Short answer: - In Prefect 3.x you cannot pass custom “pull steps” directly to Flow.deploy() from Python. - Pull steps are generated from the storage you use with flow.from_source(...). - To set the working directory inside a container, set it via the worker’s job variables (recommended), or define a pull step in prefect.yaml. What to do instead Docker worker - Set the container working directory using docker-py’s working_dir via job_variables.container_create_kwargs:

from prefect import flow

@flow
def my_flow():
    ...

# Deploy from a git repo (pull step auto-generated) and set container working dir
flow.from_source(
    source="<https://github.com/org/repo.git>",
    entrypoint="flows/my_flow.py:my_flow",
).deploy(
    name="docker-wd",
    work_pool_name="my-docker-pool",
    image="my-registry/my-image:latest",
    job_variables={
        "container_create_kwargs": {
            "working_dir": "/app"  # container’s cwd at start
        }
    },
)

Notes: - This uses docker-py’s ContainerCollection.create kwargs; Prefect passes them through, so working_dir works here. - Alternative: bake WORKDIR into your Dockerfile. Kubernetes worker - Set the pod container workingDir in the job manifest:

from prefect import flow

@flow
def my_flow():
    ...

flow.from_source(
    source="<https://github.com/org/repo.git>",
    entrypoint="flows/my_flow.py:my_flow",
).deploy(
    name="k8s-wd",
    work_pool_name="my-k8s-pool",
    job_variables={
        "namespace": "default",
        "job_manifest": {
            "apiVersion": "batch/v1",
            "kind": "Job",
            "metadata": {"labels": "{{ labels }}"},
            "spec": {
                "template": {
                    "spec": {
                        "containers": [{
                            "name": "prefect-job",
                            "image": "{{ image }}",
                            "workingDir": "/app"  # container’s cwd at start
                        }],
                        "restartPolicy": "Never",
                    }
                }
            }
        },
    },
)

If you truly want a pull step to change directories - You can only do this via prefect.yaml, not via Flow.deploy():

# prefect.yaml
pull:
  - prefect.deployments.steps.set_working_directory:
      directory: /app

- From Python, pull steps are inferred from storage: - Git -> git_clone - Remote storage -> pull_from_remote_storage - Local path -> set_working_directory - If you use flow.from_source(source="/app", ...), Prefect will generate a set_working_directory pull step to that path, but the path must exist in the runtime environment (e.g., inside the container). References - Docker worker docs: Prefect Docker integration - Kubernetes worker docs: Prefect Kubernetes integration - docker-py container create (supports working_dir): docker-py ContainerCollection.create - Deploy flows: Deploying flows in Prefect