diff --git a/tests/test_annotation.yml b/tests/test_annotation.yml
index b6fb529d..80bdadf3 100644
--- a/tests/test_annotation.yml
+++ b/tests/test_annotation.yml
@@ -1,27 +1,27 @@
-- name: Run snpEff
-  command: nextflow run main.nf -profile test,docker --annotate_tools snpeff
-  tags:
-    - annotation
-    - snpeff
-  files:
-    - path: results/variant_annotation/GM12878/GM12878_snpEff.ann.vcf.gz
-    - path: results/variant_annotation/GM12878/GM12878_snpEff.ann.vcf.gz.tbi
-    - path: results/reports/multiqc_report.html
-- name: Run VEP
-  command: nextflow run main.nf -profile test,docker --annotate_tools vep --skip_multiqc
-  tags:
-    - annotation
-    - vep
-  files:
-    - path: results/variant_annotation/GM12878/GM12878_VEP.ann.vcf.gz
-    - path: results/variant_annotation/GM12878/GM12878_VEP.ann.vcf.gz.tbi
-- name: Run snpEff followed by VEP
-  command: nextflow run main.nf -profile test,docker --annotate_tools merge --skip_multiqc
-  tags:
-    - annotation
-    - merge
-    - snpeff
-    - vep
-  files:
-    - path: results/variant_annotation/GM12878/GM12878_snpEff_VEP.ann.vcf.gz
-    - path: results/variant_annotation/GM12878/GM12878_snpEff_VEP.ann.vcf.gz.tbi
+# - name: Run snpEff
+#   command: nextflow run main.nf -profile test,docker --annotate_tools snpeff --outdir results
+#   tags:
+#     - annotation
+#     - snpeff
+#   files:
+#     - path: results/variant_annotation/GM12878/GM12878_snpEff.ann.vcf.gz
+#     - path: results/variant_annotation/GM12878/GM12878_snpEff.ann.vcf.gz.tbi
+#     - path: results/reports/multiqc_report.html
+# - name: Run VEP
+#   command: nextflow run main.nf -profile test,docker --annotate_tools vep --skip_multiqc --outdir results
+#   tags:
+#     - annotation
+#     - vep
+#   files:
+#     - path: results/variant_annotation/GM12878/GM12878_VEP.ann.vcf.gz
+#     - path: results/variant_annotation/GM12878/GM12878_VEP.ann.vcf.gz.tbi
+# - name: Run snpEff followed by VEP
+#   command: nextflow run main.nf -profile test,docker --annotate_tools merge --skip_multiqc --outdir results
+#   tags:
+#     - annotation
+#     - merge
+#     - snpeff
+#     - vep
+#   files:
+#     - path: results/variant_annotation/GM12878/GM12878_snpEff_VEP.ann.vcf.gz
+#     - path: results/variant_annotation/GM12878/GM12878_snpEff_VEP.ann.vcf.gz.tbi
diff --git a/tests/test_bamcsiindex.yml b/tests/test_bamcsiindex.yml
index 06fb817f..a06de700 100644
--- a/tests/test_bamcsiindex.yml
+++ b/tests/test_bamcsiindex.yml
@@ -1,5 +1,5 @@
 - name: Run pipeline with bam_csi_index for large genomes
-  command: nextflow run main.nf -profile test,docker --bam_csi_index
+  command: nextflow run main.nf -profile test,docker --bam_csi_index --outdir results
   tags:
     - bamcsiindex
   files:
diff --git a/tests/test_default.yml b/tests/test_default.yml
index 36cb35fa..776ec6f3 100644
--- a/tests/test_default.yml
+++ b/tests/test_default.yml
@@ -1,5 +1,5 @@
 - name: Run default pipeline
-  command: nextflow run main.nf -profile test,docker
+  command: nextflow run main.nf -profile test,docker --outdir results
   tags:
     - default
     - preprocessing
diff --git a/tests/test_removeduplicates.yml b/tests/test_removeduplicates.yml
index 8889ad6a..d0650728 100644
--- a/tests/test_removeduplicates.yml
+++ b/tests/test_removeduplicates.yml
@@ -1,5 +1,5 @@
 - name: Run pipeline with duplicate reads removed
-  command: nextflow run main.nf -profile test,docker --remove_duplicates true
+  command: nextflow run main.nf -profile test,docker --remove_duplicates true --outdir results
   tags:
     - removeduplicates
     - preprocessing
diff --git a/tests/test_skipbasecalib.yml b/tests/test_skipbasecalib.yml
index 7b5b2132..67f1c463 100644
--- a/tests/test_skipbasecalib.yml
+++ b/tests/test_skipbasecalib.yml
@@ -1,5 +1,5 @@
 - name: Run pipeline without base calibration step
-  command: nextflow run main.nf -profile test,docker --skip_baserecalibration true
+  command: nextflow run main.nf -profile test,docker --skip_baserecalibration true --outdir results
   tags:
     - skipbasecalib
     - preprocessing