diff --git a/tests/software/salmon/index/main.nf b/tests/software/salmon/index/main.nf
index 3c3dc0a4..1d79215f 100644
--- a/tests/software/salmon/index/main.nf
+++ b/tests/software/salmon/index/main.nf
@@ -5,8 +5,8 @@ nextflow.enable.dsl = 2
 include { SALMON_INDEX } from '../../../../software/salmon/index/main.nf' addParams( options: [:] )
 
 workflow test_salmon_index {
-    genome        = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
-    transcriptome = file("${launchDir}/tests/data/genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)
-
-    SALMON_INDEX ( genome, transcriptome )
+    genome_fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
+    
+    SALMON_INDEX ( genome_fasta, transcript_fasta )
 }
diff --git a/tests/software/salmon/quant/main.nf b/tests/software/salmon/quant/main.nf
index 31d54eab..7b11a5a4 100644
--- a/tests/software/salmon/quant/main.nf
+++ b/tests/software/salmon/quant/main.nf
@@ -6,26 +6,30 @@ include { SALMON_INDEX } from '../../../../software/salmon/index/main.nf' addPar
 include { SALMON_QUANT } from '../../../../software/salmon/quant/main.nf' addParams( options: [args: '--minAssignedFrags 1'] )
 
 workflow test_salmon_quant_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) 
-            ]
-    genome        = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
-    transcriptome = file("${launchDir}/tests/data/genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)
-    gtf           = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
 
-    SALMON_INDEX ( genome, transcriptome )
-    SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcriptome, false )
+    input = [ [ id:'test', single_end:true ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) 
+            ]
+    genome_fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
+    gtf              = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+
+    SALMON_INDEX ( genome_fasta, transcript_fasta )
+    SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false )
+
 }
 
 workflow test_salmon_quant_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] 
-            ]
-    genome        = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
-    transcriptome = file("${launchDir}/tests/data/genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)
-    gtf           = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
 
-    SALMON_INDEX ( genome, transcriptome )
-    SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcriptome, false )
+    input = [ [ 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) ]
+            ]
+    genome_fasta     = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
+    gtf              = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
+
+    SALMON_INDEX ( genome_fasta, transcript_fasta )
+    SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false )
+
 }
diff --git a/tests/software/salmon/quant/test.yml b/tests/software/salmon/quant/test.yml
index f1d9cafa..4bd64059 100644
--- a/tests/software/salmon/quant/test.yml
+++ b/tests/software/salmon/quant/test.yml
@@ -24,31 +24,31 @@
       md5sum: ef13c06a538e9c34ca9f84212c82f44e
     - path: ./output/salmon/test/libParams/flenDist.txt
       md5sum: 2de170bdc9f6fd237d286429b292bb28
-    - path: ./output/salmon/salmon/ref_indexing.log
-    - path: ./output/salmon/salmon/refseq.bin
+    - path: ./output/index/salmon/ref_indexing.log
+    - path: ./output/index/salmon/refseq.bin
       md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
-    - path: ./output/salmon/salmon/versionInfo.json
+    - path: ./output/index/salmon/versionInfo.json
       md5sum: 204865f645102587c4953fccb256797c
-    - path: ./output/salmon/salmon/complete_ref_lens.bin
+    - path: ./output/index/salmon/complete_ref_lens.bin
       md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/salmon/salmon/mphf.bin
+    - path: ./output/index/salmon/mphf.bin
       md5sum: 53669a47610e33e031faafd32703b714
-    - path: ./output/salmon/salmon/pre_indexing.log
-    - path: ./output/salmon/salmon/ctable.bin
-    - path: ./output/salmon/salmon/duplicate_clusters.tsv
+    - path: ./output/index/salmon/pre_indexing.log
+    - path: ./output/index/salmon/ctable.bin
+    - path: ./output/index/salmon/duplicate_clusters.tsv
       md5sum: 51b5292e3a874119c0e1aa566e95d70c
-    - path: ./output/salmon/salmon/reflengths.bin
+    - path: ./output/index/salmon/reflengths.bin
       md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/salmon/salmon/info.json
+    - path: ./output/index/salmon/info.json
       md5sum: 61ff4d3471134c280668355ddd39e99f
-    - path: ./output/salmon/salmon/refAccumLengths.bin
+    - path: ./output/index/salmon/refAccumLengths.bin
       md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
-    - path: ./output/salmon/salmon/ctg_offsets.bin
+    - path: ./output/index/salmon/ctg_offsets.bin
       md5sum: 27a76542337df436436e66017f66dd25
-    - path: ./output/salmon/salmon/rank.bin
+    - path: ./output/index/salmon/rank.bin
       md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
-    - path: ./output/salmon/salmon/pos.bin
-    - path: ./output/salmon/salmon/seq.bin
+    - path: ./output/index/salmon/pos.bin
+    - path: ./output/index/salmon/seq.bin
 
 - name: salmon quant paired end
   command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_paired_end -c tests/config/nextflow.config
@@ -76,28 +76,28 @@
       md5sum: ef13c06a538e9c34ca9f84212c82f44e
     - path: ./output/salmon/test/libParams/flenDist.txt
       md5sum: 221f754ed55dd1e34874f9b7b3f9d240
-    - path: ./output/salmon/salmon/ref_indexing.log
-    - path: ./output/salmon/salmon/refseq.bin
+    - path: ./output/index/salmon/ref_indexing.log
+    - path: ./output/index/salmon/refseq.bin
       md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
-    - path: ./output/salmon/salmon/versionInfo.json
+    - path: ./output/index/salmon/versionInfo.json
       md5sum: 204865f645102587c4953fccb256797c
-    - path: ./output/salmon/salmon/complete_ref_lens.bin
+    - path: ./output/index/salmon/complete_ref_lens.bin
       md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/salmon/salmon/mphf.bin
+    - path: ./output/index/salmon/mphf.bin
       md5sum: 53669a47610e33e031faafd32703b714
-    - path: ./output/salmon/salmon/pre_indexing.log
-    - path: ./output/salmon/salmon/ctable.bin
-    - path: ./output/salmon/salmon/duplicate_clusters.tsv
+    - path: ./output/index/salmon/pre_indexing.log
+    - path: ./output/index/salmon/ctable.bin
+    - path: ./output/index/salmon/duplicate_clusters.tsv
       md5sum: 51b5292e3a874119c0e1aa566e95d70c
-    - path: ./output/salmon/salmon/reflengths.bin
+    - path: ./output/index/salmon/reflengths.bin
       md5sum: f57562f1fca3ae7b133f895ae13c3d08
-    - path: ./output/salmon/salmon/info.json
+    - path: ./output/index/salmon/info.json
       md5sum: 61ff4d3471134c280668355ddd39e99f
-    - path: ./output/salmon/salmon/refAccumLengths.bin
+    - path: ./output/index/salmon/refAccumLengths.bin
       md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
-    - path: ./output/salmon/salmon/ctg_offsets.bin
+    - path: ./output/index/salmon/ctg_offsets.bin
       md5sum: 27a76542337df436436e66017f66dd25
-    - path: ./output/salmon/salmon/rank.bin
+    - path: ./output/index/salmon/rank.bin
       md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
-    - path: ./output/salmon/salmon/pos.bin
-    - path: ./output/salmon/salmon/seq.bin
+    - path: ./output/index/salmon/pos.bin
+    - path: ./output/index/salmon/seq.bin