diff --git a/CHANGELOG.md b/CHANGELOG.md
index 76ebdd61d9..49943ad938 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -93,6 +93,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#644](https://github.com/nf-core/sarek/pull/644) - Use `-Y` for `bwa-mem(2)` and remove `-M`
 - [#645](https://github.com/nf-core/sarek/pull/645) - Merge `tests/nextflow.config` in `conf/test.config`
 - [#646](https://github.com/nf-core/sarek/pull/646) - Update `nextflow_schema.json` to reflect new parameters and functions, removes `--annotation_cache`, removes `--ascat_chromosomes`
+- [#653](https://github.com/nf-core/sarek/pull/653) - Coherent results subfolder structure between preprocessing, variantcalling and reporting
 
 ### Fixed
 
diff --git a/conf/modules.config b/conf/modules.config
index 5bafaa61a3..6facf23688 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -143,7 +143,7 @@ process {
         publishDir       = [
             enabled: params.save_reference,
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reference" },
+            path: { "${params.outdir}/reference/cnvkit" },
             pattern: "*{bed}"
         ]
     }
@@ -154,7 +154,7 @@ process {
         publishDir       = [
             enabled: params.save_reference,
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reference" },
+            path: { "${params.outdir}/reference/cnvkit" },
             pattern: "*{cnn}"
         ]
     }
@@ -243,7 +243,7 @@ process {
             ],
             [
                 enabled: params.save_trimmed || params.save_split_fastqs,
-                path: { "${params.outdir}/preprocessing/${meta.sample}/fastp" },
+                path: { "${params.outdir}/preprocessing/fastp/${meta.sample}/" },
                 mode: params.publish_dir_mode,
                 pattern: "*.fastp.fastq.gz"
             ]
@@ -304,7 +304,7 @@ process {
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/preprocessing/" },
                 pattern: "*bam",
-                saveAs: { (params.save_bam_mapped || (params.skip_tools && params.skip_tools.split(',').contains('markduplicates'))) && (meta.size * meta.numLanes == 1) ? "${meta.id}/mapped/${it}" : null }
+                saveAs: { (params.save_bam_mapped || (params.skip_tools && params.skip_tools.split(',').contains('markduplicates'))) && (meta.size * meta.numLanes == 1) ? "mapped/${meta.id}/${it}" : null }
             ]
         }
 
@@ -317,7 +317,7 @@ process {
     withName: 'MERGE_BAM|INDEX_MERGE_BAM' {
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/preprocessing/${meta.id}/mapped" },
+            path: { "${params.outdir}/preprocessing/mapped/${meta.id}/" },
             pattern: "*{bam,bai}"
         ]
     }
@@ -342,7 +342,7 @@ process {
         publishDir       = [
             enabled: !params.save_output_as_bam,
             mode: params.publish_dir_mode,
-            path: { (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) ? "${params.outdir}/preprocessing/${meta.id}/mapped" : "${params.outdir}/preprocessing/${meta.id}/markduplicates" },
+            path: { (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) ? "${params.outdir}/preprocessing/mapped/${meta.id}/" : "${params.outdir}/preprocessing/markduplicates/${meta.id}/" },
             pattern: "*{cram,crai}"
         ]
     }
@@ -365,7 +365,7 @@ process {
             [
                 enabled: params.save_output_as_bam,
                 mode: params.publish_dir_mode,
-                path: { "${params.outdir}/preprocessing/${meta.id}/markduplicates" },
+                path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" },
                 pattern: "*{bam,bai}"
             ],
             [
@@ -383,7 +383,7 @@ process {
         publishDir       = [
             enabled: !params.save_output_as_bam,
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/preprocessing/${meta.id}/markduplicates" },
+            path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" },
             pattern: "*{cram,crai}"
         ]
     }
@@ -392,7 +392,7 @@ process {
         publishDir       = [
             enabled: !params.save_output_as_bam,
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/preprocessing/${meta.id}/markduplicates" },
+            path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" },
             pattern: "*{cram,crai}"
         ]
     }
@@ -404,7 +404,7 @@ process {
             publishDir       = [
                 enabled: params.save_output_as_bam,
                 mode: params.publish_dir_mode,
-                path: { "${params.outdir}/preprocessing/${meta.id}/markduplicates" },
+                path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" },
                 pattern: "*{md.bam,md.bam.bai}"
             ]
         }
@@ -416,9 +416,9 @@ process {
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/preprocessing/${meta.id}/" },
+            path: { "${params.outdir}/preprocessing/" },
             pattern: "*table",
-            saveAs: { meta.num_intervals > 1 ? null : "recal_table/${it}" }
+            saveAs: { meta.num_intervals > 1 ? null : "recal_table/${meta.id}/${it}" }
         ]
     }
 
@@ -427,7 +427,7 @@ process {
         ext.when         = { meta.num_intervals > 1 }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/preprocessing/${meta.id}/recal_table" },
+            path: { "${params.outdir}/preprocessing/recal_table/${meta.id}/" },
             pattern: "*table",
         ]
     }
@@ -439,9 +439,9 @@ process {
         publishDir       = [
             enabled: !params.save_output_as_bam,
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/preprocessing/${meta.id}/" },
+            path: { "${params.outdir}/preprocessing/" },
             pattern: "*cram",
-            saveAs: { meta.num_intervals > 1 ? null : "recalibrated/${it}" }
+            saveAs: { meta.num_intervals > 1 ? null : "recalibrated/${meta.id}/${it}" }
         ]
     }
 
@@ -453,7 +453,7 @@ process {
             publishDir       = [
                 enabled: !params.save_output_as_bam,
                 mode: params.publish_dir_mode,
-                path: { "${params.outdir}/preprocessing/${meta.id}/recalibrated" },
+                path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" },
                 pattern: "*cram"
             ]
         }
@@ -462,7 +462,7 @@ process {
             publishDir       = [
                 enabled: !params.save_output_as_bam,
                 mode: params.publish_dir_mode,
-                path: { "${params.outdir}/preprocessing/${meta.id}/recalibrated" },
+                path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" },
                 pattern: "*{recal.cram,recal.cram.crai}"
             ]
         }
@@ -474,7 +474,7 @@ process {
         publishDir       = [
             enabled: params.save_output_as_bam,
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/preprocessing/${meta.id}/recalibrated" },
+            path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" },
             pattern: "*{recal.bam,recal.bam.bai}"
         ]
     }
@@ -483,7 +483,7 @@ process {
         ext.prefix       = { "${meta.id}.recal" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/preprocessing/${meta.id}/recalibrated" },
+            path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" },
             pattern: "*{cram,crai}"
         ]
     }
@@ -555,7 +555,7 @@ process{
         ext.when         = { params.tools && params.tools.split(',').contains('cnvkit') }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/cnvkit" },
+            path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" },
             pattern: "*{bed,cnn,cnr,cns,pdf,png}"
         ]
     }
@@ -565,7 +565,7 @@ process{
         ext.prefix       = {"${meta.id}.deepvariant"}
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/deepvariant" },
+            path: { "${params.outdir}/variant_calling/deepvariant/${meta.id}/" },
             pattern: "*{vcf.gz,vcf.gz.tbi}"
         ]
     }
@@ -578,16 +578,16 @@ process{
         ext.when         = { params.tools && params.tools.split(',').contains('deepvariant') }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/" },
+            path: { "${params.outdir}/variant_calling/" },
             pattern: "*vcf.gz",
-            saveAs: { meta.num_intervals > 1 ? null : "deepvariant/${it}" }
+            saveAs: { meta.num_intervals > 1 ? null : "deepvariant/${meta.id}/${it}" }
         ]
     }
     withName : 'TABIX_VC_DEEPVARIANT_.*' {
         ext.prefix       = {"${meta.id}.deepvariant"}
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/deepvariant" },
+            path: { "${params.outdir}/variant_calling/deepvariant/${meta.id}/" },
             pattern: "*tbi"
         ]
     }
@@ -597,7 +597,7 @@ process{
         ext.prefix       = { "${meta.id}.freebayes" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" },
+            path: { "${params.outdir}/variant_calling/freebayes/${meta.id}/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -615,16 +615,16 @@ process{
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${vcf.minus("vcf")}.sort" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/" },
+            path: { "${params.outdir}/variant_calling/" },
             pattern: "*vcf.gz",
-            saveAs: { meta.num_intervals > 1 ? null : "freebayes/${it}" }
+            saveAs: { meta.num_intervals > 1 ? null : "freebayes/${meta.id}/${it}" }
         ]
     }
 
     withName : 'TABIX_VC_FREEBAYES' {
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" },
+            path: { "${params.outdir}/variant_calling/freebayes/${meta.id}/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -634,7 +634,7 @@ process{
         ext.prefix       = { params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller" },
+            path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -645,9 +645,9 @@ process{
         ext.when         = { params.tools && params.tools.split(',').contains('haplotypecaller') }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/"},
+            path: { "${params.outdir}/variant_calling/"},
             pattern: "*{vcf.gz,vcf.gz.tbi}",
-            saveAs: { meta.num_intervals > 1 ? null : "haplotypecaller/${it}" }
+            saveAs: { meta.num_intervals > 1 ? null : "haplotypecaller/${meta.id}/${it}" }
         ]
     }
     withName: 'CNNSCOREVARIANTS' {
@@ -660,7 +660,7 @@ process{
         ext.args         = { "--info-key CNN_1D" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller/"},
+            path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/"},
             pattern: "*{vcf.gz,vcf.gz.tbi}"
         ]
     }
@@ -670,7 +670,7 @@ process{
         ext.when         = { params.tools && params.tools.split(',').contains('haplotypecaller') && params.joint_germline}
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller"},
+            path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/"},
             pattern: "*{vcf.gz,vcf.gz.tbi}"
         ]
     }
@@ -679,7 +679,7 @@ process{
     withName: 'MERGE_MANTA.*' {
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/manta" },
+            path: { "${params.outdir}/variant_calling/manta/${meta.id}/" },
             pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}"
         ]
     }
@@ -698,9 +698,9 @@ process{
         ext.when         = { params.tools && params.tools.split(',').contains('manta') }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/" },
+            path: { "${params.outdir}/variant_calling/" },
             pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}",
-            saveAs: { meta.num_intervals > 1 ? null : "manta/${it}" }
+            saveAs: { meta.num_intervals > 1 ? null : "manta/${meta.id}/${it}" }
         ]
     }
 
@@ -708,7 +708,7 @@ process{
     withName: 'MERGE_STRELKA.*' {
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/strelka" },
+            path: { "${params.outdir}/variant_calling/strelka/${meta.id}/" },
             pattern: "*{vcf.gz,vcf.gz.tbi}"
         ]
     }
@@ -724,9 +724,9 @@ process{
         ext.when         = { params.tools && params.tools.split(',').contains('strelka') }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/" },
+            path: { "${params.outdir}/variant_calling/" },
             pattern: "*{vcf.gz,vcf.gz.tbi}",
-            saveAs: { meta.num_intervals > 1 ? null : "strelka/${it}" }
+            saveAs: { meta.num_intervals > 1 ? null : "strelka/${meta.id}/${it}" }
         ]
     }
 
@@ -737,7 +737,7 @@ process{
         ext.prefix       = { "${meta.id}.tiddit" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
+            path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" },
             pattern: "*tab",
         ]
     }
@@ -745,7 +745,7 @@ process{
         ext.prefix       = { "${meta.id}.tiddit" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
+            path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" },
             pattern: "*{vcf.gz,vcf.gz.tbi}"
         ]
     }
@@ -756,7 +756,7 @@ process{
     withName: 'ASSESS_SIGNIFICANCE' {
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
+            path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
             pattern: "*{.p.value.txt}"
         ]
     }
@@ -764,7 +764,7 @@ process{
     withName: 'CAT_MPILEUP' {
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mpileup" },
+            path: { "${params.outdir}/variant_calling/mpileup/${meta.id}/" },
             pattern: "*{mpileup.gz}",
         ]
     }
@@ -773,7 +773,7 @@ process{
         ext.when         = { params.tools && params.tools.split(',').contains('controlfreec') }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
+            path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
             pattern: "*{BedGraph,cpn,txt,_CNVs}"
         ]
     }
@@ -814,7 +814,7 @@ process{
         ext.args = { "${params.ploidy}" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
+            path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
             pattern: "*bed"
         ]
     }
@@ -823,7 +823,7 @@ process{
         ext.args = { "${params.ploidy}" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
+            path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
             pattern: "*circos.txt"
         ]
     }
@@ -832,7 +832,7 @@ process{
         ext.args = { "${params.ploidy}" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
+            path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
             pattern: "*png"
         ]
     }
@@ -841,7 +841,7 @@ process{
         ext.when         = { params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('mpileup')) }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mpileup" },
+            path: { "${params.outdir}/variant_calling/mpileup/${meta.id}/" },
             pattern: "*mpileup.gz",
             saveAs: { meta.num_intervals > 1 ? null : it }
         ]
@@ -859,7 +859,7 @@ process{
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.id}/mutect2/${filename}" }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "mutect2/${meta.id}/${filename}" }
         ]
     }
 
@@ -867,7 +867,7 @@ process{
         ext.prefix       = { "${meta.id}.mutect2" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            path: { "${params.outdir}/variant_calling/mutect2/${meta.id}" },
             pattern: "*{vcf.gz,vcf.gz.tbi}"
         ]
     }
@@ -877,7 +877,7 @@ process{
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.id}/mutect2/${filename}" }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "mutect2/${meta.id}/${filename}" }
         ]
     }
 
@@ -885,7 +885,7 @@ process{
         ext.prefix       = { "${meta.id}.mutect2" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            path: { "${params.outdir}/variant_calling/mutect2/${meta.id}/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -894,7 +894,7 @@ process{
         ext.prefix       = { "${meta.id}.mutect2" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.tumor_id}_vs_${meta.normal_id}/mutect2" },
+            path: { "${params.outdir}/variant_calling/mutect2/${meta.tumor_id}_vs_${meta.normal_id}/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -905,7 +905,7 @@ process{
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },
             pattern: "*.table",
-            saveAs: { meta.num_intervals > 1 ? null : "${meta.id}/mutect2/${it}" }
+            saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.id}/${it}" }
         ]
     }
 
@@ -915,7 +915,7 @@ process{
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },
             pattern: "*.table",
-            saveAs: { meta.num_intervals > 1 ? null : "${meta.tumor_id}_vs_${meta.normal_id}/mutect2/${it}" }
+            saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.tumor_id}_vs_${meta.normal_id}/${it}" }
         ]
     }
 
@@ -923,7 +923,7 @@ process{
         ext.prefix       = { "${meta.id}.mutect2.artifactprior" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            path: { "${params.outdir}/variant_calling/mutect2/${meta.id}/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -932,7 +932,7 @@ process{
         ext.prefix       = { "${meta.id}.mutect2" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            path: { "${params.outdir}/variant_calling/mutect2/${meta.id}/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -945,7 +945,7 @@ process{
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },
             pattern: "*{vcf.gz,vcf.gz.tbi,stats}",
-            saveAs: { meta.num_intervals > 1 ? null : "${meta.id}/mutect2/${it}" }
+            saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.id}/${it}" }
         ]
     }
 
@@ -967,7 +967,7 @@ process{
         ext.when         = { params.tools && params.tools.split(',').contains('ascat') }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/ascat" },
+            path: { "${params.outdir}/variant_calling/ascat/${meta.id}/" },
             pattern: "*{png,cnvs.txt,metrics.txt,purityploidy.txt,segments.txt,LogR.txt,BAF.txt}"
         ]
 
@@ -1076,7 +1076,7 @@ process{
     withName: 'MSISENSORPRO_MSI_SOMATIC' {
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/msisensorpro" },
+            path: { "${params.outdir}/variant_calling/msisensorpro/${meta.id}/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -1104,7 +1104,7 @@ process{
             ext.prefix       = { "${meta.id}.tiddit" }
             publishDir       = [
                 mode: params.publish_dir_mode,
-                path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
+                path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" },
                 pattern: "*vcf"
             ]
         }
@@ -1116,7 +1116,7 @@ process{
         ext.prefix       = { "${vcf.baseName.minus(".vcf")}" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reports/bcftools/${meta.id}/${meta.variantcaller}/" },
+            path: { "${params.outdir}/reports/bcftools/${meta.variantcaller}/${meta.id}/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -1126,7 +1126,7 @@ process{
         ext.prefix       = { "${variant_file.baseName.minus(".vcf")}" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reports/vcftools/${meta.id}/${meta.variantcaller}/" },
+            path: { "${params.outdir}/reports/vcftools/${meta.variantcaller}/${meta.id}/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -1154,7 +1154,7 @@ process{
             publishDir       = [
                 [
                     mode: params.publish_dir_mode,
-                    path: { "${params.outdir}/reports/snpeff/${meta.id}/${meta.variantcaller}" },
+                    path: { "${params.outdir}/reports/snpeff/${meta.variantcaller}/${meta.id}/" },
                     pattern: "*{csv,html,genes.txt}",
                     saveAs: { params.tools.split(',').contains('snpeff') ? it : null }
                 ]
@@ -1180,12 +1180,12 @@ process{
             publishDir       = [
                 [
                     mode: params.publish_dir_mode,
-                    path: { "${params.outdir}/reports/EnsemblVEP/${meta.id}/${meta.variantcaller}" },
+                    path: { "${params.outdir}/reports/EnsemblVEP/${meta.variantcaller}/${meta.id}/" },
                     pattern: "*html"
                 ],
                 [
                     mode: params.publish_dir_mode,
-                    path: { "${params.outdir}/annotation/${meta.id}/${meta.variantcaller}" },
+                    path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
                     pattern: "*{json,tab}"
                 ]
             ]
@@ -1206,7 +1206,7 @@ process{
             ext.prefix       = { input.baseName.minus(".vcf") }
             publishDir       = [
                     mode: params.publish_dir_mode,
-                    path: { "${params.outdir}/annotation/${meta.id}/${meta.variantcaller}" },
+                    path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
                     pattern: "*{gz,gz.tbi}"
             ]
         }
@@ -1216,7 +1216,7 @@ process{
         withName: 'NFCORE_SAREK:SAREK:ANNOTATE:ANNOTATION_SNPEFF:TABIX_BGZIPTABIX' {
             publishDir       = [
                 mode: params.publish_dir_mode,
-                path: { "${params.outdir}/annotation/${meta.id}/${meta.variantcaller}" },
+                path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
                 pattern: "*{gz,gz.tbi}",
                 saveAs: { params.tools.split(',').contains('snpeff') ? it : null }
             ]
diff --git a/docs/output.md b/docs/output.md
index 9cda28ff4e..0300dbfd77 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -70,10 +70,12 @@ The default directory structure is as follows
 ├── multiqc
 ├── pipeline_info
 ├── preprocessing
-│   └── <sample>
-│       ├── markduplicates
-│       ├── recal_table
-│       └── recalibrated
+│   ├── markduplicates
+│       └── <sample>
+│   ├── recal_table
+│       └── <sample>
+│   └── recalibrated
+│       └── <sample>
 ├── reference
 └── reports
     ├── <tool1>
@@ -100,7 +102,7 @@ The resulting files are intermediate and by default not kept in the final files
 <details markdown="1">
 <summary>Output files for all samples</summary>
 
-**Output directory: `{outdir}/preprocessing/<sample>/fastp/`**
+**Output directory: `{outdir}/preprocessing/fastp/<sample>`**
 
 - `<sample>_<lane>_{1,2}.fastp.fastq.gz>`
   - Bgzipped FastQ file
@@ -116,7 +118,7 @@ These files are intermediate and by default not kept in the final files delivere
 <details markdown="1">
 <summary>Output files for all samples</summary>
 
-**Output directory: `{outdir}/preprocessing/<sample>/fastp/`**
+**Output directory: `{outdir}/preprocessing/fastp/<sample>/`**
 
 - `<sample_lane_{1,2}.fastp.fastq.gz>`
   - Bgzipped FastQ file
@@ -146,7 +148,7 @@ These files are intermediate and by default not kept in the final files delivere
 <details markdown="1">
 <summary>Output files for all mappers and samples</summary>
 
-**Output directory: `{outdir}/preprocessing/<sample>/mapped`**
+**Output directory: `{outdir}/preprocessing/mapped/<sample>/`**
 
 - if `--save_bam_mapped`: `<sample>.bam` and `<sample>.bam.bai`
   - BAM file and index
@@ -170,7 +172,7 @@ The resulting CRAM files are delivered to the users.
 <details markdown="1">
 <summary>Output files for all samples</summary>
 
-**Output directory: `{outdir}/preprocessing/<sample>/markduplicates`**
+**Output directory: `{outdir}/preprocessing/markduplicates/<sample>/`**
 
 - `<sample>.md.cram` and `<sample>.md.cram.crai`
   - CRAM file and index
@@ -194,7 +196,7 @@ To use the corresponding spark implementation [GATK BaseRecalibratorSpark](https
 <details markdown="1">
 <summary>Output files for all samples</summary>
 
-**Output directory: `{outdir}/preprocessing/<sample>/recal_table`**
+**Output directory: `{outdir}/preprocessing/recal_table/<sample>/`**
 
 - `<sample>.recal.table`
   - Recalibration table associated to the duplicates-marked CRAM file.
@@ -212,7 +214,7 @@ The resulting recalibrated CRAM files are delivered to the user. Recalibrated CR
 <details markdown="1">
 <summary>Output files for all samples</summary>
 
-**Output directory: `{outdir}/preprocessing/<sample>/recalibrated`**
+**Output directory: `{outdir}/preprocessing/recalibrated/<sample>/`**
 
 - `<sample>.recal.cram` and `<sample>.recal.cram.crai`
   - CRAM file and index
@@ -262,7 +264,7 @@ For single nucleotide variants (SNVs) and small indels, multiple tools are avail
 <details markdown="1">
 <summary>Output files for normal samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<sample>/deepvariant`**
+**Output directory: `{outdir}/variantcalling/deepvariant/<sample>/`**
 
 - `<sample>.deepvariant.vcf.gz` and `<sample>.deepvariant.vcf.gz.tbi`
   - VCF with tabix index
@@ -277,7 +279,7 @@ For single nucleotide variants (SNVs) and small indels, multiple tools are avail
 <details markdown="1">
 <summary>Output files for all samples</summary>
 
-**Output directory: `{outdir}/variantcalling/{sample,normalsample_vs_tumorsample}/freebayes`**
+**Output directory: `{outdir}/variantcalling/freebayes/{sample,normalsample_vs_tumorsample}/`**
 
 - `<sample>.freebayes.vcf.gz` and `<sample>.freebayes.vcf.gz.tbi`
   - VCF with tabix index
@@ -291,7 +293,7 @@ For single nucleotide variants (SNVs) and small indels, multiple tools are avail
 <details markdown="1">
 <summary>Output files for normal samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<sample>/haplotypecaller`**
+**Output directory: `{outdir}/variantcalling/haplotypecaller/<sample>/`**
 
 - `<sample>.haplotypecaller.vcf.gz` and `<sample>.haplotypecaller.vcf.gz.tbi`
   - VCF with tabix index
@@ -308,7 +310,7 @@ If the haplotype-called VCF files are not filtered, then Sarek should be run wit
 <details markdown="1">
 <summary>Output files for normal samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<sample>/haplotypecaller`**
+**Output directory: `{outdir}/variantcalling/haplotypecaller/<sample>/`**
 
 - `<sample>.haplotypecaller.filtered.vcf.gz` and `<sample>.haplotypecaller.filtered.vcf.gz.tbi`
   - VCF with tabix index
@@ -319,7 +321,7 @@ If the haplotype-called VCF files are not filtered, then Sarek should be run wit
 
 [GATK Joint germline Variant Calling](https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-) uses Haplotypecaller per sample in `gvcf` mode. Next, the gVCFs are consolidated from multiple samples into a [GenomicsDB](https://gatk.broadinstitute.org/hc/en-us/articles/5358869876891-GenomicsDBImport) datastore. After joint [genotyping](https://gatk.broadinstitute.org/hc/en-us/articles/5358906861083-GenotypeGVCFs), [VQSR](https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator) is applied for filtering to produce the final multisample callset with the desired balance of precision and sensitivity.
 
-**Output directory: `{outdir}/variantcalling/<sample>/haplotypecaller`**
+**Output directory: `{outdir}/variantcalling/haplotypecaller/<sample>/`**
 
 _TODO_
 
@@ -332,7 +334,7 @@ It is not required, but recommended to have a [panel of normals (PON)](https://g
 <details markdown="1">
 <summary>Output files for tumor-only and tumor/normal paired samples</summary>
 
-**Output directory: `{outdir}/variantcalling/{sample,tumorsample_vs_normalsample}/mutect2`**
+**Output directory: `{outdir}/variantcalling/mutect2/{sample,tumorsample_vs_normalsample}/`**
 
 Files created:
 
@@ -363,7 +365,7 @@ For further reading and documentation see the [samtools manual](https://www.htsl
 <details markdown="1">
 <summary>Output files for all samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<sample>/mpileup`**
+**Output directory: `{outdir}/variantcalling/mpileup/<sample>/`**
 
 - `<sample>.pileup.gz`
   - The pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. Alignment records are grouped by sample (`SM`) identifiers in `@RG` header lines.
@@ -378,7 +380,7 @@ For further downstream analysis, take a look [here](https://github.com/Illumina/
 <details markdown="1">
 <summary>Output files for all single samples (normal or tumor-only)</summary>
 
-**Output directory: `{outdir}/variantcalling/<sample>/strelka`**
+**Output directory: `{outdir}/variantcalling/strelka/<sample>/`**
 
 - `<sample>.strelka.genome.vcf.gz` and `<sample>.strelka.genome.vcf.gz.tbi`
   - genome VCF with tabix index
@@ -389,7 +391,7 @@ For further downstream analysis, take a look [here](https://github.com/Illumina/
 <details markdown="1">
 <summary>Output files for tumor/normal paired samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<tumorsample_vs_normalsample>/strelka`**
+**Output directory: `{outdir}/variantcalling/strelka/<tumorsample_vs_normalsample>/`**
 
 - `<tumorsample_vs_normalsample>.strelka.somatic_indels.vcf.gz` and `<tumorsample_vs_normalsample>.strelka.somatic_indels.vcf.gz.tbi`
   - VCF with tabix index with all somatic indels inferred in the tumor sample.
@@ -409,7 +411,7 @@ It is optimized for analysis of germline variation in small sets of individuals
 <details markdown="1">
 <summary>Output files for normal samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<sample>/manta`**
+**Output directory: `{outdir}/variantcalling/manta/<sample>/`**
 
 - `<sample>.manta.diploid_sv.vcf.gz` and `<sample>.manta.diploid_sv.vcf.gz.tbi`
   - VCF with tabix index containing SVs and indels scored and genotyped under a diploid model for the sample.
@@ -418,7 +420,7 @@ It is optimized for analysis of germline variation in small sets of individuals
 <details markdown="1">
 <summary>Output files for tumor-only samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<sample>/manta`**
+**Output directory: `{outdir}/variantcalling/manta/<sample>/`**
 
 - `<sample>.manta.tumor_sv.vcf.gz` and `<sample>.manta.tumor_sv.vcf.gz.tbi`
   - VCF with tabix index containing a subset of the candidateSV.vcf.gz file after removing redundant candidates and small indels less than the minimum scored variant size (50 by default). The SVs are not scored, but include additional details: (1) paired and split read supporting evidence counts for each allele (2) a subset of the filters from the scored tumor-normal model are applied to the single tumor case to improve precision.
@@ -427,7 +429,7 @@ It is optimized for analysis of germline variation in small sets of individuals
 <details markdown="1">
 <summary>Output files for tumor/normal paired samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<tumorsample_vs_normalsample>/manta`**
+**Output directory: `{outdir}/variantcalling/manta/<tumorsample_vs_normalsample>/`**
 
 - `<tumorsample_vs_normalsample>.manta.diploid_sv.vcf.gz` and `<tumorsample_vs_normalsample>.manta.diploid_sv.vcf.gz.tbi`
   - VCF with tabix index containing SVs and indels scored and genotyped under a diploid model for the sample. In the case of a tumor/normal subtraction, the scores in this file do not reflect any information from the tumor sample.
@@ -442,7 +444,7 @@ It is optimized for analysis of germline variation in small sets of individuals
 <details markdown="1">
 <summary>Output files for normal and tumor-only samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<sample>/tiddit`**
+**Output directory: `{outdir}/variantcalling/tiddit/<sample>/`**
 
 - `<sample>.tiddit.vcf.gz` and `<sample>.tiddit.vcf.gz.tbi`
   - VCF with tabix index containing SV calls
@@ -454,7 +456,7 @@ It is optimized for analysis of germline variation in small sets of individuals
 <details markdown="1">
 <summary>Output files for tumor/normal paired samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<tumorsample_vs_normalsample>/tiddit`**
+**Output directory: `{outdir}/variantcalling/tiddit/<tumorsample_vs_normalsample>/`**
 
 - `<tumorsample_vs_normalsample>.tiddit.normal.vcf.gz` and `<tumorsample_vs_normalsample>.tiddit.normal.vcf.gz.tbi`
   - VCF with tabix index containing SV calls
@@ -480,7 +482,7 @@ This is done internally using the software [AlleleCount](https://github.com/canc
 <details markdown="1">
 <summary>Output files for tumor/normal paired samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<tumorsample_vs_normalsample>/ascat`**
+**Output directory: `{outdir}/variantcalling/ascat/<tumorsample_vs_normalsample>/`**
 
 - `<tumorsample_vs_normalsample>.tumour.ASPCF.png`
   - image with information about allele-specific copy number segmentation
@@ -527,7 +529,7 @@ The file `<tumorsample_vs_normalsample>.cnvs.txt` contains all segments predicte
 <details markdown="1">
 <summary>Output files for normal and tumor-only samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<sample>/cnvkit`**
+**Output directory: `{outdir}/variantcalling/cnvkit/<sample>/`**
 
 - `<sample>.antitargetcoverage.cnn`
   - file containing coverage information
@@ -551,7 +553,7 @@ The file `<tumorsample_vs_normalsample>.cnvs.txt` contains all segments predicte
 <details markdown="1">
 <summary>Output files for tumor/normal samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<tumorsample_vs_normalsample>/cnvkit`**
+**Output directory: `{outdir}/variantcalling/cnvkit/<tumorsample_vs_normalsample>/`**
 
 - `<normalsample>.antitargetcoverage.cnn`
   - file containing coverage information
@@ -584,7 +586,7 @@ It also detects subclonal gains and losses and evaluates the most likely average
 <details markdown="1">
 <summary>Output files for tumor-only and tumor/normal paired samples</summary>
 
-**Output directory: `{outdir}/variantcalling/{tumorsample,tumorsample_vs_normalsample}/controlfreec`**
+**Output directory: `{outdir}/variantcalling/controlfreec/{tumorsample,tumorsample_vs_normalsample}/`**
 
 - `config.txt`
   - Configuration file used to run Control-FREEC
@@ -632,7 +634,7 @@ It requires a normal sample for each tumour to differentiate the somatic and ger
 <details markdown="1">
 <summary>Output files for tumor/normal paired samples</summary>
 
-**Output directory: `{outdir}/variantcalling/<tumorsample_vs_normalsample>/msisensor`**
+**Output directory: `{outdir}/variantcalling/msisensor/<tumorsample_vs_normalsample>/`**
 
 - `<tumorsample_vs_normalsample>`
   - MSI score output, contains information about the number of somatic sites.
diff --git a/docs/usage.md b/docs/usage.md
index c88ca3cea2..9264feb458 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -30,7 +30,7 @@ results         # Finished results (configurable, see below)
 # Other nextflow hidden files, eg. history of pipeline runs and old logs.
 ```
 
-### Input: Samplesheet configurations
+### Input: Sample sheet configurations
 
 You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use the parameter `--input` to specify its location. It has to be a comma-separated file with at least 3 columns, and a header row as shown in the examples below.
 
@@ -47,7 +47,7 @@ Output from Variant Calling and/or Annotation will be in a specific directory fo
 Multiple CSV files can be specified if the path is enclosed in quotes.
 
 ```console
---input '[path to samplesheet file(s)]'
+--input '[path to sample sheet file(s)]'
 ```
 
 #### Overview: Samplesheet Columns
@@ -550,7 +550,7 @@ Some of the currently, available test profiles:
 | :-------------- | :------------------------------------------------------------------------------ |
 | annotation      | `nextflow run main.nf -profile test,annotation,docker --tools snpeff.vep,merge` |
 | no_intervals    | `nextflow run main.nf -profile test,no_intervals,docker`                        |
-| targeted        | ` nextflow run main.nf -profile test,targeted,docker`                           |
+| targeted        | `nextflow run main.nf -profile test,targeted,docker`                            |
 | tools_germline  | `nextflow run main.nf -profile test,tools_germline,docker --tools strelka`      |
 | tools_tumoronly | `nextflow run main.nf -profile test,tools_tumoronly,docker --tools strelka`     |
 | tools_somatic   | `nextflow run main.nf -profile test,tools_somatic,docker --tools strelka`       |
diff --git a/tests/test_aligner.yml b/tests/test_aligner.yml
index 6b49682e7b..86858065f5 100644
--- a/tests/test_aligner.yml
+++ b/tests/test_aligner.yml
@@ -9,11 +9,11 @@
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/reference/bwamem2/genome.fasta.0123
     - path: results/reference/bwamem2/genome.fasta.amb
     - path: results/reference/bwamem2/genome.fasta.ann
@@ -41,11 +41,11 @@
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/reference/dragmap/hash_table.cfg
     - path: results/reference/dragmap/hash_table.cfg.bin
     - path: results/reference/dragmap/hash_table.cmp
diff --git a/tests/test_bam_remap.yml b/tests/test_bam_remap.yml
index 9e91c19342..f49d42d9a8 100644
--- a/tests/test_bam_remap.yml
+++ b/tests/test_bam_remap.yml
@@ -11,7 +11,7 @@
     - path: results/csv/recalibrated.csv
     - path: results/multiqc/multiqc_report.html
     - path: results/pipeline_info
-    - path: results/preprocessing/test
+    - path: results/preprocessing/
     - path: results/reports
     - path: results/samtools
     - path: results/collate
diff --git a/tests/test_default.yml b/tests/test_default.yml
index b4103f49c0..c52b174a08 100644
--- a/tests/test_default.yml
+++ b/tests/test_default.yml
@@ -5,11 +5,11 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
@@ -34,11 +34,11 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
@@ -62,11 +62,11 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
@@ -82,7 +82,7 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools/test/test.md.cram.stats
     - path: results/reports/samtools/test/test.recal.cram.stats
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
diff --git a/tests/test_gatk_spark.yml b/tests/test_gatk_spark.yml
index 6f0cf0f78a..8f97e0e721 100644
--- a/tests/test_gatk_spark.yml
+++ b/tests/test_gatk_spark.yml
@@ -6,11 +6,11 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
diff --git a/tests/test_markduplicates.yml b/tests/test_markduplicates.yml
index d28376ffec..44b326bf03 100644
--- a/tests/test_markduplicates.yml
+++ b/tests/test_markduplicates.yml
@@ -6,11 +6,11 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
@@ -24,10 +24,10 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools/test/test.md.cram.stats
     - path: results/reports/samtools/test/test.recal.cram.stats
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
 
 - name: Run Mark Duplicates starting from CRAM
   command: nextflow run main.nf -profile test,markduplicates_cram,docker --tools strelka
@@ -37,11 +37,11 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
@@ -55,7 +55,7 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools/test/test.md.cram.stats
     - path: results/reports/samtools/test/test.recal.cram.stats
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
diff --git a/tests/test_only_paired_VC.yml b/tests/test_only_paired_VC.yml
index 58ca79ba1e..99cecd96bc 100644
--- a/tests/test_only_paired_VC.yml
+++ b/tests/test_only_paired_VC.yml
@@ -6,19 +6,19 @@
     - only_paired_variant_calling
     - copy_number_calling
   files:
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/multi_intervals.antitarget.bed
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test.paired_end.recalibrated.sorted.targetcoverage.cnn
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/reference.cnn
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted-scatter.png
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted-diagram.pdf
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.cnr
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.cns
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/multi_intervals.target.bed
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.antitarget.bed
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test.paired_end.recalibrated.sorted.targetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.bintest.cns
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/reference.cnn
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted-scatter.png
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted-diagram.pdf
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cnr
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cns
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.target.bed
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.call.cns
 
 - name: Skip variant calling on matched normal
   command: nextflow run main.nf -profile test,variantcalling_channels,docker --tools strelka --only_paired_variant_calling
@@ -27,26 +27,26 @@
     - strelka
     - variantcalling_channel
   files:
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz
       should_exist: false
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi
       should_exist: false
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz
       should_exist: false
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi
       should_exist: false
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
 
 - name: Do germline variant calling on matched normal
   command: nextflow run main.nf -profile test,variantcalling_channels,docker --tools strelka
@@ -55,19 +55,19 @@
     - strelka
     - variantcalling_channel
   files:
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
diff --git a/tests/test_pair.yml b/tests/test_pair.yml
index a74be78a17..bd283523e2 100644
--- a/tests/test_pair.yml
+++ b/tests/test_pair.yml
@@ -5,16 +5,16 @@
     - tumor_normal_pair
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
-    - path: results/preprocessing/test2/markduplicates/test2.md.cram
-    - path: results/preprocessing/test2/markduplicates/test2.md.cram.crai
-    - path: results/preprocessing/test2/recal_table/test2.recal.table
-    - path: results/preprocessing/test2/recalibrated/test2.recal.cram
-    - path: results/preprocessing/test2/recalibrated/test2.recal.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+    - path: results/preprocessing/markduplicates/test2/test2.md.cram
+    - path: results/preprocessing/markduplicates/test2/test2.md.cram.crai
+    - path: results/preprocessing/recal_table/test2/test2.recal.table
+    - path: results/preprocessing/recalibrated/test2/test2.recal.cram
+    - path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
diff --git a/tests/test_prepare_recalibration.yml b/tests/test_prepare_recalibration.yml
index caac6d3a61..6e54ec697e 100644
--- a/tests/test_prepare_recalibration.yml
+++ b/tests/test_prepare_recalibration.yml
@@ -6,19 +6,19 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/csv/recalibrated.csv
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools/test/test.recal.cram.stats
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
 
 - name: Run Prepare_recal starting from cram
   command: nextflow run main.nf -profile test,prepare_recalibration_cram,docker --tools strelka
@@ -28,19 +28,19 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/csv/recalibrated.csv
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools/test/test.recal.cram.stats
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
 
 - name: Run Prepare_recal starting from bam and skip baserecalibration
   command: nextflow run main.nf -profile test,prepare_recalibration_bam,skip_bqsr,docker --tools strelka
@@ -50,13 +50,13 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
       should_exist: false
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
       should_exist: false
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
       should_exist: false
     - path: results/csv/recalibrated.csv
       should_exist: false
@@ -70,10 +70,10 @@
       should_exist: false
     - path: results/reports/samtools/test/test.recal.cram.stats
       should_exist: false
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
 
 - name: Run Prepare_recal starting from cram and skip baserecalibration
   command: nextflow run main.nf -profile test,prepare_recalibration_cram,skip_bqsr,docker --tools strelka
@@ -83,15 +83,15 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram
       should_exist: false
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
       should_exist: false
-    - path: results/preprocessing/test/recal_table/test.recal.table
+    - path: results/preprocessing/recal_table/test/test.recal.table
       should_exist: false
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
       should_exist: false
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
       should_exist: false
     - path: results/csv/recalibrated.csv
       should_exist: false
@@ -105,7 +105,7 @@
       should_exist: false
     - path: results/reports/samtools/test/test.recal.cram.stats
       should_exist: false
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
diff --git a/tests/test_recalibrate.yml b/tests/test_recalibrate.yml
index ace325eb37..1f895fd001 100644
--- a/tests/test_recalibrate.yml
+++ b/tests/test_recalibrate.yml
@@ -6,18 +6,18 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools/test/test.recal.cram.stats
     - path: results/csv/recalibrated.csv
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
 
 - name: Run Recalibration starting from cram
   command: nextflow run main.nf -profile test,recalibrate_cram,docker --tools strelka
@@ -27,18 +27,18 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools/test/test.recal.cram.stats
     - path: results/csv/recalibrated.csv
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
 
 - name: Run Recalibration starting from bam and skip baserecalibration
   command: nextflow run main.nf -profile test,recalibrate_bam,skip_bqsr,docker --tools strelka
@@ -48,13 +48,13 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
       should_exist: false
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
       should_exist: false
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
       should_exist: false
     - path: results/csv/recalibrated.csv
       should_exist: false
@@ -68,10 +68,10 @@
       should_exist: false
     - path: results/reports/samtools/test/test.recal.cram.stats
       should_exist: false
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
 
 - name: Run Recalibration starting from cram  and skip baserecalibration
   command: nextflow run main.nf -profile test,recalibrate_cram,skip_bqsr,docker --tools strelka
@@ -81,15 +81,15 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram
       should_exist: false
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
       should_exist: false
-    - path: results/preprocessing/test/recal_table/test.recal.table
+    - path: results/preprocessing/recal_table/test/test.recal.table
       should_exist: false
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
       should_exist: false
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
       should_exist: false
     - path: results/csv/recalibrated.csv
       should_exist: false
@@ -103,7 +103,7 @@
       should_exist: false
     - path: results/reports/samtools/test/test.recal.cram.stats
       should_exist: false
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
diff --git a/tests/test_save_bam_mapped.yml b/tests/test_save_bam_mapped.yml
index 2163709ff9..19b58121ef 100644
--- a/tests/test_save_bam_mapped.yml
+++ b/tests/test_save_bam_mapped.yml
@@ -5,13 +5,13 @@
     - save_bam_mapped
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/mapped/test.bam
-    - path: results/preprocessing/test/mapped/test.bam.bai
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/mapped/test/test.bam
+    - path: results/preprocessing/mapped/test/test.bam.bai
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/csv/mapped.csv
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
diff --git a/tests/test_save_output_bam.yml b/tests/test_save_output_bam.yml
index 71f38746c8..c1bd976c9a 100644
--- a/tests/test_save_output_bam.yml
+++ b/tests/test_save_output_bam.yml
@@ -5,11 +5,11 @@
     - save_output_as_bam
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.bam
-    - path: results/preprocessing/test/markduplicates/test.md.bai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.bam
-    - path: results/preprocessing/test/recalibrated/test.recal.bam.bai
+    - path: results/preprocessing/markduplicates/test/test.md.bam
+    - path: results/preprocessing/markduplicates/test/test.md.bai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.bam
+    - path: results/preprocessing/recalibrated/test/test.recal.bam.bai
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
@@ -32,11 +32,11 @@
     - save_output_as_bam
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.bam
-    - path: results/preprocessing/test/markduplicates/test.md.bam.bai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.bam
-    - path: results/preprocessing/test/recalibrated/test.recal.bam.bai
+    - path: results/preprocessing/markduplicates/test/test.md.bam
+    - path: results/preprocessing/markduplicates/test/test.md.bam.bai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.bam
+    - path: results/preprocessing/recalibrated/test/test.recal.bam.bai
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml
index ed73a43e49..5512aef2b6 100644
--- a/tests/test_skip_markduplicates.yml
+++ b/tests/test_skip_markduplicates.yml
@@ -8,13 +8,13 @@
     - path: results/csv/markduplicates_no_table.csv # TODO These are no actually duplicate marked crams, but just mapped converted crams TODO renaming
     - path: results/csv/recalibrated.csv
     - path: results/multiqc
-    - path: results/preprocessing/test/mapped/test.bam
-    - path: results/preprocessing/test/mapped/test.bam.bai
-    - path: results/preprocessing/test/mapped/test.sorted.cram
-    - path: results/preprocessing/test/mapped/test.sorted.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/mapped/test/test.bam
+    - path: results/preprocessing/mapped/test/test.bam.bai
+    - path: results/preprocessing/mapped/test/test.sorted.cram
+    - path: results/preprocessing/mapped/test/test.sorted.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
@@ -26,10 +26,10 @@
     - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
     - path: results/reports/samtools/test/test.recal.cram.stats
     - path: results/reports/samtools/test/test.sorted.cram.stats
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
 
 - name: Run skip markduplicates bam from step markduplicates
   command: nextflow run main.nf -profile test,docker,markduplicates_bam,skip_markduplicates --tools strelka
@@ -42,11 +42,11 @@
     - path: results/csv/markduplicates_no_table.csv # TODO These are no actually duplicate marked crams, but just mapped converted crams TODO renaming
     - path: results/csv/recalibrated.csv
     - path: results/multiqc
-    - path: results/preprocessing/test/mapped/test.sorted.cram
-    - path: results/preprocessing/test/mapped/test.sorted.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/mapped/test/test.sorted.cram
+    - path: results/preprocessing/mapped/test/test.sorted.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
@@ -57,10 +57,10 @@
     - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
     - path: results/reports/samtools/test/test.recal.cram.stats
     - path: results/reports/samtools/test/test.sorted.cram.stats
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
 
 - name: Run skip markduplicates cram from step markduplicates
   command: nextflow run main.nf -profile test,docker,markduplicates_cram,skip_markduplicates --tools strelka
@@ -75,13 +75,13 @@
       should_exist: false
     - path: results/csv/recalibrated.csv
     - path: results/multiqc
-    - path: results/preprocessing/test/mapped/test.sorted.cram
+    - path: results/preprocessing/mapped/test/test.sorted.cram
       should_exist: false
-    - path: results/preprocessing/test/mapped/test.sorted.cram.crai
+    - path: results/preprocessing/mapped/test/test.sorted.cram.crai
       should_exist: false
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
@@ -92,7 +92,7 @@
     - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
     - path: results/reports/samtools/test/test.sorted.cram.stats
     - path: results/reports/samtools/test/test.recal.cram.stats
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
-    - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
diff --git a/tests/test_skip_qc.yml b/tests/test_skip_qc.yml
index 43eb376ea1..09847cae65 100644
--- a/tests/test_skip_qc.yml
+++ b/tests/test_skip_qc.yml
@@ -6,11 +6,11 @@
   files:
     - path: results/multiqc
       should_exist: false
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
@@ -47,11 +47,11 @@
   files:
     - path: results/multiqc
       should_exist: false
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
diff --git a/tests/test_split_fastq.yml b/tests/test_split_fastq.yml
index c00b9cb470..bd3602ad25 100644
--- a/tests/test_split_fastq.yml
+++ b/tests/test_split_fastq.yml
@@ -3,7 +3,7 @@
   tags:
     - split_fastq
   files:
-    - path: results/preprocessing/test/fastp/0001.test-test_L1_1.fastp.fastq.gz
-    - path: results/preprocessing/test/fastp/0001.test-test_L1_2.fastp.fastq.gz
-    - path: results/preprocessing/test/fastp/0002.test-test_L1_1.fastp.fastq.gz
-    - path: results/preprocessing/test/fastp/0002.test-test_L1_2.fastp.fastq.gz
+    - path: results/preprocessing/fastp/test/0001.test-test_L1_1.fastp.fastq.gz
+    - path: results/preprocessing/fastp/test/0001.test-test_L1_2.fastp.fastq.gz
+    - path: results/preprocessing/fastp/test/0002.test-test_L1_1.fastp.fastq.gz
+    - path: results/preprocessing/fastp/test/0002.test-test_L1_2.fastp.fastq.gz
diff --git a/tests/test_targeted.yml b/tests/test_targeted.yml
index 94ebd5c954..c94c61903a 100644
--- a/tests/test_targeted.yml
+++ b/tests/test_targeted.yml
@@ -5,11 +5,11 @@
     - targeted
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
diff --git a/tests/test_tools.yml b/tests/test_tools.yml
index 1a5af70301..59ac7bc7a0 100644
--- a/tests/test_tools.yml
+++ b/tests/test_tools.yml
@@ -6,30 +6,30 @@
     - variant_calling
     - copy_number_calling
   files:
-    - path: results/variant_calling/sample3/cnvkit/multi_intervals.antitarget.bed
-    - path: results/variant_calling/sample3/cnvkit/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn
-    - path: results/variant_calling/sample3/cnvkit/test.paired_end.recalibrated.sorted.targetcoverage.cnn
-    - path: results/variant_calling/sample3/cnvkit/reference.cnn
-    - path: results/variant_calling/sample3/cnvkit/test.paired_end.recalibrated.sorted-diagram.pdf
-    - path: results/variant_calling/sample3/cnvkit/test.paired_end.recalibrated.sorted-scatter.png
-    - path: results/variant_calling/sample3/cnvkit/test.paired_end.recalibrated.sorted.bintest.cns
-    - path: results/variant_calling/sample3/cnvkit/multi_intervals.target.bed
-    - path: results/variant_calling/sample3/cnvkit/test.paired_end.recalibrated.sorted.cnr
-    - path: results/variant_calling/sample3/cnvkit/test.paired_end.recalibrated.sorted.cns
-    - path: results/variant_calling/sample3/cnvkit/test.paired_end.recalibrated.sorted.call.cns
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/multi_intervals.antitarget.bed
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test.paired_end.recalibrated.sorted.targetcoverage.cnn
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/reference.cnn
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted-scatter.png
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted-diagram.pdf
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.cnr
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.cns
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/multi_intervals.target.bed
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
-    - path: results/variant_calling/sample4_vs_sample3/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+    - path: results/variant_calling/cnvkit/sample3/multi_intervals.antitarget.bed
+    - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.targetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample3/reference.cnn
+    - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted-diagram.pdf
+    - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted-scatter.png
+    - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.bintest.cns
+    - path: results/variant_calling/cnvkit/sample3/multi_intervals.target.bed
+    - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.cnr
+    - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.cns
+    - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.call.cns
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.antitarget.bed
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test.paired_end.recalibrated.sorted.targetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.bintest.cns
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/reference.cnn
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted-scatter.png
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted-diagram.pdf
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cnr
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cns
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.target.bed
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.call.cns
 
 - name: Run variant calling on tumor_only sample with cnvkit
   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools cnvkit
@@ -39,16 +39,16 @@
     - variant_calling
     - copy_number_calling
   files:
-    - path: results/variant_calling/sample2/cnvkit/cnvkit.reference.target-tmp.bed
-    - path: results/variant_calling/sample2/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
-    - path: results/variant_calling/sample2/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
-    - path: results/variant_calling/sample2/cnvkit/test2.paired_end.recalibrated.sorted-scatter.png
-    - path: results/variant_calling/sample2/cnvkit/cnvkit.reference.antitarget-tmp.bed
-    - path: results/variant_calling/sample2/cnvkit/test2.paired_end.recalibrated.sorted-diagram.pdf
-    - path: results/variant_calling/sample2/cnvkit/test2.paired_end.recalibrated.sorted.cnr
-    - path: results/variant_calling/sample2/cnvkit/test2.paired_end.recalibrated.sorted.cns
-    - path: results/variant_calling/sample2/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
-    - path: results/variant_calling/sample2/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+    - path: results/variant_calling/cnvkit/sample2/cnvkit.reference.target-tmp.bed
+    - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.bintest.cns
+    - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted-scatter.png
+    - path: results/variant_calling/cnvkit/sample2/cnvkit.reference.antitarget-tmp.bed
+    - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted-diagram.pdf
+    - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.cnr
+    - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.cns
+    - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.call.cns
 
 - name: Run variant calling on germline sample with cnvkit
   command: nextflow run main.nf -profile test,tools_germline,docker --tools cnvkit
@@ -58,17 +58,17 @@
     - variant_calling
     - copy_number_calling
   files:
-    - path: results/variant_calling/sample1/cnvkit/multi_intervals.antitarget.bed
-    - path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn
-    - path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted.targetcoverage.cnn
-    - path: results/variant_calling/sample1/cnvkit/reference.cnn
-    - path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted-diagram.pdf
-    - path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted-scatter.png
-    - path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted.bintest.cns
-    - path: results/variant_calling/sample1/cnvkit/multi_intervals.target.bed
-    - path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted.cnr
-    - path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted.cns
-    - path: results/variant_calling/sample1/cnvkit/test.paired_end.recalibrated.sorted.call.cns
+    - path: results/variant_calling/cnvkit/sample1/multi_intervals.antitarget.bed
+    - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.targetcoverage.cnn
+    - path: results/variant_calling/cnvkit/sample1/reference.cnn
+    - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted-diagram.pdf
+    - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted-scatter.png
+    - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.bintest.cns
+    - path: results/variant_calling/cnvkit/sample1/multi_intervals.target.bed
+    - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.cnr
+    - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.cns
+    - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.call.cns
 
 - name: Run variant calling on somatic samples with controlfreec
   command: nextflow run main.nf -profile test,tools_somatic,docker --tools controlfreec
@@ -78,22 +78,22 @@
     - variant_calling
     - copy_number_calling
   files:
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/config.txt
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3_BAF.png
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3_ratio.log2.png
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3_ratio.png
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.bed
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.circos.txt
-    - path: results/variant_calling/sample4_vs_sample3/mpileup/sample4_vs_sample3.normal.mpileup.gz
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.normal.mpileup.gz_control.cpn
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.p.value.txt
-    - path: results/variant_calling/sample4_vs_sample3/mpileup/sample4_vs_sample3.tumor.mpileup.gz
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.tumor.mpileup.gz_BAF.txt
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.tumor.mpileup.gz_CNVs
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.tumor.mpileup.gz_info.txt
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.tumor.mpileup.gz_ratio.BedGraph
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.tumor.mpileup.gz_ratio.txt
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.tumor.mpileup.gz_sample.cpn
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/config.txt
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.png
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.log2.png
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.png
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.bed
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.circos.txt
+    - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz_control.cpn
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.p.value.txt
+    - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_BAF.txt
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_CNVs
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_info.txt
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_ratio.BedGraph
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_ratio.txt
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_sample.cpn
 
 - name: Run variant calling on somatic samples with controlfreec without intervals
   command: nextflow run main.nf -profile test,tools_somatic,docker --tools controlfreec --no_intervals -stub-run
@@ -104,22 +104,22 @@
     - variant_calling
     - copy_number_calling
   files:
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/config.txt
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3_BAF.png
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3_ratio.log2.png
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3_ratio.png
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.bed
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.circos.txt
-    - path: results/variant_calling/sample4_vs_sample3/mpileup/sample4_vs_sample3.normal.mpileup.gz
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3_sample.cpn
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3.p.value.txt
-    - path: results/variant_calling/sample4_vs_sample3/mpileup/sample4_vs_sample3.tumor.mpileup.gz
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3_BAF.txt
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3_CNVs
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3_info.txt
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3_ratio.BedGraph
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3_ratio.txt
-    - path: results/variant_calling/sample4_vs_sample3/controlfreec/sample4_vs_sample3_sample.cpn
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/config.txt
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.png
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.log2.png
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.png
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.bed
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.circos.txt
+    - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_sample.cpn
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.p.value.txt
+    - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.txt
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_CNVs
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_info.txt
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.BedGraph
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.txt
+    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_sample.cpn
 
 - name: Run variant calling on tumor_only sample with controlfreec
   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools controlfreec -stub-run
@@ -129,20 +129,20 @@
     - variant_calling
     - copy_number_calling
   files:
-    - path: results/variant_calling/sample2/controlfreec/config.txt
-    - path: results/variant_calling/sample2/controlfreec/GC_profile.sample2.cpn
-    - path: results/variant_calling/sample2/controlfreec/sample2_BAF.png
-    - path: results/variant_calling/sample2/controlfreec/sample2_BAF.txt
-    - path: results/variant_calling/sample2/controlfreec/sample2_info.txt
-    - path: results/variant_calling/sample2/controlfreec/sample2_ratio.BedGraph
-    - path: results/variant_calling/sample2/controlfreec/sample2_ratio.log2.png
-    - path: results/variant_calling/sample2/controlfreec/sample2_ratio.png
-    - path: results/variant_calling/sample2/controlfreec/sample2_ratio.txt
-    - path: results/variant_calling/sample2/controlfreec/sample2_sample.cpn
-    - path: results/variant_calling/sample2/controlfreec/sample2.bed
-    - path: results/variant_calling/sample2/controlfreec/sample2.circos.txt
-    - path: results/variant_calling/sample2/mpileup/sample2.tumor.mpileup.gz
-    - path: results/variant_calling/sample2/controlfreec/sample2.p.value.txt
+    - path: results/variant_calling/controlfreec/sample2/config.txt
+    - path: results/variant_calling/controlfreec/sample2/GC_profile.sample2.cpn
+    - path: results/variant_calling/controlfreec/sample2/sample2_BAF.png
+    - path: results/variant_calling/controlfreec/sample2/sample2_BAF.txt
+    - path: results/variant_calling/controlfreec/sample2/sample2_info.txt
+    - path: results/variant_calling/controlfreec/sample2/sample2_ratio.BedGraph
+    - path: results/variant_calling/controlfreec/sample2/sample2_ratio.log2.png
+    - path: results/variant_calling/controlfreec/sample2/sample2_ratio.png
+    - path: results/variant_calling/controlfreec/sample2/sample2_ratio.txt
+    - path: results/variant_calling/controlfreec/sample2/sample2_sample.cpn
+    - path: results/variant_calling/controlfreec/sample2/sample2.bed
+    - path: results/variant_calling/controlfreec/sample2/sample2.circos.txt
+    - path: results/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz
+    - path: results/variant_calling/controlfreec/sample2/sample2.p.value.txt
 
 - name: Run variant calling on germline sample with deepvariant
   command: nextflow run main.nf -profile test,tools_germline,docker --tools deepvariant
@@ -151,10 +151,10 @@
     - germline
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.g.vcf.gz
-    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.g.vcf.gz.tbi
-    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.vcf.gz
-    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.vcf.gz.tbi
+    - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz
+    - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz.tbi
+    - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz
+    - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on germline sample with deepvariant without intervals
@@ -165,10 +165,10 @@
     - no_intervals
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.g.vcf.gz
-    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.g.vcf.gz.tbi
-    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.vcf.gz
-    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.vcf.gz.tbi
+    - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz
+    - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz.tbi
+    - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz
+    - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on germline sample with freebayes
@@ -178,8 +178,8 @@
     - germline
     - variant_calling
   files:
-    - path: results/variant_calling/test/freebayes/test.freebayes.vcf.gz
-    - path: results/variant_calling/test/freebayes/test.freebayes.vcf.gz.tbi
+    - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz
+    - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on germline sample with freebayes without intervals
@@ -190,8 +190,8 @@
     - no_intervals
     - variant_calling
   files:
-    - path: results/variant_calling/test/freebayes/test.freebayes.vcf.gz
-    - path: results/variant_calling/test/freebayes/test.freebayes.vcf.gz.tbi
+    - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz
+    - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with freebayes
@@ -201,8 +201,8 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.freebayes.vcf.gz
-    - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.freebayes.vcf.gz.tbi
+    - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz
+    - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with freebayes without intervals
@@ -213,8 +213,8 @@
     - no_intervals
     - variant_calling
   files:
-    - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.freebayes.vcf.gz
-    - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.freebayes.vcf.gz.tbi
+    - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz
+    - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 # - name: Run variant calling on tumor_only sample with freebayes
@@ -224,8 +224,8 @@
 #     - tumor_only
 #     - variant_calling
 #   files:
-#     - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz
-#     - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz.tbi
+#     - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz
+#     - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz.tbi
 
 # - name: Run variant calling on tumor_only sample with freebayes without intervals
 #   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools freebayes --no_intervals
@@ -235,8 +235,8 @@
 #     - tumor_only
 #     - variant_calling
 #   files:
-#     - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz
-#     - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz.tbi
+#     - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz
+#     - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz.tbi
 
 - name: Run variant calling on germline sample with haplotypecaller
   command: nextflow run main.nf -profile test,targeted,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller  --step variant_calling
@@ -245,15 +245,15 @@
     - haplotypecaller
     - variant_calling
   files:
-    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.vcf.gz
-    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.vcf.gz.tbi
-    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz
-    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz.tbi
+    - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz
+    - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz.tbi
+    - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz
+    - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
-    - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.vcf.gz
-    - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.vcf.gz.tbi
-    - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz
-    - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi
+    - path: results/variant_calling/haplotypecaller/test1/test1.haplotypecaller.vcf.gz
+    - path: results/variant_calling/haplotypecaller/test1/test1.haplotypecaller.vcf.gz.tbi
+    - path: results/variant_calling/haplotypecaller/test1/test1.haplotypecaller.filtered.vcf.gz
+    - path: results/variant_calling/haplotypecaller/test1/test1.haplotypecaller.filtered.vcf.gz.tbi
 
 - name: Run variant calling on germline sample with haplotypecaller without intervals
   command: nextflow run main.nf -profile test,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller  --step variant_calling --no_intervals
@@ -263,15 +263,15 @@
     - no_intervals
     - variant_calling
   files:
-    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.vcf.gz
-    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.vcf.gz.tbi
-    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz
-    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz.tbi
+    - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz
+    - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz.tbi
+    - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz
+    - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
-    - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.vcf.gz
-    - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.vcf.gz.tbi
-    - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz
-    - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi
+    - path: results/variant_calling/haplotypecaller/test1/test1.haplotypecaller.vcf.gz
+    - path: results/variant_calling/haplotypecaller/test1/test1.haplotypecaller.vcf.gz.tbi
+    - path: results/variant_calling/haplotypecaller/test1/test1.haplotypecaller.filtered.vcf.gz
+    - path: results/variant_calling/haplotypecaller/test1/test1.haplotypecaller.filtered.vcf.gz.tbi
 
 # - name: Run joint germline variant calling with haplotypecaller
 #   command: nextflow run main.nf -profile test,tools_germline,docker --tools haplotypecaller --joint_germline
@@ -281,10 +281,10 @@
 #     - haplotypecaller
 #     - variant_calling
 #   files:
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.g.vcf.gz
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.g.vcf.gz.tbi
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.vcf.gz
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.vcf.gz.tbi
+#     - path: results/variant_calling/haplotypecaller/sample1/sample1.haplotypecaller.g.vcf.gz
+#     - path: results/variant_calling/haplotypecaller/sample1/sample1.haplotypecaller.g.vcf.gz.tbi
+#     - path: results/variant_calling/haplotypecaller/sample1/sample1.haplotypecaller.vcf.gz
+#     - path: results/variant_calling/haplotypecaller/sample1/sample1.haplotypecaller.vcf.gz.tbi
 #     - path: results/csv/variantcalled.csv
 
 # - name: Run joint germline variant calling with haplotypecaller without intervals
@@ -296,10 +296,10 @@
 #     - no_intervals
 #     - variant_calling
 #   files:
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.g.vcf.gz
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.g.vcf.gz.tbi
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.vcf.gz
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.vcf.gz.tbi
+#     - path: results/variant_calling/haplotypecaller/sample1/sample1.haplotypecaller.g.vcf.gz
+#     - path: results/variant_calling/haplotypecaller/sample1/sample1.haplotypecaller.g.vcf.gz.tbi
+#     - path: results/variant_calling/haplotypecaller/sample1/sample1.haplotypecaller.vcf.gz
+#     - path: results/variant_calling/haplotypecaller/sample1/sample1.haplotypecaller.vcf.gz.tbi
 #     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on germline sample with manta
@@ -309,8 +309,8 @@
     - manta
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/manta/sample1.manta.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample1/manta/sample1.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz.tbi
 
 - name: Run variant calling on germline sample with manta without intervals
   command: nextflow run main.nf -profile test,tools_germline,docker --tools manta --no_intervals
@@ -320,8 +320,8 @@
     - no_intervals
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/manta/sample1.manta.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample1/manta/sample1.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz.tbi
 
 - name: Run variant calling on tumor_only sample with manta
   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools manta
@@ -330,8 +330,8 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/manta/sample2.manta.tumor_sv.vcf.gz
-    - path: results/variant_calling/sample2/manta/sample2.manta.tumor_sv.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz
+    - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz.tbi
 
 - name: Run variant calling on tumor_only sample with manta without intervals
   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools manta --no_intervals
@@ -341,8 +341,8 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/manta/sample2.manta.tumor_sv.vcf.gz
-    - path: results/variant_calling/sample2/manta/sample2.manta.tumor_sv.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz
+    - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz.tbi
 
 - name: Run variant calling on somatic sample with manta
   command: nextflow run main.nf -profile test,tools_somatic,docker --tools manta
@@ -351,12 +351,12 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi
 
 - name: Run variant calling on somatic sample with manta without intervals
   command: nextflow run main.nf -profile test,tools_somatic,docker --tools manta --no_intervals
@@ -366,12 +366,12 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi
 
 - name: Run variant calling on tumor_only sample to test mpileup
   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools mpileup
@@ -379,7 +379,7 @@
     - tumor_only
     - mpileup
   files:
-    - path: results/variant_calling/sample2/mpileup/sample2.tumor.mpileup.gz
+    - path: results/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz
 
 - name: Run variant calling on tumor_only sample to test mpileup without intervals
   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools mpileup --no_intervals
@@ -388,7 +388,7 @@
     - mpileup
     - no_intervals
   files:
-    - path: results/variant_calling/sample2/mpileup/sample2.tumor.mpileup.gz
+    - path: results/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz
 
 - name: Run variant calling on germline sample to test mpileup
   command: nextflow run main.nf -profile test,tools_germline,docker --tools mpileup
@@ -396,7 +396,7 @@
     - germline
     - mpileup
   files:
-    - path: results/variant_calling/sample1/mpileup/sample1.normal.mpileup.gz
+    - path: results/variant_calling/mpileup/sample1/sample1.normal.mpileup.gz
 
 - name: Run variant calling on germline sample to test mpileup without intervals
   command: nextflow run main.nf -profile test,tools_germline,docker --tools mpileup --no_intervals
@@ -405,7 +405,7 @@
     - mpileup
     - no_intervals
   files:
-    - path: results/variant_calling/sample1/mpileup/sample1.normal.mpileup.gz
+    - path: results/variant_calling/mpileup/sample1/sample1.normal.mpileup.gz
 
 - name: Run variant calling on tumoronly sample with mutect2
   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools mutect2
@@ -414,16 +414,16 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz.tbi
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz.stats
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.contamination.table
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.segmentation.table
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.artifactprior.tar.gz
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.pileupsummaries.table
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz.tbi
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz.filteringStats.tsv
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.tbi
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.stats
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.contamination.table
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.segmentation.table
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.artifactprior.tar.gz
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.pileupsummaries.table
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz.tbi
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz.filteringStats.tsv
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on tumoronly sample with mutect2 without intervals
@@ -434,17 +434,17 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.pileups.table
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz.tbi
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz.stats
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.contamination.table
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.segmentation.table
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.artifactprior.tar.gz
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.pileupsummaries.table
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz.tbi
-    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz.filteringStats.tsv
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.pileups.table
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.tbi
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.stats
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.contamination.table
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.segmentation.table
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.artifactprior.tar.gz
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.pileupsummaries.table
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz.tbi
+    - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz.filteringStats.tsv
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with mutect2
@@ -455,17 +455,17 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz.stats
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.contamination.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.segmentation.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.mutect2.pileupsummaries.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.mutect2.pileupsummaries.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.artifactprior.tar.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz.filteringStats.tsv
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.tbi
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.stats
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.contamination.table
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.segmentation.table
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample3.mutect2.pileupsummaries.table
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4.mutect2.pileupsummaries.table
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.artifactprior.tar.gz
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.filtered.vcf.gz
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.filtered.vcf.gz.tbi
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.filtered.vcf.gz.filteringStats.tsv
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with msisensor-pro
@@ -475,10 +475,10 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample4_vs_sample3/msisensorpro/sample4_vs_sample3
-    - path: results/variant_calling/sample4_vs_sample3/msisensorpro/sample4_vs_sample3_dis
-    - path: results/variant_calling/sample4_vs_sample3/msisensorpro/sample4_vs_sample3_germline
-    - path: results/variant_calling/sample4_vs_sample3/msisensorpro/sample4_vs_sample3_somatic
+    - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3
+    - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3_dis
+    - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3_germline
+    - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3_somatic
 
 - name: Run variant calling on germline sample with strelka
   command: nextflow run main.nf -profile test,tools_germline,docker --tools strelka
@@ -487,10 +487,10 @@
     - strelka
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on germline sample with strelka without intervals
@@ -501,10 +501,10 @@
     - no_intervals
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz
-    - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on tumoronly sample with strelka
@@ -514,10 +514,10 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on tumoronly sample with strelka without intervals
@@ -528,10 +528,10 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz
-    - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with strelka
@@ -541,14 +541,14 @@
     - strelka
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with strelka without intervals
@@ -559,14 +559,14 @@
     - strelka
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with strelka & manta (StrelkaBP)
@@ -576,20 +576,20 @@
     - strelkabp
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi
-    - path: results//variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz
-    - path: results//variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi
-    - path: results//variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz
-    - path: results//variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi
-    - path: results//variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz
-    - path: results//variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with & manta (StrelkaBP) without intervals
@@ -600,20 +600,20 @@
     - strelkabp
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz
+    - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz
+    - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
+    - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with tiddit
@@ -623,15 +623,15 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/tiddit/sample3.tiddit.ploidies.tab
-    - path: results/variant_calling/sample3/tiddit/sample3.tiddit.vcf.gz
-    - path: results/variant_calling/sample3/tiddit/sample3.tiddit.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.normal.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.normal.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.tumor.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.tumor.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit_sv_merge.vcf
-    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.ploidies.tab
+    - path: results/variant_calling/tiddit/sample3/sample3.tiddit.ploidies.tab
+    - path: results/variant_calling/tiddit/sample3/sample3.tiddit.vcf.gz
+    - path: results/variant_calling/tiddit/sample3/sample3.tiddit.vcf.gz.tbi
+    - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.normal.vcf.gz
+    - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.normal.vcf.gz.tbi
+    - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.tumor.vcf.gz
+    - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.tumor.vcf.gz.tbi
+    - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.vcf
+    - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.ploidies.tab
 
 - name: Run variant calling on germline sample with tiddit
   command: nextflow run main.nf -profile test,tools_germline,docker --tools tiddit
@@ -640,9 +640,9 @@
     - germline
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/tiddit/sample1.tiddit.ploidies.tab
-    - path: results/variant_calling/sample1/tiddit/sample1.tiddit.vcf.gz
-    - path: results/variant_calling/sample1/tiddit/sample1.tiddit.vcf.gz.tbi
+    - path: results/variant_calling/tiddit/sample1/sample1.tiddit.ploidies.tab
+    - path: results/variant_calling/tiddit/sample1/sample1.tiddit.vcf.gz
+    - path: results/variant_calling/tiddit/sample1/sample1.tiddit.vcf.gz.tbi
 
 - name: Run variant calling on tumor_only sample with tiddit
   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools tiddit
@@ -651,6 +651,6 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/tiddit/sample2.tiddit.ploidies.tab
-    - path: results/variant_calling/sample2/tiddit/sample2.tiddit.vcf.gz
-    - path: results/variant_calling/sample2/tiddit/sample2.tiddit.vcf.gz.tbi
+    - path: results/variant_calling/tiddit/sample2/sample2.tiddit.ploidies.tab
+    - path: results/variant_calling/tiddit/sample2/sample2.tiddit.vcf.gz
+    - path: results/variant_calling/tiddit/sample2/sample2.tiddit.vcf.gz.tbi
diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml
index 9d1a49dcaa..deda9d7b72 100644
--- a/tests/test_tools_manually.yml
+++ b/tests/test_tools_manually.yml
@@ -6,20 +6,20 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.after_correction_gc_rt.sample4_vs_sample3.tumour.germline.png
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.after_correction_gc_rt.sample4_vs_sample3.tumour.tumour.png
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.before_correction.sample4_vs_sample3.tumour.germline.png
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.before_correction.sample4_vs_sample3.tumour.tumour.png
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.cnvs.txt
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.metrics.txt
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.purityploidy.txt
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.segments.txt
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.tumour.ASPCF.png
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.tumour_normalBAF.txt
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.tumour_normalLogR.txt
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.tumour.sunrise.png
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.tumour_tumourBAF.txt
-    - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.tumour_tumourLogR.txt
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.after_correction_gc_rt.sample4_vs_sample3.tumour.germline.png
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.after_correction_gc_rt.sample4_vs_sample3.tumour.tumour.png
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.before_correction.sample4_vs_sample3.tumour.germline.png
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.before_correction.sample4_vs_sample3.tumour.tumour.png
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.cnvs.txt
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.metrics.txt
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.purityploidy.txt
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.segments.txt
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour.ASPCF.png
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_normalBAF.txt
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_normalLogR.txt
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour.sunrise.png
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourBAF.txt
+    - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourLogR.txt
 
 - name: Run variant calling on somatic sample with mutect2 without intervals
   command: nextflow run main.nf -profile test,tools_somatic,docker --tools mutect2 --no_intervals -c ./tests/nextflow.config
@@ -30,17 +30,17 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.mutect2.pileups.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.mutect2.pileups.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz.stats
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.contamination.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.segmentation.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.mutect2.pileupsummaries.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.mutect2.pileupsummaries.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.artifactprior.tar.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz.filteringStats.tsv
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample3.mutect2.pileups.table
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4.mutect2.pileups.table
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.tbi
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.stats
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.contamination.table
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.segmentation.table
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample3.mutect2.pileupsummaries.table
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4.mutect2.pileupsummaries.table
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.artifactprior.tar.gz
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.filtered.vcf.gz
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.filtered.vcf.gz.tbi
+    - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.filtered.vcf.gz.filteringStats.tsv
     - path: results/csv/variantcalled.csv
diff --git a/tests/test_trimming.yml b/tests/test_trimming.yml
index 5f18ae527c..d82668f546 100644
--- a/tests/test_trimming.yml
+++ b/tests/test_trimming.yml
@@ -5,13 +5,13 @@
     - preprocessing
   files:
     - path: results/multiqc
-    - path: results/preprocessing/test/fastp/test-test_L1_1.fastp.fastq.gz
-    - path: results/preprocessing/test/fastp/test-test_L1_2.fastp.fastq.gz
-    - path: results/preprocessing/test/markduplicates/test.md.cram
-    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
-    - path: results/preprocessing/test/recal_table/test.recal.table
-    - path: results/preprocessing/test/recalibrated/test.recal.cram
-    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/preprocessing/fastp/test/test-test_L1_1.fastp.fastq.gz
+    - path: results/preprocessing/fastp/test/test-test_L1_2.fastp.fastq.gz
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    - path: results/preprocessing/recal_table/test/test.recal.table
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv