add --dir/-d option to schema commands

[mashehu]

Fixes #3234
not sure if we want it also in pipelines create

[mirpedrol]

We already have the option for pipelines create, but on the CLI is called --outdir/-o, we could rename it or better, allow both notations.

[mashehu]

yeah, was actually thinking the same, only problem is that -d is used for description, so I think it is okay, to have that as an exemption, or what do you think, @nschan?

[nschan]

Personally, I think -o for create is reasonable. I understand -d to mean "run inside dir" whereas -o is output.

[nschan]

Looks fine to me.

[mirpedrol]

LGTM

[codecov]

Codecov Report

Attention: Patch coverage is 72.72727% with 3 lines in your changes missing coverage. Please review.

Project coverage is 75.30%. Comparing base (b87106d) to head (f49e9cf).
Report is 86 commits behind head on dev.

Files with missing lines	Patch %	Lines
nf_core/__main__.py	72.72%	3 Missing ⚠️

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