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KThorellGroup / BACTpipe

BACTpipe: An assembly and annotation pipeline for bacterial genomics
https://bactpipe.readthedocs.org
MIT License
20 stars 8 forks source link

shovill.log output as standard #152

Closed emilio-r closed 3 years ago

emilio-r commented 3 years ago

I suggest that we again make the Shovill output file shovill.log into standard output. It contains very valuable information about the assemblies and just a relatively small text file, making the storage-use rather small in comparison to the usefulness of this file.

boulund commented 3 years ago

I think this is a great suggestion! Make a PR!

emilio-r commented 3 years ago

@abhi18av, might I trouble you to implement this change at some point? I feel that I'm too unfamiliar with the structure of BACTpipe as it looks now, and would need to take too much time to get accustomed to it again before I would feel comfortable changing something like this.

boulund commented 3 years ago

I could point you to where the change needs to be made:

https://github.com/ctmrbio/BACTpipe/blob/master/modules/shovill/shovill.nf#L4

Since Nextflow v0.29.0 it is possible to add multiple publishDir directives. Should be straightforward to add a line that just publishes the log file without conditions.

emilio-r commented 3 years ago

Thank you for the assistance @boulund! I have now made the change, tested it, and made a pull request here #155 .

boulund commented 3 years ago

Nice work! Impressive that you made it so quickly! Glad to hear it worked well in testing.

boulund commented 3 years ago

Merged to develop 👍