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Warn user if signalp is missing if prokka_gram is true #148
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Yeah, I always thought it's not a nice name since it doesn't really convey anything to the end user. I think, |
Hi team, I'd like to confirm if there is a reliable cross-platform way we can check whether this By default, I'm inclined to go with |
A quick google led me here: Sounds like just trying to run I've seen variants of |
Okay, I'm just wondering whether this would be available in Let me check and circle back. |
@abhi18av Did you ever have time to check this? We can push this feature to the next release, so it's not a big deal right now. |
@boulund , not yet unfortunately 😞 I agree this could be added as a patch later. But I did take a look yesterday and it seems that the Not sure how exactly to implement this feature. Perhaps a groovy function or NF utility process to check the presence of |
I'm also not entirely sure what the best way to implement this is... Maybe it's easiest to just do it in the bash code within the prokka process itself? E.g. in https://github.com/ctmrbio/BACTpipe/blob/master/modules/prokka/prokka.nf#L50-L65 Maybe something like this could work?
It won't produce a very visible warning message, however. It will only be shown in the stdout of the prokka process, if one knows that to look for. Explanation of how I was thinking:
The value of
If the statement above evaluates to false, this part will run and set the |
Looking at it again I don't think this is the best idea. It might be better as you suggested to write a small Nextflow/groovy function to check for the presence of |
Hmm, that's an interesting point. I'm not particularly sure about that 🤔 However, I'll ask around and try to come up with solution with the utility process in the meatime. |
I would like BACTpipe to detect if
signalp
is missing ifprokka_gram
is set to true, and warn the user that prokka requires signalp if combined with theprokka_gram
option and perhaps instruct the user to run with--prokka_gram false
if they want to proceed.Now that I'm thinking of it, is
prokka_gram
really the best name for that config setting? Shouldn't it be--prokka_signal_peptides
or--use-signalp
instead, to make it more obvious to the user what it will affect?What are your opinions @thorellk @abhi18av @emilio-r ?
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