search

wtsi-hgi / gatk-cwl-generator

Generates CWL files from the GATK documentation
MIT License
7 stars 1 forks source link

short option versions don't show up anywhere in generated CWL #19

Closed jrandall closed 6 years ago

jrandall commented 6 years ago

I would have expected the short versions of options (such as -ERC instead of --emit-ref-confidence) to appear somewhere in the CWL so that when looking for an option based on an example using the short version (which most of them do!), they can be found without having to refer back to the documentation manually.

mr-c commented 6 years ago

I guess it could be mentioned in the doc for the particular input?

sersorrel commented 6 years ago

Where there is a short option available, it's now added to the doc like so:

- doc: Mode for emitting reference confidence scores [synonymous with -ERC]