Change path in yaml for ingestion tutorial

[kevinrue]

The pipeline.yml provided in the tutorial includes a path that doesn’t play well with the tutorial.

You probably want to change panpipes-tutorials/tutorials/ingesting_data/qc_genelist_1.0.csv to qc_genelist_1.0.csv.

For example, see the GitHub action workflow which uses ‘sed’ to change that file path https://github.com/DendrouLab/panpipes/blob/kra-gha/.github/workflows/ingestion-ci.yml#L88

[giuliaelgarcia]

Personally, I don't think that changing it to qc_genelist_1.0.csv will help since it assumes that the file is in your current directory, which for example my case wasn't. I think the way to go around it (especially for new users) would be to make it clear in the tutorials that each user will have to adapt the yml to the correct path based on their own setup. Since this has to be done all throughout the various tutorials.

[kevinrue]

I'm confused. Why would it assume that it's in the current directory if the pipeline.yml declares a path to another directory?

[kevinrue]

Side note: the tutorial generally does a good job of indicating bits that need to be adjusted by users. However, this is the only place in the whole tutorial where the example file is not immediately usable as is. All the other example files contain values that point to the place where the tutorial files are located/downloaded.

[bio-la]

Hey @giuliaelgarcia I see your point but I do agree with @kevinrue. Plus, it would make it foolproof for new users to just take the yml and run the tutorial. ( If someone mistakenly modified a path in the config they can always go back to the original one which surely will work)

Please add a section on the ingestion tutorial on how to organize all the input files (do so by adding a new header in the tutorial) and clarifying that the config we provide expects the files to be in the current directory (or the data.dir depending on where they are). You can move the statement about our suggestions on how to organize the project directory to the top of the tutorial then.
Happy to talk tomorrow in case you need clarification!

Thank you!