Add option of writing module diff to file

[ErikDanielsson]

EDIT from @ewels: Description is outdated. Usage is now via interactive prompt or --save-diff.

Original description kept below for context:

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Added option of writing the diffs in nf-core modules update between a locally installed module and a remote version in two ways:

• If --diff is specified, the user is asked whether the diffs should be displayed directly in the terminal or written to a file
• Added --diff-file <filename> option to specify a file, without using any interactive prompts

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

[ewels]

Note to self: need to think about flag naming with this to avoid potential confusion with #1312

Potentially:

• nf-core modules update --show-diff > nf-core modules update --update-diff
• nf-core modules update --diff > nf-core modules update --update-diff

So collapse into one file, use - to print to stdout? (or allow empty input string if that's possible?)

[ewels]

Coming back to this comment, update-diff sounds horrible as it sounds like an action. Maybe we stick with --show-diff but remove the --diff flag 🤔

Could also have a nf-core modules patch --show-diff flag alongside, I think that would be logical (x-ref #1312 )

[ewels]

ok after a bit of back and forth on this I think I'm happy - not finished yet but moving in the right direction.

• Removed --diff entirely and rely on the interactive prompt
• Rename --diff-file to --save-diff
• Some other refactoring / bugfixes

Still to do before merge:

• Fix logic when previewing diffs and saving them to a file
• Maybe: Fix diff file output so that we can use git apply

[ewels]

Can't do the git diff thing as we also need to update the modules.json file.

Unless we add the changes to that file to the diff as well 🤔

[ewels]

ok that's pretty cool, can do git apply mychanges.patch after reviewing it all..

[FriederikeHanssen]

lgtm