nf-core / nf-core/modules

Implement unit-test for full datasets

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enhancement hackathon2023 tests wishlist
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Description

Is your feature request related to a problem?

Some of the module features can not be tested using the self-contained data-set of the repository.

Describe the solution you'd like

Implement unit testing that can fetch real datasets and this way could test that modules work with real data and that features such as default resource allocations etc. work as expected.

Describe alternatives you've considered

@KevinMenden, @MaxUlysse @drpatelh and myself(@JoseEspinosa) have discussed several ideas on Slack (see additional context) such as:

  • Create a new repository to host the full datasets (or the pointers to them) similar to the test-datasets for modules
  • Create a branch on the test-datasets that contains the links to the full modules data-sets.

However how to implement the tests and even how the data should be host still needs a lot of discussions and that is why we opened the issue, so feel free to contribute with your ideas 😃

Additional context

This issue has been opened following a discussion on Slack about how to organize test datasets and that the idea that at some point we may want to test the modules on real data.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

No files, tests, or entry points are named. Start by reviewing the proposed full-dataset repository or branch approaches and the referenced Slack discussion, then determine how datasets should be hosted and fetched for module tests. Done requires an agreed testing and data-hosting design, which this issue does not yet define.

Written by the indexing model from the issue text.

Assessment

Domain
data, testing-qa
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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