diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index f0267fb0..a393d021 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -24,14 +24,8 @@ params {
                 kraken2                                   = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
                 kraken2_tar_gz                            = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
 
-                test_wig_gz                               = "${test_data_dir}/genomics/sarscov2/genome/gcwiggle/test.wig.gz"
-
                 all_sites_fas                             = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas"
                 informative_sites_fas                     = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas"
-
-                contigs_fasta                             = "${test_data_dir}/genomics/sarscov2/genome/contigs.fasta"
-                scaffolds_fasta                           = "${test_data_dir}/genomics/sarscov2/genome/scaffolds.fasta"
-                assembly_gfa                              = "${test_data_dir}/genomics/sarscov2/genome/assembly.gfa"
             }
             'illumina' {
                 test_single_end_bam                       = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.bam"
@@ -66,6 +60,10 @@ params {
                 test3_vcf                                 = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf"
                 test3_vcf_gz                              = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz"
                 test3_vcf_gz_tbi                          = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi"
+
+                contigs_fasta                             = "${test_data_dir}/genomics/sarscov2/illumina/fasta/contigs.fasta"
+                scaffolds_fasta                           = "${test_data_dir}/genomics/sarscov2/illumina/fasta/scaffolds.fasta"
+                assembly_gfa                              = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa"
             }
             'nanopore' {
                 test_sorted_bam                           = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam"
diff --git a/tests/software/abacas/main.nf b/tests/software/abacas/main.nf
index 49f1b444..00020039 100644
--- a/tests/software/abacas/main.nf
+++ b/tests/software/abacas/main.nf
@@ -7,7 +7,7 @@ include { ABACAS } from '../../../software/abacas/main.nf' addParams ( options:
 workflow test_abacas {
 
     input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['scaffolds_fasta'], checkIfExists: true)
+              file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
             ]
 
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/software/plasmidid/main.nf b/tests/software/plasmidid/main.nf
index ea450694..44a022df 100644
--- a/tests/software/plasmidid/main.nf
+++ b/tests/software/plasmidid/main.nf
@@ -7,7 +7,7 @@ include { PLASMIDID } from '../../../software/plasmidid/main.nf' addParams ( opt
 workflow test_plasmidid {
 
     contigs = [ [ id:'test' ], // meta map
-                file(params.test_data['sarscov2']['genome']['contigs_fasta'], checkIfExists: true)
+                file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
               ]
 
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)