diff --git a/modules/nf-core/ampir/tests/main.nf.test b/modules/nf-core/ampir/tests/main.nf.test
index 35943624332..0ed40ef50df 100644
--- a/modules/nf-core/ampir/tests/main.nf.test
+++ b/modules/nf-core/ampir/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
                 """
                 input[0] = [
                             [ id:'test', single_end:false ], // meta map
-                            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true),
                 ]
                 input[1] = "precursor" // model
                 input[2] = 10          // min_length
@@ -42,7 +42,7 @@ nextflow_process {
                 """
                 input[0] = [
                             [ id:'test', single_end:false ], // meta map
-                            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true),
                 ]
                 input[1] = "precursor" // model
                 input[2] = 10          // min_length
diff --git a/modules/nf-core/bowtie2/align/tests/main.nf.test b/modules/nf-core/bowtie2/align/tests/main.nf.test
index 03aeaf9eef3..0de5950fee6 100644
--- a/modules/nf-core/bowtie2/align/tests/main.nf.test
+++ b/modules/nf-core/bowtie2/align/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)
                     ]
                     """
                 }
@@ -30,10 +30,10 @@ nextflow_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] = BOWTIE2_BUILD.out.index
-                input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
                 input[4] = false //sort
                 """
@@ -64,7 +64,7 @@ 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)
                     ]
                     """
                 }
@@ -76,10 +76,10 @@ nextflow_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] = BOWTIE2_BUILD.out.index
-                input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
                 input[4] = false //sort
                 """
@@ -110,7 +110,7 @@ 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)
                     ]
                     """
                 }
@@ -122,10 +122,10 @@ nextflow_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] = BOWTIE2_BUILD.out.index
-                input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
                 input[4] = false //sort
                 """
@@ -155,7 +155,7 @@ 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)
                     ]
                     """
                 }
@@ -167,10 +167,10 @@ nextflow_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] = BOWTIE2_BUILD.out.index
-                input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
                 input[4] = false //sort
                 """
@@ -200,7 +200,7 @@ 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)
                     ]
                     """
                 }
@@ -213,12 +213,12 @@ 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] = BOWTIE2_BUILD.out.index
-                input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
                 input[4] = false //sort
                 """
@@ -248,7 +248,7 @@ 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)
                     ]
                     """
                 }
@@ -261,12 +261,12 @@ 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] = BOWTIE2_BUILD.out.index
-                input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
                 input[4] = false //sort
                 """
@@ -297,7 +297,7 @@ 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)
                     ]
                     """
                 }
@@ -309,10 +309,10 @@ nextflow_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] = BOWTIE2_BUILD.out.index
-                input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
                 input[4] = false //sort
                 """
@@ -343,7 +343,7 @@ 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)
                     ]
                     """
                 }
@@ -356,12 +356,12 @@ 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] = BOWTIE2_BUILD.out.index
-                input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
                 input[4] = false //sort
                 """
@@ -391,7 +391,7 @@ 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)
                     ]
                     """
                 }
@@ -404,12 +404,12 @@ 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] = BOWTIE2_BUILD.out.index
-                input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
                 input[4] = false //sort
                 """
@@ -439,7 +439,7 @@ 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)
                     ]
                     """
                 }
@@ -451,10 +451,10 @@ nextflow_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] = BOWTIE2_BUILD.out.index
-                input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
                 input[4] = false //sort
                 """
@@ -486,7 +486,7 @@ 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)
                     ]
                     """
                 }
@@ -499,12 +499,12 @@ 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] = BOWTIE2_BUILD.out.index
-                input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
                 input[4] = true //sort
                 """
@@ -533,7 +533,7 @@ 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)
                     ]
                     """
                 }
@@ -546,12 +546,12 @@ 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] = BOWTIE2_BUILD.out.index
-                input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
                 input[4] = false //sort
                 """
@@ -583,7 +583,7 @@ 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)
                     ]
                     """
                 }
@@ -595,10 +595,10 @@ nextflow_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] = BOWTIE2_BUILD.out.index
-                input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
                 input[4] = false //sort
                 """
diff --git a/modules/nf-core/checkm2/predict/tests/main.nf.test b/modules/nf-core/checkm2/predict/tests/main.nf.test
index b380faa7856..cd7dda4ed25 100644
--- a/modules/nf-core/checkm2/predict/tests/main.nf.test
+++ b/modules/nf-core/checkm2/predict/tests/main.nf.test
@@ -23,7 +23,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [id: 'test'], [file(params.test_data['sarscov2']['illumina']['contigs_fasta'])] ]
+                input[0] = [ [id: 'test'], [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)] ]
                 input[1] = CHECKM2_DATABASEDOWNLOAD.out.database
                 """
             }
diff --git a/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test b/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test
index 13c802643d6..13caaceabb4 100644
--- a/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test
+++ b/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id: 'test' ],
-                    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)
                 ]
                 """
             }
@@ -44,7 +44,7 @@ nextflow_process {
         when {
             process {
                 """
-                def input_file_lines = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true).text.split('\\n')
+                def input_file_lines = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true).text.split('\\n')
                 def file_with_adapters = file('sarscov2_with_adapters.fasta')
                 file_with_adapters.text = (
                     input_file_lines[0..<(input_file_lines.size()/2)]
@@ -89,7 +89,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id: 'test' ],
-                    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)
                 ]
                 """
             }
diff --git a/modules/nf-core/foldseek/createdb/tests/main.nf.test b/modules/nf-core/foldseek/createdb/tests/main.nf.test
index 7cd7189467f..03064df16ba 100644
--- a/modules/nf-core/foldseek/createdb/tests/main.nf.test
+++ b/modules/nf-core/foldseek/createdb/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [ [id:'test'], file(params.test_data['proteomics']['pdb']['tim1_pdb'], checkIfExists: true) ]
+                input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'proteomics/pdb/1tim.pdb', checkIfExists: true) ]
                 """
             }
         }
@@ -34,7 +34,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [ [id:'test'], file(params.test_data['proteomics']['pdb']['tim1_pdb'], checkIfExists: true) ]
+                input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'proteomics/pdb/1tim.pdb', checkIfExists: true) ]
                 """
             }
         }
diff --git a/modules/nf-core/foldseek/easysearch/tests/main.nf.test b/modules/nf-core/foldseek/easysearch/tests/main.nf.test
index f229cc26911..c71e2743ed1 100644
--- a/modules/nf-core/foldseek/easysearch/tests/main.nf.test
+++ b/modules/nf-core/foldseek/easysearch/tests/main.nf.test
@@ -14,7 +14,7 @@ nextflow_process {
             script "../../createdb/main.nf"
             process {
                 """
-                input[0] = [ [ id:'test_db' ], [ file(params.test_data['proteomics']['pdb']['tim1_pdb'], checkIfExists: true) ] ]
+                input[0] = [ [ id:'test_db' ], [ file(params.modules_testdata_base_path + 'proteomics/pdb/1tim.pdb', checkIfExists: true) ] ]
                 """
             }
         }
@@ -25,7 +25,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [ [ id:'test_search' ], [ file(params.test_data['proteomics']['pdb']['tim8_pdb'], checkIfExists: true) ] ]
+                input[0] = [ [ id:'test_search' ], [ file(params.modules_testdata_base_path + 'proteomics/pdb/8tim.pdb', checkIfExists: true) ] ]
                 input[1] = FOLDSEEK_CREATEDB.out.db
                 """
             }
@@ -48,7 +48,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [ [ id:'test_search' ], [ file(params.test_data['proteomics']['pdb']['tim8_pdb'], checkIfExists: true) ] ]
+                input[0] = [ [ id:'test_search' ], [ file(params.modules_testdata_base_path + 'proteomics/pdb/8tim.pdb', checkIfExists: true) ] ]
                 input[1] = FOLDSEEK_CREATEDB.out.db
                 """
             }
diff --git a/modules/nf-core/isoseq3/tag/tests/main.nf.test b/modules/nf-core/isoseq3/tag/tests/main.nf.test
index 55ea4fdb93d..2f7816e3be8 100644
--- a/modules/nf-core/isoseq3/tag/tests/main.nf.test
+++ b/modules/nf-core/isoseq3/tag/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'mini'], // meta map
-                    file(params.test_data['homo_sapiens']['pacbio']['tag'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/mini.5p--3p.bam', checkIfExists: true)
                     ]
                 input[1] = "T-12U-16B"
                 """
@@ -44,7 +44,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'mini'], // meta map
-                    file(params.test_data['homo_sapiens']['pacbio']['tag'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/mini.5p--3p.bam', checkIfExists: true)
                     ]
                 input[1] = "T-12U-16B"
                 """
diff --git a/modules/nf-core/mosdepth/tests/main.nf.test b/modules/nf-core/mosdepth/tests/main.nf.test
index 21eebc1fa5e..0b3c860d321 100644
--- a/modules/nf-core/mosdepth/tests/main.nf.test
+++ b/modules/nf-core/mosdepth/tests/main.nf.test
@@ -15,8 +15,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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),
                     []
                 ]
                 input[1] = [[],[]]
@@ -40,9 +40,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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] = [[],[]]
                 """
@@ -65,13 +65,13 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
                     []
                 ]
                 input[1] = [
                     [ id:'test' ],
-                    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)
                 ]
                 """
             }
@@ -93,13 +93,13 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
                 ]
                 input[1] = [
                     [ id:'test' ],
-                    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)
                 ]
                 """
             }
@@ -122,8 +122,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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),
                     []
                 ]
                 input[1] = [[],[]]
@@ -148,8 +148,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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),
                     []
                 ]
                 input[1] = [[],[]]
@@ -174,9 +174,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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] = [[],[]]
                 """
@@ -200,9 +200,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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] = [[],[]]
                 """
@@ -225,9 +225,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:true ],
-                    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] = [[],[]]
                 """
diff --git a/modules/nf-core/stringtie/merge/tests/main.nf.test b/modules/nf-core/stringtie/merge/tests/main.nf.test
index 358c561a00b..bcc648bc76f 100644
--- a/modules/nf-core/stringtie/merge/tests/main.nf.test
+++ b/modules/nf-core/stringtie/merge/tests/main.nf.test
@@ -50,7 +50,7 @@ nextflow_process {
             process {
                 """
                 input[0] = STRINGTIE_STRINGTIE.out.transcript_gtf.map { it -> it[1] }
-                input[1] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
                 """
             }
         }