Matthias Zepper

> Sorry, good in principle now for me (maybe some factoring out we can do later). Just need to get tests to run + pass. Well, it appears the issue...

Just to give a brief update: I have finally [found some time to update the tests](https://github.com/nf-core/modules/pull/7075). Therefore, I hope the module tests will soon be updated in the repo and...

@maxulysse: Let me know, when you have synced the test data to the S3 bucket. Ultimately, that sounds like something we could automate in the future with a CI on...

> @nf-core-bot fix linting Thanks! Strange, that the linter is unhappy, since I literally copy and pasted that from the current `dev`...anyway.

I don't think that any of my changes could have caused this test failure? Admittedly, I do not even know what kind of test that is...

Admittedly, my changes apparently introduced an issue with the config parsing. When running `pytest tests/pipelines/test_create_app.py -k test_github` the `manifest.version` key is missing from the configuration: ```Python sorted(wf_config.keys()) 'manifest.contributors', 'manifest.defaultBranch', 'manifest.description',...

Ok, this looks much better now. The only test that is still failing is Refgenie as expected. But I could fix the other test failures that indeed indicated a serious...

Indeed, a massive refactoring and rewrite of the `nf-core download` tool is required, that should - Refactor the whole codebase into separate, more modular classes - Make use of `nextflow...

I just learned that Phil has already come up with a similar solution. Like him, I was also thinking of a custom config file with container specifications, like in [POC1](https://github.com/seqeralabs/nf-aggregate/pull/43)....

For the `--tower` download, this is exactly what it already does. Check the `WorkflowRepo` class and associated methods. When `DownloadWorkflow.download_workflow_tower()` is executed, the repo is checked out at every requested...