diff --git a/aggregate_and_plot.cwl b/aggregate_and_plot.cwl
index f55e0552068db2fa71d62be06d544a194364e69f..7fc1214572dd34a1d39d7459f32500afdc60a39e 100644
--- a/aggregate_and_plot.cwl
+++ b/aggregate_and_plot.cwl
@@ -15,4 +15,16 @@ inputs:
     inputBinding:
       position: 1  # The first argument after the script will be the workdir
 
-outputs: []
+outputs:
+- id: plots
+  type: File[]
+  outputBinding:
+    glob: "*.png"
+- id: outputs
+  type: File
+  outputBinding:
+    glob: "outputs.txt"
+- id: inspect
+  type: File
+  outputBinding:
+    glob: "inspect.h5"
diff --git a/aggregate_and_plot.py b/aggregate_and_plot.py
index 8eb79cb6573088f2a51b8991471d8c6474669f55..858865688001c0624a3268e6c402c2d36620f2de 100644
--- a/aggregate_and_plot.py
+++ b/aggregate_and_plot.py
@@ -31,14 +31,14 @@ def main():
                 logging.info(f"Could not find the following input file: {line}")
         logging.info(f"Found {len(h5_paths)} h5 files")
 
-    h5_output_path = workdir / "inspect.h5"
+    h5_output_path = "inspect.h5"
     join_inspect_ds(h5_paths, h5_output_path)
     plot_paths = plot_inspect_ds(h5_output_path, workdir, min_elevation=15)
 
-    with open(workdir / "outputs.txt", "w") as file:
-        file.write(str(h5_output_path.absolute()) + "\n")
+    with open("outputs.txt", "w") as file:
+        file.write(str(h5_output_path) + "\n")
         for file_path in plot_paths:
-            path = Path(file_path).absolute()
+            path = Path(file_path)
             file.write(str(path) + "\n")
 
 if __name__ == "__main__":
diff --git a/aggregate_and_plot.sh b/aggregate_and_plot.sh
index 63ae9d4149a8801e4b59fb6ececd5a492f00198f..36fcbf428b3a7349a291ba7430ea3fe21f1be107 100644
--- a/aggregate_and_plot.sh
+++ b/aggregate_and_plot.sh
@@ -14,4 +14,4 @@ else
 fi
 export SINGULARITY_BIND="/project:/project"
 export TOIL_SLURM_ARGS=""
-toil-cwl-runner "${SCRIPT_DIR}/imaging_compress_pipeline.git/aggregate_and_plot.cwl" --workdir $SCRIPT_DIR --logDebug --singularity --batchSystem slurm --batchLogsDir ./logs --jobStore ./job_store
+toil-cwl-runner "${SCRIPT_DIR}/imaging_compress_pipeline.git/aggregate_and_plot.cwl" --workdir $SCRIPT_DIR --outdir $SCRIPT_DIR --logDebug --singularity --batchSystem slurm --batchLogsDir ./logs --jobStore ./job_store --clean always