Add a check for step dependencies ?

[enricotagliavini]

It can happen to skip a step by mistake and get an unlcear error due to missing inputs. For example task 03 can fail with

[2023-03-20 10:15:36+0100] INFO - prefect.TaskRunner | Task 'link_nuclei_task[1]': Starting task run...
Measurment regionprops_ovr_C01 does not exist in C03:[].
[2023-03-20 10:15:36+0100] INFO - prefect.TaskRunner | Task 'link_nuclei_task[0]': Starting task run...
Measurment regionprops_ovr_C01 does not exist in C03:[].
[2023-03-20 10:15:36+0100] ERROR - prefect.TaskRunner | Task 'link_nuclei_task[1]': Exception encountered during task execution!
Traceback (most recent call last):
  File "/tungstenfs/nobackup/gliberal/taglenri/nicole/scmp_venv/lib64/python3.8/site-packages/prefect/engine/task_runner.py", line 880, in get_task_run_state
    value = prefect.utilities.executors.run_task_with_timeout(
  File "/tungstenfs/nobackup/gliberal/taglenri/nicole/scmp_venv/lib64/python3.8/site-packages/prefect/utilities/executors.py", line 468, in run_task_with_timeout
    return task.run(*args, **kwargs)  # type: ignore
  File "./scripts/prefect/03_nuclear_multiplex.py", line 62, in link_nuclei_task
    link_nuclei(
  File "/tungstenfs/nobackup/gliberal/taglenri/nicole/gliberal-scMultipleX/src/scmultiplex/linking/NucleiLinking.py", line 39, in link_nuclei
    R0_df_ovr, R0_df_org = load_organoid_measurement(organoid, org_seg_ch)
  File "/tungstenfs/nobackup/gliberal/taglenri/nicole/gliberal-scMultipleX/src/scmultiplex/linking/NucleiLinking.py", line 21, in load_organoid_measurement
    df_ovr = df_ovr.set_index("org_id")
AttributeError: 'NoneType' object has no attribute 'set_index'
[2023-03-20 10:15:36+0100] ERROR - prefect.TaskRunner | Task 'link_nuclei_task[0]': Exception encountered during task execution!
Traceback (most recent call last):
  File "/tungstenfs/nobackup/gliberal/taglenri/nicole/scmp_venv/lib64/python3.8/site-packages/prefect/engine/task_runner.py", line 880, in get_task_run_state
    value = prefect.utilities.executors.run_task_with_timeout(
  File "/tungstenfs/nobackup/gliberal/taglenri/nicole/scmp_venv/lib64/python3.8/site-packages/prefect/utilities/executors.py", line 468, in run_task_with_timeout
    return task.run(*args, **kwargs)  # type: ignore
  File "./scripts/prefect/03_nuclear_multiplex.py", line 62, in link_nuclei_task
    link_nuclei(
  File "/tungstenfs/nobackup/gliberal/taglenri/nicole/gliberal-scMultipleX/src/scmultiplex/linking/NucleiLinking.py", line 39, in link_nuclei
    R0_df_ovr, R0_df_org = load_organoid_measurement(organoid, org_seg_ch)
  File "/tungstenfs/nobackup/gliberal/taglenri/nicole/gliberal-scMultipleX/src/scmultiplex/linking/NucleiLinking.py", line 21, in load_organoid_measurement
    df_ovr = df_ovr.set_index("org_id")
AttributeError: 'NoneType' object has no attribute 'set_index'
[2023-03-20 10:15:36+0100] INFO - prefect.TaskRunner | Task 'link_nuclei_task[1]': Finished task run for task with final state: 'Failed'
[2023-03-20 10:15:36+0100] INFO - prefect.TaskRunner | Task 'link_nuclei_task[0]': Finished task run for task with final state: 'Failed'
[2023-03-20 10:15:36+0100] INFO - prefect.FlowRunner | Flow run FAILED: some reference tasks failed.