Pipeline template: Fix the faulty Download test / GitHub action

[MatthiasZepper]

In #3351, I refactored the nf-core pipelines download test to use $GITHUB_OUTPUT instead of the environment for improved security.

However, splitting the test into two independent jobs introduced the possibility of them running on different runners, which resulted in the second job lacking the correct setup. I have now resolved this issue by ensuring that all necessary setup setups are retained within the main job. Only the potentially vulnerable step remains isolated from the main job, but also does not require any setup.

The new version of the CI pipeline was successfully tested in my Test pipeline repository. Any further independent tests are highly appreciated.

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 76.16%. Comparing base (570ae2b) to head (737b515).
Report is 5 commits behind head on dev.

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[mirpedrol]

Looks good!
Also tested with the nf-core/testpipeline https://github.com/nf-core/testpipeline/actions/runs/12744809455/job/35517501873?pr=101

[MatthiasZepper]

Great! I think, it was by now already manually incorporated to the development version of the Taxprofiler pipeline, so that also suggests it does now work.

Also tested with the nf-core/testpipeline https://github.com/nf-core/testpipeline/actions/runs/12744809455/job/35517501873?pr=101

Did you by chance also test the conditional part? Because I have never created a pipeline with a cherry-picked template, and there is this {% if test_config %} clause in there that I do not understand at all. I vaguely recall you one mentioned that it allows customizing the template in the creation process, but I have not tested the non-default action. Would that then be only the upper part without everying enclosed between {% if test_config %} and {% endif %}?

[mirpedrol]

Exactly, it won't contain anything that is between {% if test_config %} and {% endif %}. I haven't tested that case, but it should be ok as it will only test the first part of the action, which is passing on the tests pe made