Can we specify file names of input assemblies?

[MostafaYA]

This is not really an issue, but may be a feature request. I see that chewbbaca allele call takes as input the directory containing the assemblies / file of paths to the assemblies.
Chewbbaca then predicts the names of the fasta files as a prefix before the first dot "." - in a few cases (such as different NCBI assembly versions) the names may contain dots.
I try to use chewbbaca as part of a pipeline, and this behavior leads to inconsistencies in the samples' name.

As a solution, instead of passing a file with paths, can we pass a file with two columns, column 1 for sample name and column 2 for the file's path?
e.g.
#Isolate_name path
Sample.1 /path/2/sample.1.fasta
Sample.2 /path/2/sample.2.fasta

Thanks

[rfm-targa]

Hello @MostafaYA,

Sorry for the delayed response. We can implement that for the AlleleCall module. I'll try to add it to one of the following versions (I don't know if it'll be possible in the next version, v3.2.0, but it should be included in the version after that).
Thanks for suggesting that feature. It'll help us improve chewBBACA.
I'll let you know when it's been implemented.

Rafael