add code to create raw tsv and make a markdown table + add submodules

[marcobarilari]

No description provided.

[pep8speaks]

Hello @marcobarilari! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file tools/list_raw.py:

Line 1:80: E501 line too long (81 > 79 characters)

• In the file tools/utils.py:

Line 29:80: E501 line too long (82 > 79 characters)
Line 138:80: E501 line too long (85 > 79 characters)
Line 149:80: E501 line too long (81 > 79 characters)
Line 172:80: E501 line too long (83 > 79 characters)
Line 174:80: E501 line too long (84 > 79 characters)
Line 177:80: E501 line too long (88 > 79 characters)
Line 190:80: E501 line too long (86 > 79 characters)

Comment last updated at 2023-11-08 09:11:57 UTC

[marcobarilari]

@Remi-Gau will merge tomorrow morning (around 10:15) to have some basic stuff to show around. However, if you think you want to review this first one to start with the right step I am happy to leave it open for a little while more.

[Remi-Gau]

for the moment I would drop the columns :

• has_participant_tsv
• has_participant_json
• has_phenotype_dir
• participant_columns

[Remi-Gau]

drop some of the columns we do not care about

[Remi-Gau]

you probably want to:

• rerun the script
• delete and gitignore the pycache folder

[Remi-Gau]

also if you want to jsut reformat your code to get less complaints like this one,
just run in the repo.

pip install black
black .

[Remi-Gau]

will push a couple of changes and merge