diff --git a/software/bwa/mem/main.nf b/software/bwa/mem/main.nf
index be6d8977..fb7d848d 100644
--- a/software/bwa/mem/main.nf
+++ b/software/bwa/mem/main.nf
@@ -11,11 +11,11 @@ process BWA_MEM {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
     } else {
-        container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
+        container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
     }
 
     input:
diff --git a/software/bwamem2/index/main.nf b/software/bwamem2/index/main.nf
index b54d5897..7f9dbf19 100644
--- a/software/bwamem2/index/main.nf
+++ b/software/bwamem2/index/main.nf
@@ -11,11 +11,11 @@ process BWAMEM2_INDEX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
 
-    conda (params.enable_conda ? "bioconda::bwa-mem2=2.1" : null)
+    conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bwa-mem2:2.1--he513fc3_0"
+        container "https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0"
     } else {
-        container "quay.io/biocontainers/bwa-mem2:2.1--he513fc3_0"
+        container "quay.io/biocontainers/bwa-mem2:2.2.1--he513fc3_0"
     }
 
     input:
diff --git a/software/bwamem2/mem/main.nf b/software/bwamem2/mem/main.nf
index afe15e76..427caa3a 100644
--- a/software/bwamem2/mem/main.nf
+++ b/software/bwamem2/mem/main.nf
@@ -11,11 +11,11 @@ process BWAMEM2_MEM {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? "bioconda::bwa-mem2=2.1 bioconda::samtools=1.11" : null)
+    conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:e6f0d20c9d78572ddbbf00d8767ee6ff865edd4e-0"
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0"
     } else {
-        container "quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:e6f0d20c9d78572ddbbf00d8767ee6ff865edd4e-0"
+        container "quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0"
     }
 
     input:
diff --git a/tests/software/bwa/index/main.nf b/tests/software/bwa/index/main.nf
index a12aa35d..db3d0200 100644
--- a/tests/software/bwa/index/main.nf
+++ b/tests/software/bwa/index/main.nf
@@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
 include { BWA_INDEX } from '../../../../software/bwa/index/main.nf' addParams( options: [:] )
 
 workflow test_bwa_index {
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BWA_INDEX ( fasta )
 }
diff --git a/tests/software/bwa/index/test.yml b/tests/software/bwa/index/test.yml
index f9d16f13..413fa74e 100644
--- a/tests/software/bwa/index/test.yml
+++ b/tests/software/bwa/index/test.yml
@@ -4,13 +4,13 @@
     - bwa
     - bwa_index
   files:
-    - path: ./output/index/bwa/test_genome.bwt
+    - path: ./output/index/bwa/genome.bwt
       md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: ./output/index/bwa/test_genome.amb
+    - path: ./output/index/bwa/genome.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/index/bwa/test_genome.sa
+    - path: ./output/index/bwa/genome.sa
       md5sum: ab3952cabf026b48cd3eb5bccbb636d1
-    - path: ./output/index/bwa/test_genome.pac
+    - path: ./output/index/bwa/genome.pac
       md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/index/bwa/test_genome.ann
+    - path: ./output/index/bwa/genome.ann
       md5sum: c32e11f6c859f166c7525a9c1d583567
diff --git a/tests/software/bwa/mem/main.nf b/tests/software/bwa/mem/main.nf
index 04453da1..9b65d437 100644
--- a/tests/software/bwa/mem/main.nf
+++ b/tests/software/bwa/mem/main.nf
@@ -10,9 +10,9 @@ include { BWA_MEM } from '../../../../software/bwa/mem/main.nf' addParams( optio
  */
 workflow test_bwa_mem_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
             ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BWA_INDEX ( fasta )
     BWA_MEM ( input, BWA_INDEX.out.index )
@@ -23,10 +23,10 @@ workflow test_bwa_mem_single_end {
  */
 workflow test_bwa_mem_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) ]
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BWA_INDEX ( fasta )
     BWA_MEM ( input, BWA_INDEX.out.index )
diff --git a/tests/software/bwa/mem/test.yml b/tests/software/bwa/mem/test.yml
index 7cbe6619..aa1f9fbf 100644
--- a/tests/software/bwa/mem/test.yml
+++ b/tests/software/bwa/mem/test.yml
@@ -6,16 +6,16 @@
     - bwa_mem_single_end
   files:
     - path: ./output/bwa/test.bam
-      md5sum: c0d98ef222409eca3b7347bfd91484ba
-    - path: ./output/bwa/bwa/test_genome.bwt
+      md5sum: 9165508bf914baee0e6347711aa7b23a
+    - path: ./output/index/bwa/genome.bwt
       md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: ./output/bwa/bwa/test_genome.amb
+    - path: ./output/index/bwa/genome.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwa/bwa/test_genome.ann
+    - path: ./output/index/bwa/genome.ann
       md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: ./output/bwa/bwa/test_genome.pac
+    - path: ./output/index/bwa/genome.pac
       md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwa/bwa/test_genome.sa
+    - path: ./output/index/bwa/genome.sa
       md5sum: ab3952cabf026b48cd3eb5bccbb636d1
 
 - name: bwa mem paired-end
@@ -26,14 +26,14 @@
     - bwa_mem_paired_end
   files:
     - path: ./output/bwa/test.bam
-      md5sum: dcb1c0d42496b582ddb4e8e892b47c4e
-    - path: ./output/bwa/bwa/test_genome.bwt
+      md5sum: 670a53bddee62d6bd14ed7adaf103e7c
+    - path: ./output/index/bwa/genome.bwt
       md5sum: 0469c30a1e239dd08f68afe66fde99da
-    - path: ./output/bwa/bwa/test_genome.amb
+    - path: ./output/index/bwa/genome.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwa/bwa/test_genome.ann
+    - path: ./output/index/bwa/genome.ann
       md5sum: c32e11f6c859f166c7525a9c1d583567
-    - path: ./output/bwa/bwa/test_genome.pac
+    - path: ./output/index/bwa/genome.pac
       md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwa/bwa/test_genome.sa
+    - path: ./output/index/bwa/genome.sa
       md5sum: ab3952cabf026b48cd3eb5bccbb636d1
diff --git a/tests/software/bwamem2/index/main.nf b/tests/software/bwamem2/index/main.nf
index 3c2adfe2..747ecc4f 100644
--- a/tests/software/bwamem2/index/main.nf
+++ b/tests/software/bwamem2/index/main.nf
@@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
 include { BWAMEM2_INDEX } from '../../../../software/bwamem2/index/main.nf' addParams( options: [:] )
 
 workflow test_bwamem2_index {
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BWAMEM2_INDEX ( fasta )
 }
diff --git a/tests/software/bwamem2/index/test.yml b/tests/software/bwamem2/index/test.yml
index 27a0f533..7ec9435f 100644
--- a/tests/software/bwamem2/index/test.yml
+++ b/tests/software/bwamem2/index/test.yml
@@ -4,13 +4,13 @@
     - bwamem2
     - bwamem2_index
   files:
-    - path: ./output/index/bwamem2/test_genome.fasta.amb
+    - path: ./output/index/bwamem2/genome.fasta.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/index/bwamem2/test_genome.fasta.pac
+    - path: ./output/index/bwamem2/genome.fasta.pac
       md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/index/bwamem2/test_genome.fasta.0123
+    - path: ./output/index/bwamem2/genome.fasta.0123
       md5sum: b02870de80106104abcb03cd9463e7d8
-    - path: ./output/index/bwamem2/test_genome.fasta.bwt.2bit.64
+    - path: ./output/index/bwamem2/genome.fasta.bwt.2bit.64
       md5sum: d097a1b82dee375d41a1ea69895a9216
-    - path: ./output/index/bwamem2/test_genome.fasta.ann
+    - path: ./output/index/bwamem2/genome.fasta.ann
       md5sum: c32e11f6c859f166c7525a9c1d583567
diff --git a/tests/software/bwamem2/mem/main.nf b/tests/software/bwamem2/mem/main.nf
index ee7a93d6..312178fb 100644
--- a/tests/software/bwamem2/mem/main.nf
+++ b/tests/software/bwamem2/mem/main.nf
@@ -10,9 +10,9 @@ include { BWAMEM2_MEM   } from '../../../../software/bwamem2/mem/main.nf'   addP
  */
 workflow test_bwamem2_mem_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] 
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
             ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BWAMEM2_INDEX ( fasta )
     BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index )
@@ -23,10 +23,10 @@ workflow test_bwamem2_mem_single_end {
  */
 workflow test_bwamem2_mem_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) ] 
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     BWAMEM2_INDEX ( fasta )
     BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index )
diff --git a/tests/software/bwamem2/mem/test.yml b/tests/software/bwamem2/mem/test.yml
index a058115b..f5acaf83 100644
--- a/tests/software/bwamem2/mem/test.yml
+++ b/tests/software/bwamem2/mem/test.yml
@@ -6,16 +6,16 @@
     - bwamem2_mem_single_end
   files:
     - path: ./output/bwamem2/test.bam
-      md5sum: b0823bb56a248a6870be51d26851214e
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.amb
+      md5sum: 2133c011119ea11f06f0a9b1621ba05b
+    - path: ./output/index/bwamem2/genome.fasta.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.pac
+    - path: ./output/index/bwamem2/genome.fasta.pac
       md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.0123
+    - path: ./output/index/bwamem2/genome.fasta.0123
       md5sum: b02870de80106104abcb03cd9463e7d8
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.bwt.2bit.64
+    - path: ./output/index/bwamem2/genome.fasta.bwt.2bit.64
       md5sum: d097a1b82dee375d41a1ea69895a9216
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.ann
+    - path: ./output/index/bwamem2/genome.fasta.ann
       md5sum: c32e11f6c859f166c7525a9c1d583567
 
 - name: bwamem2 mem paired-end
@@ -26,14 +26,14 @@
     - bwamem2_mem_paired_end
   files:
     - path: ./output/bwamem2/test.bam
-      md5sum: bd938bf4038759be9c872394927eec05
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.amb
+      md5sum: d8fadab5cef04faff1851a8162fc30b5
+    - path: ./output/index/bwamem2/genome.fasta.amb
       md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.pac
+    - path: ./output/index/bwamem2/genome.fasta.pac
       md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.0123
+    - path: ./output/index/bwamem2/genome.fasta.0123
       md5sum: b02870de80106104abcb03cd9463e7d8
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.bwt.2bit.64
+    - path: ./output/index/bwamem2/genome.fasta.bwt.2bit.64
       md5sum: d097a1b82dee375d41a1ea69895a9216
-    - path: ./output/bwamem2/bwamem2/test_genome.fasta.ann
+    - path: ./output/index/bwamem2/genome.fasta.ann
       md5sum: c32e11f6c859f166c7525a9c1d583567