Documentation out of sync

The documentation has not been updated with recent code changes and is now out-of-sync. Please update such that the documentation is in sync with the current state of the workflow.

added high priority label

assigned to @iris.mestrespascual

When updating the section Usage section, now that there's no RUNS/ directory, should I make the user to make a clean copy of the test directory and change names?

Also, in order to fully update the documentation I also have to remove the images we have now and create new ones accordingly to the workflow. Should I do it in this same issue?

Of course! Create a single Snakemake rule graph for the entire combined workflow and use that instead of the current images.

And regarding the Usage section?

I will much prefer if you suggest what you wanna do, in detail and in a single message. I can then check and sign it off or ask for some changes.

In principle I think the issue is quite clear: the documentation, in its entirety, should reflect the current state of the workflow at all times.

Okay, I'll update the README.md to reflect what we have right now and think of how to solve the usage part later on.

created branch 39-sync-documentation to address this issue

An update of the README.md has been done in a different branch but the pull request not due to:

1. The usage part has a "step-by-step" on how to run the workflow with the user's data but this decision has not been approved yet.
2. I'll wait to make the pull request when the open pull request is merged; that way I can update too the prepare subworkflow from downloading to using local files.