
         }
@@ -158,15 +158,15 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true)
                     ]
 
-                input[1] = [[id:'genome'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
-                input[2] = [[id:'genome'], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)]
-                input[3] = [[id:'genome'], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)]
+                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
+                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
                 """
             }
         }
diff --git a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test
index 7a552e7a63c..33eb40de6fa 100644
--- a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test
+++ b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test
@@ -18,16 +18,16 @@ nextflow_process {
                 input[0] = [
                             [ id:'test', single_end:false ], //meta
                             [
-                                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true)
                             ],  // input1
                             [
-                                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai', checkIfExists: true)
                             ], // input1_index
                             [], // input2
                             [], // input2_index
-                            file(params.test_data['homo_sapiens']['genome']['haplotype_map'], checkIfExists: true) // haplotype_map
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt', checkIfExists: true) // haplotype_map
                         ]
                 input[1] = [[:],[]]
                 """
@@ -53,16 +53,16 @@ nextflow_process {
                 input[0] = [
                             [ id:'test', single_end:false ], //meta
                             [
-                                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true)
                             ],  // input1
                             [
-                                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai', checkIfExists: true)
                             ], // input1_index
                             [], // input2
                             [], // input2_index
-                            file(params.test_data['homo_sapiens']['genome']['haplotype_map'], checkIfExists: true) // haplotype_map
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt', checkIfExists: true) // haplotype_map
                         ]
                 input[1] = [[:],[]]
                 """
diff --git a/modules/nf-core/picard/extractfingerprint/tests/main.nf.test b/modules/nf-core/picard/extractfingerprint/tests/main.nf.test
index 13f8534009b..065e3909aee 100644
--- a/modules/nf-core/picard/extractfingerprint/tests/main.nf.test
+++ b/modules/nf-core/picard/extractfingerprint/tests/main.nf.test
@@ -17,13 +17,13 @@ nextflow_process {
                 """
                 bam = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
                 ]
-                fasta = [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]
-                fai   = [file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]
-                dict  = [file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]
-                haplotype_map  = [file(params.test_data['homo_sapiens']['genome']['haplotype_map'], checkIfExists: true)]
+                fasta = [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
+                fai   = [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
+                dict  = [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]
+                haplotype_map  = [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt', checkIfExists: true)]
 
                 input[0] = bam
                 input[1] = haplotype_map
diff --git a/modules/nf-core/pigz/compress/tests/main.nf.test b/modules/nf-core/pigz/compress/tests/main.nf.test
index 248d40fb78c..b3cb25e3667 100644
--- a/modules/nf-core/pigz/compress/tests/main.nf.test
+++ b/modules/nf-core/pigz/compress/tests/main.nf.test
@@ -14,7 +14,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test'], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                 """
             }
@@ -34,7 +34,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test'], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                 """
             }
@@ -42,7 +42,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.archive[0][1]).name).match() }
+                { assert snapshot(
+                    file(process.out.archive[0][1]).name,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
diff --git a/modules/nf-core/pigz/compress/tests/main.nf.test.snap b/modules/nf-core/pigz/compress/tests/main.nf.test.snap
index 6e50456f3db..4d8df9f1bb3 100644
--- a/modules/nf-core/pigz/compress/tests/main.nf.test.snap
+++ b/modules/nf-core/pigz/compress/tests/main.nf.test.snap
@@ -26,12 +26,23 @@
                 ]
             }
         ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
         "timestamp": "2023-12-11T22:39:53.350546"
     },
     "sarscov2 - genome - fasta - stub": {
         "content": [
-            "genome.fasta.gz"
+            "genome.fasta.gz",
+            [
+                "versions.yml:md5,ca30e9e1ffa1394ba7eefdac8cf3a3ad"
+            ]
         ],
-        "timestamp": "2023-12-11T22:52:24.309192"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T12:18:32.339508"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/pigz/uncompress/tests/main.nf.test b/modules/nf-core/pigz/uncompress/tests/main.nf.test
index b079098262b..62ab27e2b64 100644
--- a/modules/nf-core/pigz/uncompress/tests/main.nf.test
+++ b/modules/nf-core/pigz/uncompress/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test'],
-                                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                             ]
                 """
             }
diff --git a/modules/nf-core/plink/epistasis/main.nf b/modules/nf-core/plink/epistasis/main.nf
index a407cde1d23..1020ee3bd15 100644
--- a/modules/nf-core/plink/epistasis/main.nf
+++ b/modules/nf-core/plink/epistasis/main.nf
@@ -55,7 +55,7 @@ process PLINK_EPISTASIS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        plink: \$(samtools --version |& sed '1!d ; s/samtools //')
+        plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
     END_VERSIONS
     """
 
diff --git a/modules/nf-core/plink/epistasis/tests/main.nf.test b/modules/nf-core/plink/epistasis/tests/main.nf.test
index b178db561ea..8e75f355739 100644
--- a/modules/nf-core/plink/epistasis/tests/main.nf.test
+++ b/modules/nf-core/plink/epistasis/tests/main.nf.test
@@ -21,12 +21,12 @@ nextflow_process {
                 input[0] = [ [id:"null"], [], [], []]
                 input[1] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.vcf.gz', checkIfExists: true)
                 ]
                 input[2] = [ [id:"null"], []]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phe'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.phe', checkIfExists: true)
                 ]
                 """
             }
@@ -34,13 +34,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.version).match("version") },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.epi,
                     process.out.episummary,
-                    process.out.nosex
-                    ).match() },
-                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.nosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -58,12 +59,12 @@ nextflow_process {
                 input[0] = [ [id:"null"], [], [], []]
                 input[1] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.vcf.gz', checkIfExists: true)
                 ]
                 input[2] = [ [id:"null"], []]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phenoname'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated_phenoname.phe', checkIfExists: true)
                 ]
                 """
             }
@@ -71,12 +72,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.epi,
                     process.out.episummary,
-                    process.out.nosex
-                    ).match() },
-                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.nosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -93,9 +96,9 @@ nextflow_process {
                 """
                 input[0] = [
                         [id:"test"],
-                        file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bed'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bim'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['popgen']['plink_case_control_fam'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
                 ]
                 input[1] = [ [id:"null"], []]
                 input[2] = [ [id:"null"], []]
@@ -106,12 +109,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.epi,
                     process.out.episummary,
-                    process.out.nosex
-                    ).match() },
-                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.nosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -130,11 +135,11 @@ nextflow_process {
                 input[1] = [ [id:"null"], []]
                 input[2] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bcf.gz', checkIfExists: true)
                 ]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phe'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.phe', checkIfExists: true)
                 ]
                 """
             }
@@ -142,12 +147,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.epi,
                     process.out.episummary,
-                    process.out.nosex
-                    ).match() },
-                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.nosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -165,12 +172,12 @@ nextflow_process {
                 input[0] = [ [id:"null"], [], [], []]
                 input[1] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.vcf.gz', checkIfExists: true)
                 ]
                 input[2] = [ [id:"null"], []]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phenoname'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated_phenoname.phe', checkIfExists: true)
                 ]
                 """
             }
@@ -178,12 +185,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.epi,
                     process.out.episummary,
-                    process.out.nosex
-                    ).match() },
-                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.nosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
diff --git a/modules/nf-core/plink/epistasis/tests/main.nf.test.snap b/modules/nf-core/plink/epistasis/tests/main.nf.test.snap
index 151792673ad..af21eed8f95 100644
--- a/modules/nf-core/plink/epistasis/tests/main.nf.test.snap
+++ b/modules/nf-core/plink/epistasis/tests/main.nf.test.snap
@@ -24,13 +24,16 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,ecc19d016e365a8c5d625dfc5f381cf1"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-22T15:44:06.676203832"
+        "timestamp": "2024-07-30T18:22:17.817238"
     },
     "plink - BCF with phenotype name": {
         "content": [
@@ -57,13 +60,16 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,ecc19d016e365a8c5d625dfc5f381cf1"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-22T15:44:36.743772181"
+        "timestamp": "2024-07-30T18:22:22.418078"
     },
     "plink - VCF with phenotype name": {
         "content": [
@@ -90,13 +96,16 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,ecc19d016e365a8c5d625dfc5f381cf1"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-22T15:43:29.573025062"
+        "timestamp": "2024-07-30T18:22:08.177602"
     },
     "plink - binary": {
         "content": [
@@ -118,13 +127,16 @@
             ],
             [
                 
+            ],
+            [
+                "versions.yml:md5,ecc19d016e365a8c5d625dfc5f381cf1"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-22T15:43:51.26229668"
+        "timestamp": "2024-07-30T18:22:13.263003"
     },
     "plink - VCF": {
         "content": [
@@ -151,20 +163,15 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,ecc19d016e365a8c5d625dfc5f381cf1"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-22T15:43:14.573129885"
-    },
-    "version": {
-        "content": null,
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-22T15:43:14.558983227"
+        "timestamp": "2024-07-30T18:22:03.126913"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/plink/fastepistasis/main.nf b/modules/nf-core/plink/fastepistasis/main.nf
index 8bdd30b1322..bf46d3c44e3 100644
--- a/modules/nf-core/plink/fastepistasis/main.nf
+++ b/modules/nf-core/plink/fastepistasis/main.nf
@@ -55,7 +55,7 @@ process PLINK_FASTEPISTASIS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        plink: \$(samtools --version |& sed '1!d ; s/samtools //')
+        plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
     END_VERSIONS
     """
 
diff --git a/modules/nf-core/plink/fastepistasis/tests/main.nf.test b/modules/nf-core/plink/fastepistasis/tests/main.nf.test
index ac234c4b494..e4e43375604 100644
--- a/modules/nf-core/plink/fastepistasis/tests/main.nf.test
+++ b/modules/nf-core/plink/fastepistasis/tests/main.nf.test
@@ -21,12 +21,12 @@ nextflow_process {
                 input[0] = [ [id:"null"], [], [], []]
                 input[1] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.vcf.gz', checkIfExists: true)
                 ]
                 input[2] = [ [id:"null"], []]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phe'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.phe', checkIfExists: true)
                 ]
                 """
             }
@@ -34,13 +34,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.version).match("version") },
+                { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.fepi,
                     process.out.fepisummary,
-                    process.out.fnosex
-                    ).match() },
-                { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.fnosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -58,12 +59,12 @@ nextflow_process {
                 input[0] = [ [id:"null"], [], [], []]
                 input[1] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.vcf.gz', checkIfExists: true)
                 ]
                 input[2] = [ [id:"null"], []]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phenoname'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated_phenoname.phe', checkIfExists: true)
                 ]
                 """
             }
@@ -71,12 +72,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.fepi,
                     process.out.fepisummary,
-                    process.out.fnosex
-                    ).match() },
-                { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.fnosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -93,9 +96,9 @@ nextflow_process {
                 """
                 input[0] = [
                         [id:"test"],
-                        file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bed'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bim'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['popgen']['plink_case_control_fam'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
                 ]
                 input[1] = [ [id:"null"], []]
                 input[2] = [ [id:"null"], []]
@@ -106,12 +109,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.fepi,
                     process.out.fepisummary,
-                    process.out.fnosex
-                    ).match() },
-                { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.fnosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -130,11 +135,11 @@ nextflow_process {
                 input[1] = [ [id:"null"], []]
                 input[2] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bcf.gz', checkIfExists: true)
                 ]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phe'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.phe', checkIfExists: true)
                 ]
                 """
             }
@@ -142,12 +147,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.fepi,
                     process.out.fepisummary,
-                    process.out.fnosex
-                    ).match() },
-                { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.fnosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -165,12 +172,12 @@ nextflow_process {
                 input[0] = [ [id:"null"], [], [], []]
                 input[1] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.vcf.gz', checkIfExists: true)
                 ]
                 input[2] = [ [id:"null"], []]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phenoname'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated_phenoname.phe', checkIfExists: true)
                 ]
                 """
             }
@@ -178,12 +185,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.fepi,
                     process.out.fepisummary,
-                    process.out.fnosex
-                    ).match() },
-                { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.fnosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
diff --git a/modules/nf-core/plink/fastepistasis/tests/main.nf.test.snap b/modules/nf-core/plink/fastepistasis/tests/main.nf.test.snap
index 919ae910d2c..86f4d344e12 100644
--- a/modules/nf-core/plink/fastepistasis/tests/main.nf.test.snap
+++ b/modules/nf-core/plink/fastepistasis/tests/main.nf.test.snap
@@ -24,13 +24,16 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,bb3141f8ba161f147c0b705025f7ee90"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-25T15:54:18.804673977"
+        "timestamp": "2024-07-30T18:10:34.769209"
     },
     "plink - BCF with phenotype name": {
         "content": [
@@ -57,13 +60,16 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,bb3141f8ba161f147c0b705025f7ee90"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-25T15:54:28.893162946"
+        "timestamp": "2024-07-30T18:10:39.897157"
     },
     "plink - VCF with phenotype name": {
         "content": [
@@ -90,13 +96,16 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,bb3141f8ba161f147c0b705025f7ee90"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-25T15:53:56.070572393"
+        "timestamp": "2024-07-30T18:10:23.305229"
     },
     "plink - binary": {
         "content": [
@@ -118,13 +127,16 @@
             ],
             [
                 
+            ],
+            [
+                "versions.yml:md5,bb3141f8ba161f147c0b705025f7ee90"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-25T15:54:08.487963135"
+        "timestamp": "2024-07-30T18:10:29.480795"
     },
     "plink - VCF": {
         "content": [
@@ -151,20 +163,15 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,bb3141f8ba161f147c0b705025f7ee90"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-25T15:53:44.711384951"
-    },
-    "version": {
-        "content": null,
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-25T15:53:44.699910482"
+        "timestamp": "2024-07-30T18:10:17.534118"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/plink/gwas/tests/main.nf.test b/modules/nf-core/plink/gwas/tests/main.nf.test
index 89529f3376c..38236e13412 100644
--- a/modules/nf-core/plink/gwas/tests/main.nf.test
+++ b/modules/nf-core/plink/gwas/tests/main.nf.test
@@ -21,12 +21,12 @@ nextflow_process {
                 input[0] = [ [id:"null"], [], [], []]
                 input[1] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.vcf.gz', checkIfExists: true)
                 ]
                 input[2] = [ [id:"null"], []]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phe'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.phe', checkIfExists: true)
                 ]
                 """
             }
@@ -35,11 +35,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.assoc,
-                    process.out.nosex
-                    ).match() },
-                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.nosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -57,12 +59,12 @@ nextflow_process {
                 input[0] = [ [id:"null"], [], [], []]
                 input[1] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.vcf.gz', checkIfExists: true)
                 ]
                 input[2] = [ [id:"null"], []]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phenoname'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated_phenoname.phe', checkIfExists: true)
                 ]
                 """
             }
@@ -71,11 +73,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.assoc,
-                    process.out.nosex
-                    ).match() },
-                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.nosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -92,9 +96,9 @@ nextflow_process {
                 """
                 input[0] = [
                         [id:"test"],
-                        file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bed'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bim'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['popgen']['plink_case_control_fam'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
                 ]
                 input[1] = [ [id:"null"], []]
                 input[2] = [ [id:"null"], []]
@@ -106,8 +110,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.assoc).match() },
-                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" },
+                { assert snapshot(
+                    process.out.assoc,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -126,11 +134,11 @@ nextflow_process {
                 input[1] = [ [id:"null"], []]
                 input[2] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bcf.gz', checkIfExists: true)
                 ]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phe'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.phe', checkIfExists: true)
                 ]
                 """
             }
@@ -139,11 +147,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.assoc,
-                    process.out.nosex
-                    ).match() },
-                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.nosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -161,12 +171,12 @@ nextflow_process {
                 input[0] = [ [id:"null"], [], [], []]
                 input[1] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.vcf.gz', checkIfExists: true)
                 ]
                 input[2] = [ [id:"null"], []]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phenoname'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated_phenoname.phe', checkIfExists: true)
                 ]
                 """
             }
@@ -175,11 +185,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.assoc,
-                    process.out.nosex
-                    ).match() },
-                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.nosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
diff --git a/modules/nf-core/plink/gwas/tests/main.nf.test.snap b/modules/nf-core/plink/gwas/tests/main.nf.test.snap
index 7dc5749b175..3a0c7507301 100644
--- a/modules/nf-core/plink/gwas/tests/main.nf.test.snap
+++ b/modules/nf-core/plink/gwas/tests/main.nf.test.snap
@@ -16,13 +16,16 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,6201877470ebd48d6b5cb97ca0641641"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-22T13:55:49.239817224"
+        "timestamp": "2024-07-30T18:03:08.363934"
     },
     "plink - BCF with phenotype name": {
         "content": [
@@ -41,13 +44,16 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,6201877470ebd48d6b5cb97ca0641641"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-22T13:56:02.903429935"
+        "timestamp": "2024-07-30T18:01:33.223256"
     },
     "plink - VCF with phenotype name": {
         "content": [
@@ -66,13 +72,16 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,6201877470ebd48d6b5cb97ca0641641"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-22T13:55:30.436423207"
+        "timestamp": "2024-07-30T18:01:15.485141"
     },
     "plink - binary": {
         "content": [
@@ -83,13 +92,16 @@
                     },
                     "test.assoc:md5,ab8f91519a605cd9f2b2f89e18c3df9b"
                 ]
+            ],
+            [
+                "versions.yml:md5,6201877470ebd48d6b5cb97ca0641641"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-22T13:55:40.069724205"
+        "timestamp": "2024-07-30T18:01:22.136918"
     },
     "plink - VCF": {
         "content": [
@@ -108,12 +120,15 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,6201877470ebd48d6b5cb97ca0641641"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-22T13:55:18.428110102"
+        "timestamp": "2024-07-30T18:01:09.222434"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/plink/hwe/main.nf b/modules/nf-core/plink/hwe/main.nf
index 5f521fa83c8..bda1274c83c 100644
--- a/modules/nf-core/plink/hwe/main.nf
+++ b/modules/nf-core/plink/hwe/main.nf
@@ -14,8 +14,8 @@ process PLINK_HWE {
 
 
     output:
-    tuple val(meta), path("*.hwe"), emit: hwe
-    path "versions.yml"              , emit: versions
+    tuple val(meta), path("*.hwe")      , emit: hwe
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/plink/hwe/tests/main.nf.test b/modules/nf-core/plink/hwe/tests/main.nf.test
index 5f70fd41714..474c8eda9a1 100644
--- a/modules/nf-core/plink/hwe/tests/main.nf.test
+++ b/modules/nf-core/plink/hwe/tests/main.nf.test
@@ -19,7 +19,7 @@ nextflow_process {
                 input[0] = [ [id:"null"], [], [], []]
                 input[1] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.vcf.gz', checkIfExists: true)
                 ]
                 input[2] = [ [id:"null"], []]
                 """
@@ -28,8 +28,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.version).match("version") },
-                { assert snapshot(process.out.hwe).match() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -44,9 +43,9 @@ nextflow_process {
                 """
                 input[0] = [
                         [id:"test"],
-                        file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bed'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bim'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['popgen']['plink_case_control_fam'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
                 ]
                 input[1] = [ [id:"null"], []]
                 input[2] = [ [id:"null"], []]
@@ -56,7 +55,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.hwe).match() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -73,7 +72,7 @@ nextflow_process {
                 input[1] = [ [id:"null"], []]
                 input[2] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bcf.gz', checkIfExists: true)
                 ]
                 """
             }
@@ -81,7 +80,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.hwe).match() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/modules/nf-core/plink/hwe/tests/main.nf.test.snap b/modules/nf-core/plink/hwe/tests/main.nf.test.snap
index 4d9907e69ea..d89067a8c53 100644
--- a/modules/nf-core/plink/hwe/tests/main.nf.test.snap
+++ b/modules/nf-core/plink/hwe/tests/main.nf.test.snap
@@ -1,61 +1,101 @@
 {
     "plink - BCF": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.hwe:md5,41eee2205e83463d1bf6fefed2ea663e"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.hwe:md5,41eee2205e83463d1bf6fefed2ea663e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7b957939528f3a12d7d8e9988f7f6dcd"
+                ],
+                "hwe": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.hwe:md5,41eee2205e83463d1bf6fefed2ea663e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7b957939528f3a12d7d8e9988f7f6dcd"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-11T16:21:44.80953873"
+        "timestamp": "2024-07-30T17:56:01.116096"
     },
     "plink - binary": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.hwe:md5,23c235dea4f587c0348703c2eac84d84"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.hwe:md5,23c235dea4f587c0348703c2eac84d84"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7b957939528f3a12d7d8e9988f7f6dcd"
+                ],
+                "hwe": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.hwe:md5,23c235dea4f587c0348703c2eac84d84"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7b957939528f3a12d7d8e9988f7f6dcd"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-11T16:17:35.872152911"
+        "timestamp": "2024-07-30T17:55:54.21925"
     },
     "plink - VCF": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.hwe:md5,41eee2205e83463d1bf6fefed2ea663e"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.hwe:md5,41eee2205e83463d1bf6fefed2ea663e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7b957939528f3a12d7d8e9988f7f6dcd"
+                ],
+                "hwe": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.hwe:md5,41eee2205e83463d1bf6fefed2ea663e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7b957939528f3a12d7d8e9988f7f6dcd"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-15T14:02:26.089453664"
-    },
-    "version": {
-        "content": null,
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-11T16:12:19.889326788"
+        "timestamp": "2024-07-30T17:55:46.409999"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/plink/ld/tests/main.nf.test b/modules/nf-core/plink/ld/tests/main.nf.test
index 66384aae897..ca5fb86e273 100644
--- a/modules/nf-core/plink/ld/tests/main.nf.test
+++ b/modules/nf-core/plink/ld/tests/main.nf.test
@@ -20,12 +20,12 @@ nextflow_process {
                 input[0] = [ [id:"null"], [], [], []]
                 input[1] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.vcf.gz', checkIfExists: true)
                     ]
                 input[2] = [ [id:"null"], []]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_random_selected_snp'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_random_selected_snp.txt', checkIfExists: true)
                     ]
                 """
             }
@@ -33,12 +33,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.version).match("version") },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.ld,
-                    process.out.nosex
-                    ).match() },
-                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.nosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -53,15 +54,15 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bed'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bim'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_fam'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
                     ]
                 input[1] = [ [id:"null"], []]
                 input[2] = [ [id:"null"], []]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_random_selected_snp'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_random_selected_snp.txt', checkIfExists: true)
                     ]
                 """
             }
@@ -69,10 +70,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
-                    process.out.ld
-                ).match() },
-            { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.ld,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -89,11 +92,11 @@ nextflow_process {
                 input[1] = [ [id:"null"], []]
                 input[2] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bcf.gz', checkIfExists: true)
                     ]
                 input[3] = [
                     [id:"test"],
-                    file(params.test_data['homo_sapiens']['popgen']['plink_random_selected_snp'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_random_selected_snp.txt', checkIfExists: true)
                     ]
                 """
             }
@@ -101,11 +104,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" },
                 { assert snapshot(
                     process.out.ld,
-                    process.out.nosex
-                    ).match() },
-                { assert process.out.log.get(0).get(1) ==~ ".*/*.log" }
+                    process.out.nosex,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
diff --git a/modules/nf-core/plink/ld/tests/main.nf.test.snap b/modules/nf-core/plink/ld/tests/main.nf.test.snap
index fccd93e6b4d..3badf481811 100644
--- a/modules/nf-core/plink/ld/tests/main.nf.test.snap
+++ b/modules/nf-core/plink/ld/tests/main.nf.test.snap
@@ -16,13 +16,16 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,123cceed9f2bb99eedfe3e15b2087a07"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-22T13:56:51.1545332"
+        "timestamp": "2024-07-30T17:44:30.177855"
     },
     "plink - binary": {
         "content": [
@@ -33,13 +36,16 @@
                     },
                     "test.ld:md5,647636ceb985a3ff66b17c79004d284f"
                 ]
+            ],
+            [
+                "versions.yml:md5,123cceed9f2bb99eedfe3e15b2087a07"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-22T13:56:40.371392669"
+        "timestamp": "2024-07-30T17:44:23.476975"
     },
     "plink - VCF": {
         "content": [
@@ -58,20 +64,15 @@
                     },
                     "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9"
                 ]
+            ],
+            [
+                "versions.yml:md5,123cceed9f2bb99eedfe3e15b2087a07"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-22T13:56:29.029809559"
-    },
-    "version": {
-        "content": null,
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-22T13:56:29.02167666"
+        "timestamp": "2024-07-30T17:44:16.291871"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/porechop/abi/environment.yml b/modules/nf-core/porechop/abi/environment.yml
index f9beb5c2483..4dd2eab15c4 100644
--- a/modules/nf-core/porechop/abi/environment.yml
+++ b/modules/nf-core/porechop/abi/environment.yml
@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 name: porechop_abi
 channels:
   - conda-forge
diff --git a/modules/nf-core/porechop/abi/main.nf b/modules/nf-core/porechop/abi/main.nf
index ca71169e97d..88ec5bd0ea9 100644
--- a/modules/nf-core/porechop/abi/main.nf
+++ b/modules/nf-core/porechop/abi/main.nf
@@ -11,23 +11,37 @@ process PORECHOP_ABI {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.fastq.gz"), emit: reads
-    tuple val(meta), path("*.log")     , emit: log
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path("*.fastq.gz") , emit: reads
+    tuple val(meta), path("*.log")      , emit: log
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}.porechop_abi"
+    if ("$reads" == "${prefix}.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     porechop_abi \\
         --input $reads \\
         --threads $task.cpus \\
         $args \\
         --output ${prefix}.fastq.gz \\
-        > ${prefix}.log
+        | tee ${prefix}.log
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        porechop_abi: \$( porechop_abi --version )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}.porechop_abi"
+    """
+    echo "" | gzip > ${prefix}.fastq.gz
+    touch ${prefix}.log
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         porechop_abi: \$( porechop_abi --version )
diff --git a/modules/nf-core/porechop/abi/meta.yml b/modules/nf-core/porechop/abi/meta.yml
index 67d9ff486d5..a856ffbe65c 100644
--- a/modules/nf-core/porechop/abi/meta.yml
+++ b/modules/nf-core/porechop/abi/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/bonsai-team/Porechop_ABI"
       tool_dev_url: "https://github.com/bonsai-team/Porechop_ABI"
       doi: "10.1101/2022.07.07.499093"
-      licence: "['GPL v3']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
@@ -35,12 +35,14 @@ output:
   - reads:
       type: file
       description: Adapter-trimmed fastq.gz file
-      pattern: "*fastq.gz"
+      pattern: "*.fastq.gz"
   - log:
       type: file
       description: Log file containing stdout information
       pattern: "*.log"
 authors:
   - "@sofstam"
+  - "LilyAnderssonLee"
 maintainers:
   - "@sofstam"
+  - "LilyAnderssonLee"
diff --git a/modules/nf-core/porechop/abi/tests/main.nf.test b/modules/nf-core/porechop/abi/tests/main.nf.test
new file mode 100644
index 00000000000..b5a29f90846
--- /dev/null
+++ b/modules/nf-core/porechop/abi/tests/main.nf.test
@@ -0,0 +1,59 @@
+nextflow_process {
+
+    name "Test Process PORECHOP_ABI"
+    script "../main.nf"
+    process "PORECHOP_ABI"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "porechop"
+    tag "porechop/abi"
+
+    test("sarscov2-nanopore") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.reads,
+                    file(process.out.log.get(0).get(1)).readLines()[20..40],
+                    process.out.versions).match()
+                }
+            )
+        }
+    }
+
+    test("sarscov2-nanopore - stub") {
+
+        options "-stub"
+
+        when {
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/porechop/abi/tests/main.nf.test.snap b/modules/nf-core/porechop/abi/tests/main.nf.test.snap
new file mode 100644
index 00000000000..ad63f4edb9b
--- /dev/null
+++ b/modules/nf-core/porechop/abi/tests/main.nf.test.snap
@@ -0,0 +1,94 @@
+{
+    "sarscov2-nanopore": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.porechop_abi.fastq.gz:md5,886fdb859fb50e0dddd35007bcff043e"
+                ]
+            ],
+            [
+                "                                        Best               \u001b[0m",
+                "                                        read       Best    \u001b[0m",
+                "                                        start      read end\u001b[0m",
+                "  \u001b[4mSet                                   %ID        %ID     \u001b[0m",
+                "  \u001b[32mSQK-NSK007                               100.0       73.1\u001b[0m",
+                "  Rapid                                     40.4        0.0",
+                "  RBK004_upstream                           77.5        0.0",
+                "  SQK-MAP006                                75.8       72.7",
+                "  SQK-MAP006 short                          65.5       66.7",
+                "  PCR adapters 1                            73.9       69.6",
+                "  PCR adapters 2                            80.0       72.7",
+                "  PCR adapters 3                            70.8       69.6",
+                "  1D^2 part 1                               71.4       70.0",
+                "  1D^2 part 2                               84.8       75.8",
+                "  cDNA SSP                                  63.0       61.7",
+                "  \u001b[32mBarcode 1 (reverse)                      100.0      100.0\u001b[0m",
+                "  Barcode 2 (reverse)                       70.8       69.2",
+                "  Barcode 3 (reverse)                       76.0       70.4",
+                "  Barcode 4 (reverse)                       74.1       71.4",
+                "  Barcode 5 (reverse)                       77.8       80.8",
+                "  Barcode 6 (reverse)                       73.1       70.8"
+            ],
+            [
+                "versions.yml:md5,0e9e5e0d35a68ff8e6490c949b257f98"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-07-29T13:50:49.318599"
+    },
+    "sarscov2-nanopore - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.porechop_abi.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.porechop_abi.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,0e9e5e0d35a68ff8e6490c949b257f98"
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.porechop_abi.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.porechop_abi.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0e9e5e0d35a68ff8e6490c949b257f98"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-07-29T13:50:54.425389"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/porechop/abi/tests/tags.yml b/modules/nf-core/porechop/abi/tests/tags.yml
new file mode 100644
index 00000000000..e19350cd61b
--- /dev/null
+++ b/modules/nf-core/porechop/abi/tests/tags.yml
@@ -0,0 +1,2 @@
+porechop/abi:
+  - "modules/nf-core/porechop/abi/**"
diff --git a/modules/nf-core/presto/filterseq/tests/main.nf.test b/modules/nf-core/presto/filterseq/tests/main.nf.test
index 2f0bd169ad7..62ced75c389 100644
--- a/modules/nf-core/presto/filterseq/tests/main.nf.test
+++ b/modules/nf-core/presto/filterseq/tests/main.nf.test
@@ -21,7 +21,7 @@ nextflow_process {
                     """
                     input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_airrseq_1_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_airrseq_umi_R1.fastq.gz', checkIfExists: true)
                     ]
                     """
                 }
diff --git a/modules/nf-core/prokka/tests/main.nf.test b/modules/nf-core/prokka/tests/main.nf.test
index 3b59ef3af50..dca19bba717 100644
--- a/modules/nf-core/prokka/tests/main.nf.test
+++ b/modules/nf-core/prokka/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
                 """
                 input[0] =  Channel.fromList([
                         tuple([ id:'test', single_end:false ], // meta map
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true))
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true))
                     ])
                 input[1] = []
                 input[2] = []
@@ -26,18 +26,22 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gff).match("gff") },
-                { assert snapshot(process.out.fna).match("fna") },
-                { assert snapshot(process.out.faa).match("faa") },
-                { assert snapshot(process.out.ffn).match("ffn") },
-                { assert snapshot(process.out.fsa).match("fsa") },
-                { assert snapshot(process.out.tbl).match("tbl") },
-                { assert snapshot(process.out.err).match("err") },
-                { assert snapshot(process.out.txt).match("txt") },
-                { assert snapshot(process.out.tsv).match("tsv") },
                 { assert path(process.out.gbk.get(0).get(1)).exists() },
                 { assert path(process.out.log.get(0).get(1)).exists() },
-                { assert path(process.out.sqn.get(0).get(1)).exists() }
+                { assert path(process.out.sqn.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.gff,
+                    process.out.fna,
+                    process.out.faa,
+                    process.out.ffn,
+                    process.out.fsa,
+                    process.out.tbl,
+                    process.out.err,
+                    process.out.txt,
+                    process.out.tsv,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
 
diff --git a/modules/nf-core/prokka/tests/main.nf.test.snap b/modules/nf-core/prokka/tests/main.nf.test.snap
index 859e8df8244..874c989d7a6 100644
--- a/modules/nf-core/prokka/tests/main.nf.test.snap
+++ b/modules/nf-core/prokka/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "txt": {
+    "Prokka - sarscov2 - genome.fasta": {
         "content": [
             [
                 [
@@ -7,122 +7,89 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.txt:md5,b40e485ffc8eaf1feacf8d79d9751a33"
+                    "test.gff:md5,5dbfb8fcf2db020564c16045976a0933"
                 ]
-            ]
-        ],
-        "timestamp": "2023-12-14T15:19:54.84139118"
-    },
-    "err": {
-        "content": [
+            ],
             [
                 [
                     {
                         "id": "test",
                         "single_end": false
                     },
-                    "test.err:md5,b3daedc646fddd422824e2b3e5e9229d"
+                    "test.fna:md5,787307f29a263e5657cc276ebbf7e2b3"
                 ]
-            ]
-        ],
-        "timestamp": "2023-12-14T15:19:54.837204155"
-    },
-    "fsa": {
-        "content": [
+            ],
             [
                 [
                     {
                         "id": "test",
                         "single_end": false
                     },
-                    "test.fsa:md5,71bbefcb7f12046bcd3263f58cfd5404"
+                    "test.faa:md5,a4ceda83262b3c222a6b1f508fb9e24b"
                 ]
-            ]
-        ],
-        "timestamp": "2023-12-14T15:19:54.803513721"
-    },
-    "gff": {
-        "content": [
+            ],
             [
                 [
                     {
                         "id": "test",
                         "single_end": false
                     },
-                    "test.gff:md5,5dbfb8fcf2db020564c16045976a0933"
+                    "test.ffn:md5,80f474b5367b7ea5ed23791935f65e34"
                 ]
-            ]
-        ],
-        "timestamp": "2023-12-14T15:19:54.710100529"
-    },
-    "tsv": {
-        "content": [
+            ],
             [
                 [
                     {
                         "id": "test",
                         "single_end": false
                     },
-                    "test.tsv:md5,da7c720c3018c5081d6a70b517b7d450"
+                    "test.fsa:md5,71bbefcb7f12046bcd3263f58cfd5404"
                 ]
-            ]
-        ],
-        "timestamp": "2023-12-14T15:19:54.846026731"
-    },
-    "faa": {
-        "content": [
+            ],
             [
                 [
                     {
                         "id": "test",
                         "single_end": false
                     },
-                    "test.faa:md5,a4ceda83262b3c222a6b1f508fb9e24b"
+                    "test.tbl:md5,d8f816a066ced94b62d9618b13fb8add"
                 ]
-            ]
-        ],
-        "timestamp": "2023-12-14T15:19:54.722112433"
-    },
-    "fna": {
-        "content": [
+            ],
             [
                 [
                     {
                         "id": "test",
                         "single_end": false
                     },
-                    "test.fna:md5,787307f29a263e5657cc276ebbf7e2b3"
+                    "test.err:md5,b3daedc646fddd422824e2b3e5e9229d"
                 ]
-            ]
-        ],
-        "timestamp": "2023-12-14T15:19:54.717325796"
-    },
-    "ffn": {
-        "content": [
+            ],
             [
                 [
                     {
                         "id": "test",
                         "single_end": false
                     },
-                    "test.ffn:md5,80f474b5367b7ea5ed23791935f65e34"
+                    "test.txt:md5,b40e485ffc8eaf1feacf8d79d9751a33"
                 ]
-            ]
-        ],
-        "timestamp": "2023-12-14T15:19:54.727149899"
-    },
-    "tbl": {
-        "content": [
+            ],
             [
                 [
                     {
                         "id": "test",
                         "single_end": false
                     },
-                    "test.tbl:md5,d8f816a066ced94b62d9618b13fb8add"
+                    "test.tsv:md5,da7c720c3018c5081d6a70b517b7d450"
                 ]
+            ],
+            [
+                "versions.yml:md5,e83a22fe02167e290d90853b45650db9"
             ]
         ],
-        "timestamp": "2023-12-14T15:19:54.831206944"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T12:34:20.447734"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/pycoqc/tests/main.nf.test b/modules/nf-core/pycoqc/tests/main.nf.test
index afc15a98015..0df42e226b5 100644
--- a/modules/nf-core/pycoqc/tests/main.nf.test
+++ b/modules/nf-core/pycoqc/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_process {
                 """
                 input[0] =  [
                                 [ id:'test' ], // meta map
-                                file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true)
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt', checkIfExists: true)
                             ]
 
                 """
diff --git a/modules/nf-core/pyrodigal/tests/main.nf.test b/modules/nf-core/pyrodigal/tests/main.nf.test
index 95ea3b2bbd6..faa7c8ece69 100644
--- a/modules/nf-core/pyrodigal/tests/main.nf.test
+++ b/modules/nf-core/pyrodigal/tests/main.nf.test
@@ -14,7 +14,7 @@ nextflow_process {
                 """
                 input[0] = [
                              [id:'test', single_end:false ], // meta map
-                             file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                             file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                             ]
                  input[1] = 'gff'
                 """
@@ -35,7 +35,7 @@ nextflow_process {
                 """
                 input[0] = [
                              [id:'test', single_end:false ], // meta map
-                             file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                             file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                             ]
                  input[1] = 'gbk'
                 """
@@ -45,7 +45,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    path(process.out.annotations.get(0).get(1)).linesGzip[14..22],
+                    process.out.faa,
+                    process.out.fna,
+                    process.out.score,
+                    process.out.versions,
+                ).match() }
             )
         }
     }
@@ -57,7 +63,7 @@ nextflow_process {
                 """
                 input[0] = [
                              [id:'test', single_end:false ], // meta map
-                             file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                             file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                             ]
                 input[1] = 'gff'
                 """
@@ -83,7 +89,7 @@ nextflow_process {
                 """
                 input[0] = [
                              [id:'test', single_end:false ], // meta map
-                             file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                             file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                             ]
                 input[1] = 'gbk'
                 """
diff --git a/modules/nf-core/pyrodigal/tests/main.nf.test.snap b/modules/nf-core/pyrodigal/tests/main.nf.test.snap
index 82f4c48d93a..827fdaaa357 100644
--- a/modules/nf-core/pyrodigal/tests/main.nf.test.snap
+++ b/modules/nf-core/pyrodigal/tests/main.nf.test.snap
@@ -16,92 +16,53 @@
     },
     "pyrodigal - sarscov2 - gbk": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.gbk.gz:md5,2dcc29d50022d1d74ea1133a60c5bd51"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.score.gz:md5,c0703a9e662ae0b21c7bbb082ef3fb5f"
-                    ]
-                ],
-                "4": [
-                    "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3"
-                ],
-                "annotations": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.gbk.gz:md5,2dcc29d50022d1d74ea1133a60c5bd51"
-                    ]
-                ],
-                "faa": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7"
-                    ]
-                ],
-                "fna": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b"
-                    ]
-                ],
-                "score": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.score.gz:md5,c0703a9e662ae0b21c7bbb082ef3fb5f"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3"
+            [
+                "     CDS             310..13476",
+                "                     /codon_start=1",
+                "                     /inference=\"ab initio prediction:pyrodigal:3.3.0\"",
+                "                     /locus_tag=\"MT192765.1_1\"",
+                "                     /transl_table=11",
+                "                     /translation=\"MPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLP",
+                "                     QLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKV",
+                "                     LLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG",
+                "                     AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIA"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7"
                 ]
-            }
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.score.gz:md5,c0703a9e662ae0b21c7bbb082ef3fb5f"
+                ]
+            ],
+            [
+                "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3"
+            ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-03-18T15:42:04.374845155"
+        "timestamp": "2024-07-30T06:09:40.289778252"
     },
     "pyrodigal - sarscov2 - gff": {
         "content": [
diff --git a/modules/nf-core/samtools/dict/tests/main.nf.test b/modules/nf-core/samtools/dict/tests/main.nf.test
new file mode 100644
index 00000000000..c467081f82f
--- /dev/null
+++ b/modules/nf-core/samtools/dict/tests/main.nf.test
@@ -0,0 +1,62 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_DICT"
+    script "../main.nf"
+    process "SAMTOOLS_DICT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/dict"
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.dict[0][1]).readLines()[0],
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/samtools/dict/tests/main.nf.test.snap b/modules/nf-core/samtools/dict/tests/main.nf.test.snap
new file mode 100644
index 00000000000..66d7b1fcff5
--- /dev/null
+++ b/modules/nf-core/samtools/dict/tests/main.nf.test.snap
@@ -0,0 +1,50 @@
+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.dict:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,47f9e889ed1e779cb54e61d707a7135d"
+                ],
+                "dict": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.dict:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,47f9e889ed1e779cb54e61d707a7135d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-18T09:43:30.509703257"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            "@HD\tVN:1.0\tSO:unsorted",
+            [
+                "versions.yml:md5,0af6b2d2d6d9d96bc5abe98b99b91446"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T12:12:31.201483952"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/scimap/spatiallda/tests/main.nf.test b/modules/nf-core/scimap/spatiallda/tests/main.nf.test
index 90924a3b82a..688977ab305 100644
--- a/modules/nf-core/scimap/spatiallda/tests/main.nf.test
+++ b/modules/nf-core/scimap/spatiallda/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['imaging']['downstream']['phenotyped'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'imaging/downstream/phenotyped.csv', checkIfExists: true)
                 ]
                 """
             }
@@ -28,8 +28,7 @@ nextflow_process {
                 { assert process.out.spatial_lda_output },
                 { assert process.out.composition_plot },
                 { assert process.out.motif_location_plot },
-                { assert process.out.versions },
-                { assert snapshot(process.out.versions).match("versions") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -40,7 +39,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['imaging']['downstream']['phenotyped'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'imaging/downstream/phenotyped.csv', checkIfExists: true)
                 ]
                 """
             }
@@ -48,7 +47,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/modules/nf-core/sentieon/qualcal/main.nf b/modules/nf-core/sentieon/qualcal/main.nf
index 54f916f9e82..d1d4f4258d9 100644
--- a/modules/nf-core/sentieon/qualcal/main.nf
+++ b/modules/nf-core/sentieon/qualcal/main.nf
@@ -95,10 +95,11 @@ process SENTIEON_QUALCAL {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def file_suffix = input.name.endsWith(".bam") ? "bam" : "cram"
     def recalibrated_bam = generate_recalibrated_bams ? "${prefix}.recalibrated.${file_suffix}" : ""
+    def recalibrated_bam_cmd = generate_recalibrated_bams ? "touch $recalibrated_bam" : ""
     """
     touch ${prefix}.table
     touch ${prefix}.table.post
-    touch ${recalibrated_bam}
+    ${recalibrated_bam_cmd}
     touch ${prefix}.csv
     touch ${prefix}.pdf
 
diff --git a/modules/nf-core/sentieon/qualcal/tests/main.nf.test b/modules/nf-core/sentieon/qualcal/tests/main.nf.test
index 9b71ece49f8..feb6463d55f 100644
--- a/modules/nf-core/sentieon/qualcal/tests/main.nf.test
+++ b/modules/nf-core/sentieon/qualcal/tests/main.nf.test
@@ -202,6 +202,36 @@ nextflow_process {
 
     }
 
+    test("no recal BAM - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [ [ id:'fasta' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+                input[2] = [ [ id:'fasta' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
+
+                input[3] = [ [ id:'knownSites' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
+                input[4] = [ [ id:'knownSites' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ]
+                input[5] = [[:],[]]
+                input[6] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
 
 
 }
diff --git a/modules/nf-core/smoothxg/tests/main.nf.test b/modules/nf-core/smoothxg/tests/main.nf.test
index ed19da0be12..1a2ee9188dd 100644
--- a/modules/nf-core/smoothxg/tests/main.nf.test
+++ b/modules/nf-core/smoothxg/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true)
                     ]
                 """
             }
@@ -38,7 +38,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['pangenome']['pangenome_seqwish_gfa'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.seqwish.gfa', checkIfExists: true)
                     ]
                 """
             }
diff --git a/modules/nf-core/staramr/search/environment.yml b/modules/nf-core/staramr/search/environment.yml
index 935337eb349..78d2dd7be46 100644
--- a/modules/nf-core/staramr/search/environment.yml
+++ b/modules/nf-core/staramr/search/environment.yml
@@ -8,3 +8,4 @@ channels:
 dependencies:
   - bioconda::mlst=2.23.0
   - bioconda::staramr=0.10.0
+  - conda-forge::numpy=1.25.2
diff --git a/modules/nf-core/staramr/search/tests/main.nf.test b/modules/nf-core/staramr/search/tests/main.nf.test
index 01e60659aa1..fa72c63b776 100644
--- a/modules/nf-core/staramr/search/tests/main.nf.test
+++ b/modules/nf-core/staramr/search/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)
                 ]
                 """
             }
@@ -36,4 +36,4 @@ nextflow_process {
             )
         }
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/survivor/bedpetovcf/tests/main.nf.test b/modules/nf-core/survivor/bedpetovcf/tests/main.nf.test
index 5ab24e66f28..58be3136fd1 100644
--- a/modules/nf-core/survivor/bedpetovcf/tests/main.nf.test
+++ b/modules/nf-core/survivor/bedpetovcf/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['genome']['test_bedpe'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bedpe', checkIfExists: true)
                     ]
                 """
             }
@@ -41,7 +41,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['genome']['test_bedpe'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bedpe', checkIfExists: true)
                     ]
                 """
             }
diff --git a/modules/nf-core/survivor/stats/tests/main.nf.test b/modules/nf-core/survivor/stats/tests/main.nf.test
index e83df576a31..d725a17f5ff 100644
--- a/modules/nf-core/survivor/stats/tests/main.nf.test
+++ b/modules/nf-core/survivor/stats/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                     input[0] = [
                         [ id:'test' ], // meta map
-                        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true)
                         ]
                     input[1] = -1
                     input[2] = -1
@@ -47,7 +47,7 @@ nextflow_process {
                 """
                     input[0] = [
                         [ id:'test' ], // meta map
-                        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true)
                         ]
                     input[1] = -1
                     input[2] = -1
diff --git a/modules/nf-core/svdb/query/tests/main.nf.test b/modules/nf-core/svdb/query/tests/main.nf.test
index edf801f78c8..72e829158c6 100644
--- a/modules/nf-core/svdb/query/tests/main.nf.test
+++ b/modules/nf-core/svdb/query/tests/main.nf.test
@@ -14,13 +14,13 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of([ [ id:'test' ], // meta map
-                        [ file(params.test_data['homo_sapiens']['illumina']['test_sv_vcf'], checkIfExists: true) ]
+                        [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) ]
                         ])
                 input[1] = ['AC']
                 input[2] = ['AF']
                 input[3] = ['gnomad_svAC']
                 input[4] = ['gnomad_svAF']
-                input[5] = Channel.of([file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_sv_vcf_gz'], checkIfExists: true)])
+                input[5] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz', checkIfExists: true)])
                 input[6] = []
                 """
             }
diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test b/modules/nf-core/tabix/bgzip/tests/main.nf.test
index 95fd4c506a8..d784aa07078 100644
--- a/modules/nf-core/tabix/bgzip/tests/main.nf.test
+++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
                 """
                 input[0] = [
                                 [ id:'bgzip_test' ],
-                                [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ]
                 ]
                 """
             }
@@ -39,7 +39,7 @@ nextflow_process {
                 """
                 input[0] = [
                             [ id:'bedgz_test' ],
-                            [ file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) ]
+                            [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed.gz', checkIfExists: true) ]
                 ]
                 """
             }
@@ -66,7 +66,7 @@ nextflow_process {
                 """
                 input[0] = [
                                 [ id:"test_stub" ],
-                                [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ]
                 ]
                 """
             }
@@ -91,7 +91,7 @@ nextflow_process {
                 """
                 input[0] = [
                                 [ id:"gzi_compress_test" ],
-                                [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ]
                 ]
                 """
             }
diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
index 87ea2c84f9e..1a84d74fc0d 100644
--- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
                                 [ id:'tbi_test' ],
-                                [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ]
                 ]
                 """
             }
@@ -43,7 +43,7 @@ nextflow_process {
                 """
                 input[0] = [
                                 [ id:'csi_test' ],
-                                [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ]
                 ]
                 """
             }
@@ -72,7 +72,7 @@ nextflow_process {
                 """
                 input[0] = [
                                 [ id:'test' ],
-                                [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ]
                 ]
                 """
             }
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index 38fbdfdd34f..102b0d7bf38 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
                 """
                 input[0] = [
                                 [ id:'tbi_bed' ],
-                                [ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ]
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true) ]
                             ]
                 """
             }
@@ -40,7 +40,7 @@ nextflow_process {
                 """
                 input[0] = [
                                 [ id:'tbi_gff' ],
-                                [ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ]
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) ]
                             ]
                 """
             }
@@ -64,7 +64,7 @@ nextflow_process {
                 """
                 input[0] =  [
                                 [ id:'tbi_vcf' ],
-                                [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
                             ]
                 """
             }
@@ -89,7 +89,7 @@ nextflow_process {
                 """
                 input[0] =  [
                                 [ id:'vcf_csi' ],
-                                [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
                             ]
                 """
             }
@@ -115,7 +115,7 @@ nextflow_process {
                 """
                 input[0] =  [
                                 [ id:'vcf_csi_stub' ],
-                                [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
                             ]
                 """
             }
diff --git a/modules/nf-core/tiddit/cov/tests/main.nf.test b/modules/nf-core/tiddit/cov/tests/main.nf.test
index 72746648a7f..24c273d86dc 100644
--- a/modules/nf-core/tiddit/cov/tests/main.nf.test
+++ b/modules/nf-core/tiddit/cov/tests/main.nf.test
@@ -16,12 +16,12 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
                 ]
 
                 input[1] = [
                     [:],  // meta map
-                    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)
                 ]
                 """
             }
@@ -30,9 +30,12 @@ nextflow_process {
         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") }
+                { assert snapshot(
+                    process.out.cov,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
 
@@ -45,7 +48,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
                 ]
                 input[1] = [ [:], [] ]
                 """
@@ -55,9 +58,12 @@ nextflow_process {
         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") }
+                { assert snapshot(
+                    process.out.cov,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
 
@@ -72,12 +78,12 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
                 ]
 
                 input[1] = [
                     [:],  // meta map
-                    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)
                 ]
                 """
             }
@@ -86,9 +92,12 @@ nextflow_process {
         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") }
+                { assert snapshot(
+                    process.out.wig,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
 
@@ -103,7 +112,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
                 ]
 
                 input[1] = [ [:], [] ]
@@ -114,9 +123,12 @@ nextflow_process {
         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") }
+                { assert snapshot(
+                    process.out.wig,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
 
@@ -133,12 +145,12 @@ nextflow_process {
 
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
                 ]
 
                 input[1] = [
                     [:],  // meta map
-                    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)
                 ]
                 """
             }
@@ -147,11 +159,14 @@ nextflow_process {
         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") }
+                { assert snapshot(
+                    process.out.cov,
+                    process.out.wig,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
 
diff --git a/modules/nf-core/tiddit/cov/tests/main.nf.test.snap b/modules/nf-core/tiddit/cov/tests/main.nf.test.snap
index dcd24edca90..5067886d6dc 100644
--- a/modules/nf-core/tiddit/cov/tests/main.nf.test.snap
+++ b/modules/nf-core/tiddit/cov/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "wig": {
+    "homo_sapiens - bam - wig": {
         "content": [
             [
                 [
@@ -9,11 +9,18 @@
                     },
                     "test.wig:md5,7c46b6ef30574acdce0ad854f40126ae"
                 ]
+            ],
+            [
+                "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a"
             ]
         ],
-        "timestamp": "2023-12-22T11:24:06.649602"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T09:44:07.66262"
     },
-    "wig - stub": {
+    "homo_sapiens - cram - wig": {
         "content": [
             [
                 [
@@ -21,21 +28,50 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    "test.wig:md5,7c46b6ef30574acdce0ad854f40126ae"
                 ]
+            ],
+            [
+                "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a"
             ]
         ],
-        "timestamp": "2023-12-22T11:30:00.831686"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T09:44:01.397993"
     },
-    "versions": {
+    "homo_sapiens - stub": {
         "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
             [
                 "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a"
             ]
         ],
-        "timestamp": "2023-12-22T11:23:58.227251"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T09:44:12.873466"
     },
-    "cov": {
+    "homo_sapiens - bam - bed": {
         "content": [
             [
                 [
@@ -45,19 +81,18 @@
                     },
                     "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"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T09:43:54.542951"
     },
-    "cov - stub": {
+    "homo_sapiens - cram - bed": {
         "content": [
             [
                 [
@@ -65,10 +100,17 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    "test.bed:md5,caf0742f2d4a6f713ceb85268dd48c14"
                 ]
+            ],
+            [
+                "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a"
             ]
         ],
-        "timestamp": "2023-12-22T11:30:00.826974"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T09:43:47.441318"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/trinity/tests/main.nf.test b/modules/nf-core/trinity/tests/main.nf.test
index 49e89a57711..8717518bd87 100644
--- a/modules/nf-core/trinity/tests/main.nf.test
+++ b/modules/nf-core/trinity/tests/main.nf.test
@@ -16,8 +16,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 """
@@ -27,13 +27,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
+                { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN7_c0_g1_i1 len=299 path=[0:0-151 2:152-298]") },
                 { assert snapshot(
                     process.out.versions
-                    ).match("versions")
-                },
-                { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
-                { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN7_c0_g1_i1 len=299 path=[0:0-151 2:152-298]") }
-
+                    ).match()
+                }
             )
         }
     }
@@ -45,7 +44,7 @@ nextflow_process {
                 input[0] = [
                     [ id:'test', single_end:true ], // meta map
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 """
@@ -55,12 +54,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
+                { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN10_c0_g1_i1 len=534 path=[0:0-533]") },
                 { assert snapshot(
                     process.out.versions
-                    ).match("versions")
+                    ).match()
                 },
-                { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
-                { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN10_c0_g1_i1 len=534 path=[0:0-533]") }
             )
         }
     }
@@ -72,10 +71,10 @@ nextflow_process {
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 """
@@ -85,12 +84,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
+                { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=225 path=[0:0-224]") },
                 { assert snapshot(
                     process.out.versions
-                    ).match("versions")
-                },
-                { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
-                { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=225 path=[0:0-224]") }
+                    ).match()
+                }
 
             )
         }
@@ -103,8 +102,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test', single_end:true ], // meta map
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 """
@@ -114,12 +113,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
+                { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=268 path=[0:0-267]") },
                 { assert snapshot(
                     process.out.versions
-                    ).match("versions")
-                },
-                { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
-                { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=268 path=[0:0-267]") }
+                    ).match()
+                }
             )
         }
     }
@@ -134,8 +133,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 """
@@ -145,12 +144,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                        process.out.transcript_fasta,
-                        process.out.log
-                    ).match()
-                },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/modules/nf-core/trinity/tests/main.nf.test.snap b/modules/nf-core/trinity/tests/main.nf.test.snap
index d543fc4406e..61217a2e33d 100644
--- a/modules/nf-core/trinity/tests/main.nf.test.snap
+++ b/modules/nf-core/trinity/tests/main.nf.test.snap
@@ -1,33 +1,103 @@
 {
-    "versions": {
+    "homo_sapiens-test_rnaseq-paired-multiple": {
         "content": [
             [
                 "versions.yml:md5,f77f7a5b3e84ea0ee771e0df95895cfb"
             ]
         ],
-        "timestamp": "2024-01-15T19:10:42.684367037"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T16:43:56.823365"
     },
-    "homo_sapiens-test_rnaseq-stub": {
+    "homo_sapiens-test_rnaseq-single": {
         "content": [
             [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ]
-            ],
+                "versions.yml:md5,f77f7a5b3e84ea0ee771e0df95895cfb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T16:41:17.496781"
+    },
+    "homo_sapiens-test_rnaseq-paired": {
+        "content": [
             [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ]
+                "versions.yml:md5,f77f7a5b3e84ea0ee771e0df95895cfb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T16:39:34.89455"
+    },
+    "homo_sapiens-test_rnaseq-single-multiple": {
+        "content": [
+            [
+                "versions.yml:md5,f77f7a5b3e84ea0ee771e0df95895cfb"
             ]
         ],
-        "timestamp": "2024-01-15T19:11:49.900582628"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T16:46:07.157559"
+    },
+    "homo_sapiens-test_rnaseq-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,f77f7a5b3e84ea0ee771e0df95895cfb"
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "transcript_fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f77f7a5b3e84ea0ee771e0df95895cfb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-30T16:46:18.056478"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/vardictjava/tests/main.nf.test b/modules/nf-core/vardictjava/tests/main.nf.test
index 483a753a896..8e5fec10266 100644
--- a/modules/nf-core/vardictjava/tests/main.nf.test
+++ b/modules/nf-core/vardictjava/tests/main.nf.test
@@ -17,17 +17,17 @@ nextflow_process {
                 """
                 input[0] = Channel.value([
                     [ id:'test' ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ])
                 input[1] = [
                     [id:"ref"],
-                    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[2] = [
                     [id:"ref"],
-                    file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 """
             }
@@ -55,22 +55,22 @@ nextflow_process {
                 input[0] = Channel.value([
                     [ id:'test' ], // meta map
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true)
                     ],
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai', checkIfExists: true)
                     ],
-                    file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ])
                 input[1] = [
                     [id:"ref"],
-                    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[2] = [
                     [id:"ref"],
-                    file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/vcfanno/tests/main.nf.test b/modules/nf-core/vcfanno/tests/main.nf.test
index b28431b2778..8bbcfd8942f 100644
--- a/modules/nf-core/vcfanno/tests/main.nf.test
+++ b/modules/nf-core/vcfanno/tests/main.nf.test
@@ -15,11 +15,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test_compressed', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists:true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true)
                 ]
-                input[1] = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml', checkIfExists: true)
                 input[2] = []
                 input[3] = [
                     file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true),
@@ -45,11 +45,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test_uncompressed', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true),
                     [],
-                    file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists:true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true)
                 ]
-                input[1] = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml', checkIfExists: true)
                 input[2] = []
                 input[3] = [
                     file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true),
@@ -77,11 +77,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test_compressed', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists:true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true)
                 ]
-                input[1] = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml', checkIfExists: true)
                 input[2] = []
                 input[3] = [
                     file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true),
diff --git a/modules/nf-core/windowmasker/convert/tests/main.nf.test b/modules/nf-core/windowmasker/convert/tests/main.nf.test
index 55a6589bf48..8118cdf3100 100644
--- a/modules/nf-core/windowmasker/convert/tests/main.nf.test
+++ b/modules/nf-core/windowmasker/convert/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id: "test" ],
-                    [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 ]
                 """
             }
@@ -90,7 +90,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id: "test" ],
-                    [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 ]
                 """
             }
diff --git a/modules/nf-core/windowmasker/mkcounts/tests/main.nf.test b/modules/nf-core/windowmasker/mkcounts/tests/main.nf.test
index 18c4977c609..bf53d7fa642 100644
--- a/modules/nf-core/windowmasker/mkcounts/tests/main.nf.test
+++ b/modules/nf-core/windowmasker/mkcounts/tests/main.nf.test
@@ -20,7 +20,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id: "test" ],
-                    [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 ]
                 """
             }
@@ -43,7 +43,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id: "test" ],
-                    [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 ]
                 """
             }
diff --git a/modules/nf-core/windowmasker/ustat/tests/main.nf.test b/modules/nf-core/windowmasker/ustat/tests/main.nf.test
index 58d91b1386b..6e02c9c18c4 100644
--- a/modules/nf-core/windowmasker/ustat/tests/main.nf.test
+++ b/modules/nf-core/windowmasker/ustat/tests/main.nf.test
@@ -19,7 +19,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id: "test" ],
-                    [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 ]
                 """
             }
@@ -33,7 +33,7 @@ nextflow_process {
                 input[0] = WINDOWMASKER_MKCOUNTS.out.counts
                 input[1] = [
                     [id: "test" ],
-                    [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 ]
                 """
             }
@@ -51,7 +51,7 @@ nextflow_process {
                 input[0] = WINDOWMASKER_MKCOUNTS.out.counts
                 input[1] = [
                     [id: "test" ],
-                    [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 ]
                 """
             }
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 5eace824d5e..e6529a07ed5 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1229,9 +1229,6 @@ pmdtools/filter:
 pneumocat:
   - modules/nf-core/pneumocat/**
   - tests/modules/nf-core/pneumocat/**
-porechop/abi:
-  - modules/nf-core/porechop/abi/**
-  - tests/modules/nf-core/porechop/abi/**
 preseq/ccurve:
   - modules/nf-core/preseq/ccurve/**
   - tests/modules/nf-core/preseq/ccurve/**
@@ -1334,9 +1331,6 @@ samtools/collatefastq:
 samtools/depth:
   - modules/nf-core/samtools/depth/**
   - tests/modules/nf-core/samtools/depth/**
-samtools/dict:
-  - modules/nf-core/samtools/dict/**
-  - tests/modules/nf-core/samtools/dict/**
 samtools/fasta:
   - modules/nf-core/samtools/fasta/**
   - tests/modules/nf-core/samtools/fasta/**
@@ -1641,9 +1635,6 @@ transdecoder/longorf:
 transdecoder/predict:
   - modules/nf-core/transdecoder/predict/**
   - tests/modules/nf-core/transdecoder/predict/**
-trinity:
-  - modules/nf-core/trinity/**
-  - tests/modules/nf-core/trinity/**
 truvari/bench:
   - modules/nf-core/truvari/bench/**
   - tests/modules/nf-core/truvari/bench/**
diff --git a/tests/modules/nf-core/samtools/dict/main.nf b/tests/modules/nf-core/samtools/dict/main.nf
deleted file mode 100644
index 7bac114a4f1..00000000000
--- a/tests/modules/nf-core/samtools/dict/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_DICT } from '../../../../../modules/nf-core/samtools/dict/main.nf'
-
-workflow test_samtools_dict {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    SAMTOOLS_DICT ( input )
-}
diff --git a/tests/modules/nf-core/samtools/dict/nextflow.config b/tests/modules/nf-core/samtools/dict/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/samtools/dict/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/samtools/dict/test.yml b/tests/modules/nf-core/samtools/dict/test.yml
deleted file mode 100644
index a037744fc8a..00000000000
--- a/tests/modules/nf-core/samtools/dict/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: samtools dict test_samtools_dict
-  command: nextflow run ./tests/modules/nf-core/samtools/dict -entry test_samtools_dict -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/dict/nextflow.config
-  tags:
-    - samtools/dict
-    - samtools
-  files:
-    - path: output/samtools/genome.fasta.dict
-      contains:
-        - "SN:MT192765.1"
-        - "LN:29829"
-        - "M5:c95f3e5592d0ad9974e41e7f0ea14eb0"
-    - path: output/samtools/versions.yml