diff --git a/containers/azimuth/Dockerfile b/containers/azimuth/Dockerfile
index 7dc880d..cf12acf 100644
--- a/containers/azimuth/Dockerfile
+++ b/containers/azimuth/Dockerfile
@@ -5,4 +5,4 @@ RUN pip install -r requirements-freeze.txt
 
 COPY context/* .
 
-ENTRYPOINT ["python3", "/main.py"]
\ No newline at end of file
+CMD ["python3", "/main.py"]
\ No newline at end of file
diff --git a/containers/azimuth/pipeline.cwl b/containers/azimuth/pipeline.cwl
index 488cc8b..75ca43c 100644
--- a/containers/azimuth/pipeline.cwl
+++ b/containers/azimuth/pipeline.cwl
@@ -9,7 +9,9 @@ requirements:
     types:
       - $import: ./options.yml
 
-baseCommand: python3 /main.py
+baseCommand: python3
+arguments:
+  - /main.py
 
 inputs:
   matrix:
diff --git a/containers/celltypist/Dockerfile b/containers/celltypist/Dockerfile
index 95e2fc6..ef436de 100644
--- a/containers/celltypist/Dockerfile
+++ b/containers/celltypist/Dockerfile
@@ -8,4 +8,4 @@ RUN python -c "import celltypist; celltypist.models.download_models()"
 
 COPY context/* .
 
-ENTRYPOINT ["python", "/main.py"]
\ No newline at end of file
+CMD ["python", "/main.py"]
\ No newline at end of file
diff --git a/containers/celltypist/pipeline.cwl b/containers/celltypist/pipeline.cwl
index 1442ee2..b9590cc 100644
--- a/containers/celltypist/pipeline.cwl
+++ b/containers/celltypist/pipeline.cwl
@@ -9,7 +9,9 @@ requirements:
     types:
       - $import: ./options.yml
 
-baseCommand: python /main.py
+baseCommand: python
+arguments:
+  - /main.py
 
 inputs:
   matrix:
diff --git a/containers/extract-summary/Dockerfile b/containers/extract-summary/Dockerfile
index aa850e9..a7588b2 100644
--- a/containers/extract-summary/Dockerfile
+++ b/containers/extract-summary/Dockerfile
@@ -5,4 +5,4 @@ RUN pip install -r requirements-freeze.txt
 
 COPY context/* .
 
-ENTRYPOINT ["python", "/main.py"]
+CMD ["python", "/main.py"]
diff --git a/containers/extract-summary/pipeline.cwl b/containers/extract-summary/pipeline.cwl
index 8238925..861f891 100644
--- a/containers/extract-summary/pipeline.cwl
+++ b/containers/extract-summary/pipeline.cwl
@@ -9,7 +9,9 @@ requirements:
     types:
       - $import: ./options.yml
 
-baseCommand: python /main.py
+baseCommand: python
+arguments:
+  - /main.py
 
 inputs:
   annotations:
diff --git a/containers/popv/Dockerfile b/containers/popv/Dockerfile
index 5fddb58..dba4287 100644
--- a/containers/popv/Dockerfile
+++ b/containers/popv/Dockerfile
@@ -14,4 +14,4 @@ RUN pip install -r requirements-freeze.txt
 
 COPY context/* .
 
-ENTRYPOINT ["python", "/main.py"]
+CMD ["python", "/main.py"]
diff --git a/containers/popv/pipeline.cwl b/containers/popv/pipeline.cwl
index a558d45..c5fc5e8 100644
--- a/containers/popv/pipeline.cwl
+++ b/containers/popv/pipeline.cwl
@@ -9,7 +9,9 @@ requirements:
     types:
       - $import: ./options.yml
 
-baseCommand: python /main.py
+baseCommand: python
+arguments:
+  - /main.py
 
 inputs:
   matrix:
diff --git a/containers/preprocess/Dockerfile b/containers/preprocess/Dockerfile
index be1d754..5d0bd8c 100644
--- a/containers/preprocess/Dockerfile
+++ b/containers/preprocess/Dockerfile
@@ -5,4 +5,4 @@ RUN pip install -r requirements-freeze.txt
 
 COPY context/* .
 
-ENTRYPOINT ["python", "/main.py"]
\ No newline at end of file
+CMD ["python", "/main.py"]
\ No newline at end of file
diff --git a/containers/preprocess/pipeline.cwl b/containers/preprocess/pipeline.cwl
index 163754c..60f01ff 100644
--- a/containers/preprocess/pipeline.cwl
+++ b/containers/preprocess/pipeline.cwl
@@ -9,7 +9,9 @@ requirements:
     types:
       - $import: ./options.yml
 
-baseCommand: python /main.py
+baseCommand: python
+arguments:
+  - /main.py
 
 inputs:
   matrix: