Remove 'Tower' from almost everywhere..

[ewels]

Tried to replace "Nextflow Tower" with "Seqera Platform" everywhere I could.

Special note:

• nf-core download --tower now uses --platform
  • The short flag is still -t as -s and -p were already taken
  • I left --tower in place for now but hid it from help text. We can remove it fully in the future.
• I replaced mention of tower in the code as well as docs, wherever possible
• Some stuff can't be switched yet and needs updating in the future, eg. action-tower-launch
• I didn't bother updating the Changelog

I didn't change the secret names, such as secrets.TOWER_WORKSPACE_ID. Though I guess we could do.

Haven't done loads of testing at this point, so any help on that front would be much appreciated 🙏🏻

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Codecov Report

Attention: Patch coverage is 85.71429% with 2 lines in your changes are missing coverage. Please review.

Project coverage is 74.79%. Comparing base (189a4af) to head (3b78154).

❗ Current head 3b78154 differs from pull request most recent head 9f9b75d. Consider uploading reports for the commit 9f9b75d to get more accurate results

Files	Patch %	Lines
nf_core/download.py	84.61%	2 Missing ⚠️

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[ewels]

@nf-core-bot fix linting

[MatthiasZepper]

Before going into detailed review here: Why now --platform ?

I thought we had long settled for the neutral --bare on Slack? (I know for sure, because I preferred archive but then went with the majority vote). Using Tower was making a bow to Seqera, but in retrospect, I think it was a poor judgement to depend on any corporate naming choices, in particular since those pipelines can still be run without Tower/Platform/Whatever future rebranding.

[MatthiasZepper]

Just a typo when replacing Tower in one file and the overall discontent with the branding. --collection would be my pick.

But if other (non-Seqera affiliated people!) agree, then I will survive having it changed to --platform.

[MatthiasZepper]

Not at all happy with using --platform, but neither with --bare.

Still would strongly prefer something neutral that suggests that multiple pipeline revisions can be contained: --collection, --package or --multi.

The strongest argument against --collection or --package was that the -c respectively -p short parameters were already taken (or in the case of -c reserved for config). But if that isn't paramount and any letter within the word will do, then collection also contains a -t. That will of course be nice to preserve backwards compatibility.

[ewels]

Wow, how many times can I mis-spell the name of my employer? 😆 Thanks @MatthiasZepper!

I don't have particularly strong opinions about the CLI flag, other than it should be obvious and easy for find for folks who want to use it. Personally I don't think that any of --collection, --package or --multi really fulfil that - I would assume that each did something different just from the flag name.

Do we know of any other practical uses for this flag apart from running Seqera Platform?

[edmundmiller]

Think the discussion is outside the scope of this PR. This is just a style change.

I think you should open an issue or reopen the old issue if you'd like to continue to discuss @MatthiasZepper.

[ewels]

Thanks all!

[MatthiasZepper]

Do we know of any other practical uses for this flag apart from running Seqera Platform?

You can nextflow run such a download with a file:/absolute/path/to/pipeline.git. If one wishes to keep multiple pipeline revisions in a convenient, space-saving multi-revision collection/package, then those downloads are perfectly suitable and easier to handle than the classic multi-revision download, that creates subfolders for each revision.

[MatthiasZepper]

Think the discussion is outside the scope of this PR. This is just a style change.

Just a style change? I wish I had known that when I wanted to change some CLI arguments of the nf-core download command a year ago. Oh boy, that was an uphill battle, discussing every single change ad nauseam and in the end settling with a half-way compromise.

I think you should open an issue or reopen the old issue if you'd like to continue to discuss @MatthiasZepper.

No, I won't. I am obviously a pushover, but I do also not what to stubbornly escalate this into a Wikipedia-style edit war. Merged is merged.