diff --git a/workflows/heatmap/heatmap.py b/workflows/heatmap/heatmap.py
index 79efcbdc16dc06035f59dc970df3cee28fa32756..facb4055f976af6aac838548306bf1f8a259eae4 100644
--- a/workflows/heatmap/heatmap.py
+++ b/workflows/heatmap/heatmap.py
@@ -3,11 +3,11 @@ import plotly.express as px
 import sys
 
 # Read command line arguments
-MeasurementTableCSV=sys.argv[0]
-FigureFileName=sys.argv[1]
+MeasurementTableCSV=sys.argv[1]
+FigureFileName=sys.argv[2]
 
 # Read the CSV file
-data = pd.read_csv(MeasurementTableCSV, index_col=0)
+data = pd.read_csv(MeasurementTableCSV, index_col=0, on_bad_lines='skip')
 
 # Create a heatmap
 fig = px.imshow(data, 
@@ -17,5 +17,3 @@ fig = px.imshow(data,
 
 # Save heatmap to file
 fig.write_image(FigureFileName + ".svg")
-
-
diff --git a/workflows/heatmap/workflow.cwl b/workflows/heatmap/workflow.cwl
index f0800704e16bc3834550043e5b42611b71810a2b..5ccb946b210b42dc2eeea5810ee0ad297e7a80c2 100644
--- a/workflows/heatmap/workflow.cwl
+++ b/workflows/heatmap/workflow.cwl
@@ -2,9 +2,6 @@
 
 cwlVersion: v1.2
 class: CommandLineTool
-# hints:
-#   DockerRequirement:
-#     dockerPull: 
 requirements:
   - class: InitialWorkDirRequirement
     listing:
@@ -13,7 +10,7 @@ requirements:
           $include: heatmap.py
   - class: NetworkAccess
     networkAccess: true
-baseCommand: [python, heatmap.py]
+baseCommand: [python3, heatmap.py]
 inputs:
   MeasurementTableCSV:
     type: File