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For instance, the app-maxwell-filter
takes as inputs the meg/fif
datatype (for the meg.fif) and also optionaly optionnaly the meg/fif-override
datatype. The inputs from the meg/fif-override
datatype are optional because we don’t know if an App user will run the whole pipeline on Brainlife (i.e. compute the destination.fif, then the headshape.pos, detect bad channels, and eventually run Maxwell filter), maybe he will want to run only the app-maxwell-filter
and he will provide the headshape.pos and channels.tsv without computing them with the BL Apps, and these files will be directly into the data staged under the meg/fif
datatype.
But, maybe the user will run the pipeline from the beginning and still provide the headshape.pos and channels.tsv in when the data is staged underr the meg/fif
datatype. So, for app-maxwell-filter
we will have two versions of each file. So, in this case, only the files computed by the BL Apps will be taken into account.
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We decided not to inform the App user that the optional file previously computed by an App (so a file from the meg/fif-override
datatype) will overwrite the optional file linked to the meg/fif
datatype because we supposed that, if the User computed computes a new file he doesn’t want to use the file he gave at first when the data was staged.
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In the config.json
created by BL we will have the keys linked to the meg/fif-override
datatype, but these keys won’t be present if the App is run locally because the datatype issue is specific to BL (that’s why we check if the key is present at the beginning.
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