search

nf-core / hlatyping

Precision HLA typing from next-generation sequencing data
https://nf-co.re/hlatyping
MIT License
61 stars 30 forks source link

Parse parameters.settings.json and display params with description in --help #57

Closed sven1103 closed 4 years ago

sven1103 commented 5 years ago

x-ref: https://github.com/nf-core/tools/issues/267

Proof of concept implementation.

christopher-mohr commented 5 years ago

In one of the recent commits I noticed that parameter value ranges are currently displayed like that in the help message:

--beta [0.0, 0.1] Shows additional n-1 suboptimal solutions from OptiType --enumerations [1, 150] Shows additional n-1 suboptimal solutions from OptiType.

Maybe it would be better to use a different notation for ranges than for "valid values", e.g.:

--beta [0.0:0.1] Shows additional n-1 suboptimal solutions from OptiType --enumerations [1:150] Shows additional n-1 suboptimal solutions from OptiType.

sven1103 commented 5 years ago

x-ref https://github.com/nf-core/tools/issues/267

@KochTobi can you change this in the template? Ranges should be assigned with :, enums separated with ,.

christopher-mohr commented 4 years ago

I guess this will be handled by the upcoming JSON schema and can be closed?

KochTobi commented 4 years ago

I guess so, yes