Issue with options when calling subcommand for "gapseq doall". about gapseq HOT 3 CLOSED

hi @ArnaudBelcour
Thank you for your thoughtful comment! You are right; the current approach does not match the expected behavior.

And sure, it would be great to have a pull request for this!

The only thing why I am a bit hesitating is that gapseq doall is supposed to perform a default and recommended settings. Adding parameters for all sub-processes would probably add too much complexity, and for these use cases, advanced users should, in my opinion, better call the sub-processes like gapseq find or gapseq fill directly.

For -K, it makes total sense to add it, and maybe also for -v although I am not so completely sure here because doall starts the pipeline and is not primarily for getting general information and version numbers. What do you think?

from gapseq.

I understand your point of using only default option with gapseq doall and yes, only the -K option could be added. I will make this minimal modification and we can discuss it on the PR.

For the other option, I was more thinking of -n, which allows to have a more verbose output when using gapseq doall. Because indeed, -v is not very useful to such command, but I was using it as the difference of outputs were the most striking.

from gapseq.

I agree that -v and -K both make sense for gapseq doall!

If you still want to implement it, feel free to open a PR, otherwise, I can also do it.

from gapseq.