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.

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.

[mashehu]

I would keep it as a flag. Pointing towards the one-liner approach suggested by @ewels should be enough.

[MatthiasZepper]

I would keep it as a flag. Pointing towards the one-liner approach suggested by @ewels should be enough.

But the download configuration prompt and the $NXF_SINGULARITY_CACHEDIR are two different things ?!?

[mashehu]

okay, then I misunderstood why you linked the issue... just for clarity's sake: one can add the also the download-configuration with $NFCORE_DOWNLOAD-CONFIGURATION

[mirpedrol]

LGTM, we are only missing updating the docs for these changes. Is this PR ready to be merged @MatthiasZepper ?

[MatthiasZepper]

just for clarity's sake: one can add the also the download-configuration with $NFCORE_DOWNLOAD-CONFIGURATION

I did not know that. I also do not find it in the code. So how does that work?

            if not self.platform and self.include_configs is None:
                self.prompt_config_inclusion()

LGTM, we are only missing updating the docs for these changes. Is this PR ready to be merged @MatthiasZepper ?

From my side, absolutely, since there is seemingly no need to address the CACHE DIR issue, since the OP did never reply. But I do not think that @mashehu is happy with the other changes yet?

[mashehu]

the env. variable thing comes with click: https://click.palletsprojects.com/en/8.1.x/options/#values-from-environment-variables