diff --git a/tests/software/bowtie/align/test.yml b/tests/software/bowtie/align/test.yml
index eded71f2..4c12905f 100644
--- a/tests/software/bowtie/align/test.yml
+++ b/tests/software/bowtie/align/test.yml
@@ -1,5 +1,5 @@
 - name: bowtie align single-end
-  command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
   tags:
     - bowtie
     - bowtie_align
@@ -23,7 +23,7 @@
       should_exist: true
 
 - name: bowtie align paired-end
-  command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
   tags:
     - bowtie
     - bowtie_align
diff --git a/tests/software/bowtie/build/test.yml b/tests/software/bowtie/build/test.yml
index 145836d6..4b8cfd7a 100644
--- a/tests/software/bowtie/build/test.yml
+++ b/tests/software/bowtie/build/test.yml
@@ -1,5 +1,5 @@
 - name: bowtie build
-  command: nextflow run ./tests/software/bowtie -entry test_bowtie_build -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie/build -entry test_bowtie_build -c tests/config/nextflow.config
   tags:
     - bowtie
     - bowtie_build