diff --git a/tests/software/trimgalore/test.yml b/tests/software/trimgalore/test.yml
index a37ffdb6..a3fba07b 100644
--- a/tests/software/trimgalore/test.yml
+++ b/tests/software/trimgalore/test.yml
@@ -5,8 +5,8 @@
   files:
     # These can't be md5'd reliably
     # TODO Test for includes
-    - path: output/test_single_end/test.fastq.gz_trimming_report.txt
-    - path: output/test_single_end/test_trimmed.fq.gz
+    - path: output/trimgalore/test.fastq.gz_trimming_report.txt
+    - path: output/trimgalore/test_trimmed.fq.gz
 
 - name: trimgalore paired-end
   command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_paired_end -c tests/config/nextflow.config
@@ -15,7 +15,7 @@
   files:
     # These can't be md5'd reliably
     # TODO Test for includes
-    - path: output/test_paired_end/test_1.fastq.gz_trimming_report.txt
-    - path: output/test_paired_end/test_1_val_1.fq.gz
-    - path: output/test_paired_end/test_2.fastq.gz_trimming_report.txt
-    - path: output/test_paired_end/test_2_val_2.fq.gz
+    - path: output/trimgalore/test_1.fastq.gz_trimming_report.txt
+    - path: output/trimgalore/test_1_val_1.fq.gz
+    - path: output/trimgalore/test_2.fastq.gz_trimming_report.txt
+    - path: output/trimgalore/test_2_val_2.fq.gz