diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 738e995..32030e9 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -32,4 +32,6 @@ jobs:
           pip install .[dev,test]
       - name: Test stub run
         run: |
+          cd tests/
+          cruise init
           cruise run -profile ci_stub -stub
diff --git a/conf/ci_stub.config b/conf/ci_stub.config
index eca857a..e7a60d0 100644
--- a/conf/ci_stub.config
+++ b/conf/ci_stub.config
@@ -2,10 +2,10 @@ params {
     config_profile_name = 'Test single-end stubs'
     config_profile_description = 'Minimal test dataset with blank references to run stubs with continuous integration'
 
-    input = 'tests/assets/samplesheet.csv' // adapted from https://github.com/nf-core/test-datasets/blob/chipseq/samplesheet/v2.0/samplesheet_test.csv
+    input = 'assets/samplesheet.csv' // adapted from https://github.com/nf-core/test-datasets/blob/chipseq/samplesheet/v2.0/samplesheet_test.csv
     library = 'assets/lib/yusa_library.csv'
     outdir = 'results/test'
-    design_matrix = 'tests/data/designmat.txt'
+    design_matrix = 'data/designmat.txt'
 
     max_cpus = 2        // for GitHub Actions https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
     max_memory = '6.GB'
diff --git a/tests/assets/samplesheet.csv b/tests/assets/samplesheet.csv
index 66c2ed1..fb271da 100644
--- a/tests/assets/samplesheet.csv
+++ b/tests/assets/samplesheet.csv
@@ -1,3 +1,3 @@
 sample,fastq_1,fastq_2,treat_or_ctrl
-s1_rep1,tests/data/file1.fastq.gz,,treatment
-s2_rep1,tests/data/file2.fastq.gz,,control
+s1_rep1,data/file1.fastq.gz,,treatment
+s2_rep1,data/file2.fastq.gz,,control