Ega download module

[Kdreval]

Pull Request Checklists

Important: When opening a pull request, keep only the applicable checklist and delete all other sections.

Checklist for New Module

Required

• [X] I used the cookiecutter template and updated the placeholder rules.

• [X] The snakemake rules follow the design guidelines.

  • [X] All references to the rules object (e.g. for input files) are wrapped with str().

• [X] Every rule in the module is either listed under localrules or has the threads and resources directives.

• [X] Input and output files are being symlinked into the CFG["inputs"] and CFG["outputs"] subdirectories, respectively.

• [X] I updated the final target rule (*_all) to include every output rule.

• [X] I explained important module design decisions in CHANGELOG.md.

• [X] I tested the module on real data for all supported seq_type values.

• [X] I updated the default.yaml configuration file to provide default values for each rule in the module snakefile.

• [X] I did not set any global wildcard constraints. Any/all wildcard constraints are set on a per-rule basis.

• [X] I ensured that all symbolic links are relative and self-contained (i.e. do not point outside of the repository).

• [X] I replaced every value that should (or might need to) be updated in the default configuration file with __UPDATE__.

• [X] I recursively searched for all comments containing TODO to ensure none were left. For example:

  grep -r TODO modules/<module_name>/1.0

[Kdreval]

Yep, this was tested and all the samples in the recent gambl dataset are downloaded with this module. They live here: /projects/rmorin_scratch/ega_download/ and this is the gambl PR that added that specific cohort: https://github.com/morinlab/gambl/pull/322

[Kdreval]

Thanks for the quick turnaround @gillissierra !