Hello group!
In my Jupyter notebook, I specify a list of input files to be processed like this:
files = [‘msCam1.avi’, ‘msCam2.avi’]
data_folder = ‘/work/imaging-analysis/data/raw_movies’
When running the notebook from the command line through papermill
, the list can also be specified and everything runs fine:
papermill --kernel Python3 \
notebooks/01_cnmfE_MotionCorrect.ipynb \
notebooks/01_cnmfE_MotionCorrect.ran.ipynb \
-p data_folder /work/imaging-analysis/data/raw_movies \
-y '{files:[msCam1.avi, msCam2.avi]}'
But if I try to run the exact same command through renku run
I get an error(after the notebook has completed):
Input Notebook: notebooks/01_cnmfE_MotionCorrect.ipynb
Output Notebook: notebooks/01_cnmfE_MotionCorrect.ran.ipynb
Executing: 100%|██████████████████████████████████████████████████████████████████████████████████████| 17/17 [01:01<00:00, 3.64s/cell]
Error: The output directory "data/raw_movies" is not empty.
Delete existing files before running the command:
(use "git rm <file>..." to remove them first)
data/raw_movies/msCam1.avi
data/raw_movies/msCam2.avi
Once you have removed files that should be used as outputs,
you can safely rerun the previous command.
Why does it complain about the input files in this case?