Error when running a pipeline with optional files

The Apps created as part of the MEEG Brainlife project are supposed to be run one after another (see How to run Apps one after another). Thus the output of an App will be the input of another.

To test how it works, I decided to apply app-bad-channels and then app-maxfilter

First attempt

• app-bad-channels: no optional files present in file mapping

• app-maxfilter: no optional files listes in file mapping

Result: it works fine

Second attempt

• app-bad-channels: optional files present in file mapping

• app-maxfilter: optional files present in file mapping

Result: app-bad-channels works but app-maxfilter failed:

The optional file is indeed not in out_dir_bad_channels.

Indeed, the app-maxfilter takes in input the files corresponding to the datatype meg/fif present in out_dir_bad_channels, but here only meg.fif is in this folder.

How to address this issue

The only way to solve this issue is to save in the output directory the files you want to use as optional inputs of the next App. So here, the destination file must be saved in out_dir_bad_channels.

To do so, we add the following line to the helper.py (see Create a helper.py file) for each optional file: