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

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 76.04%. Comparing base (b685800) to head (c67027d).

Additional details and impacted files

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