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Published 20 hours ago • verified publisher icon bactopia

[bug] output in json format only

Open shlomobl opened this issue 2 years ago • 1 comments

Hi, After updating to the last version of Bactopia, most output files are in json format. For example, BLAST, MLST, AMR... no txt files, only json. Any ideas what could be causing/how to solve this? Thanks!

shlomobl avatar Jun 16 '22 18:06 shlomobl

There was an issue with the Ariba recipe which forced me to removed it temporarily.

I've since fixed the recipe (https://github.com/bioconda/bioconda-recipes/pull/35383) and will look to adding it back. Although I might have to move to strictly a Bactopia Tool due to it no longer being maintained.

rpetit3 avatar Jun 16 '22 21:06 rpetit3

Hi @shlomobl

I've released v2.2.0, there is now an alternate mlst tool available. I'm going to go ahead and close this.

Cheers, Robert

rpetit3 avatar Nov 29 '22 00:11 rpetit3