Changes to nf-core pipelines download CLI

[MatthiasZepper]

This PR suggests a change to the CLI of nf-core download respectively now nf-core pipelines download.

To free the -p flag for Seqera Platform, the -d flag was needed for --parallel-downloads and thus --download-configs had to change from -d to -c.

This is also more consistent, since most short flags use the first letter of the last word as the short flag, e.g. -l for --container-library or -u for --container-cache-utilisation.

Furthermore, -t / --tower has now been entirely removed as it was deprecated before. Therefore -t could have been used for --tag in the future, but there is hardly a point of having a short flag for a three letter argument, so I refrained from introducing it.

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 Does that still apply? I looked into the new docs folder, but it seems the old manual Markdown was replaced by some autogenerated API documentation: docs/api/_src/api/pipelines/download.md

[mirpedrol]

Hi @MatthiasZepper, thanks for this PR. Docs are now on the website repo here.
May I ask why --download-configuration has changed to yes/no instead of being a flag?

[MatthiasZepper]

Thanks for taking a look already. There are some more tweaks coming...

May I ask why --download-configuration has changed to yes/no instead of being a flag?

Because I have occasionally received complaints similar to #3043 and the prompt for downloading the configs was one of them. Technically, if stderr.is_interactive: should prevent prompts in non-interactive shells, but apparently there are users where this fails.

I never felt it was a pressing issue, but kept it in the back of my head for the next major version jump.