Cohort-creator

Added

- [ENH] Add non-openneuro datasets (ABIDE, CORR, ADHD200, Neuromod...). (124 Remi-Gau)
- [ENH] Add Dash app to help browse and visualizse all known datasets.
- [ENH] Improved listing of knonwn datasets to include:
- "scan duration"
- presence of `physio.tsv.gz` or `stim.tsv.gz` files
- presence of a `stimuli` directory
- numbers of the different file formats for EEG, MEG, iEEG
- references and links associated to each dataset
- dataset license

Fixed

- [FIX] Improve datasets listing for datasets with a mix of session level folders absent or present (for example: `sub-01/meg` and `sub-emptyroom/ses-20221212/meg`)
- [FIX] Make datasets URI more generic. (169 Remi-Gau)
- [FIX] handle datasets with fMRIPrep data in subfolders. (173 Remi-Gau)

Changed

- Adapt to neurobagel query tools new outputs formats by using a participant
and a dataset input files. 55 Remi-Gau

Added

- [ENH] turns output into a yoda datalad dataset. 84 Remi-Gau
- [ENH] pass dataset listings as list of strings via the CLI. 82 Remi-Gau
- [ENH] Index dataset and return participant listing if not provided. 81 Remi-Gau
- [ENH] Skip mriqc if requested. 80 Remi-Gau
- [ENH] Add an "all" sub command that runs install, get and copy in sequence. 65 Remi-Gau
- [ENH] Add a dockerfile for the package. 64 Remi-Gau
- [ENH] Call MRIQC docker to regenerate group level plots after copying mriqc data. 32 Remi-Gau
- [ENH] Create a bagel.csv file for a new cohort to list
what pipeline has been run on which subject / session pair. 29 Remi-Gau
- [ENH] Change output layout output to comply with recommendations
from the "Mega" extension to BIDS. 24 Remi-Gau
- [ENH] Implement the usage of a "bids filter file" to define "suffix groups"
with their own datatype, BIDS entities and suffix and extensions
to flexibly allow to copy data from any datatype for each dataset type. 35 Remi-Gau
- [ENH] Allow to run without using any participant file.
In this case all participants of each datasets are downloaded. 75 Remi-Gau

Removed

- Only use the participants file and not the dataset listing file. 34 Remi-Gau
- Change output layout output to now comply with recommendations
from the "Mega" extension to BIDS. 24 Remi-Gau