diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a3c5ca8..4c09b46 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -41,8 +41,13 @@ jobs:
       - name: Nextflow DAG
         # Catches a rewiring mistake without running anything. The stub needs the synthetic
         # dataset, which is generated rather than committed.
+        # pysceptre's scripts/ (sceptre_io, which watteg-make-test-data imports) is not in its
+        # wheel, so it is fetched at the pinned tag and put on PYTHONPATH, as the container does.
         run: |
+          git clone --quiet --depth 1 --branch v0.2.0 \
+            https://github.com/broadinstitute/pysceptre.git /tmp/pysceptre
+          export PYTHONPATH=/tmp/pysceptre/scripts
           curl -fsSL https://get.nextflow.io | bash
           uv run watteg-make-test-data --out tests/data/synthetic.h5mu
-          ./nextflow run . -profile standard -params-file config/test.yml -stub-run \
+          ./nextflow run . -profile stub -params-file config/test.yml -stub-run \
             --samplesheet assets/samplesheet_synthetic.csv --outdir /tmp/stub
diff --git a/pyproject.toml b/pyproject.toml
index 8b3af8a..afc2aed 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,6 +11,8 @@ dependencies = [
     "pandas>=2.0",
     "h5py>=3.8",
     "pyarrow>=14",
+    "anndata",   # reading the .h5mu pysceptre's export writes (pixi.toml has them too)
+    "mudata",
     "pysceptre",
 ]