diff --git a/tests/test_bam_remap.yml b/tests/test_bam_remap.yml
index 9e91c1934..f49d42d9a 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 80f7288ab..c52b174a0 100644
--- a/tests/test_default.yml
+++ b/tests/test_default.yml
@@ -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_markduplicates.yml b/tests/test_markduplicates.yml
index a136c9cfb..44b326bf0 100644
--- a/tests/test_markduplicates.yml
+++ b/tests/test_markduplicates.yml
@@ -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
@@ -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_split_fastq.yml b/tests/test_split_fastq.yml
index c00b9cb47..bd3602ad2 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