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LanguageMachines / PICCL

A set of workflows for corpus building through OCR, post-correction and normalisation
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Frog does not honour --skip option #28

Closed zeusttu closed 6 years ago

zeusttu commented 6 years ago

We can now select which individual Frog features should and should not run, but it turns out this information is ultimately ignored. I found that picclservice_wrapper.py does correctly call frog.nf with the correct --skip option, but that Frog then proceeds to ignore it. I suspect that the following line is the culprit: https://github.com/LanguageMachines/PICCL/blob/0d370b84aebf70ddfc6abe906c8eb08429cc120d/frog.nf#L23

proycon commented 6 years ago

Hmm, that is odd. That line shouldn't be the issue really cause that's where the defaults are set for the parameters, nextflow superimposes the actual values on it (I guess that happens for each process), but it seems a bit counter-intuitive yes.

proycon commented 6 years ago

I think that should fix it.

zeusttu commented 6 years ago

I am unfamiliar with the Nextflow language so I believe your word about it. I ran a test and it seems your commit indeed fixed it! :tada: Thanks!

Looking at the code it looks like the same bug should still exist for the test2folia workflow though. (We don't use that one but it should still be worth fixing.)