search

kevlar-dev / kevlar

Reference-free variant discovery in large eukaryotic genomes
https://kevlar.readthedocs.io
MIT License
41 stars 9 forks source link

Report kevlar version when running a script #61

Open standage opened 7 years ago

standage commented 7 years ago

...for reproducibility's sake, yo.

ctb commented 7 years ago

@mr-c and I and others have thought about doing this in a more systematic way using a JSON output format - note that e.g. Salmon does this.

khmer issue:

https://github.com/dib-lab/khmer/issues/676

standage commented 7 years ago

Minimal reporting added in #65. Leaving this thread open to entertain considerations raised by @ctb.

standage commented 5 years ago

The introduction of Snakemake workflows in #305 and #306 raises the possibility of recommending Snakemake as the primary interface for most users, with the kevlar command documented for users that are curious or need to tweak results. In any case, I think with a small amount of effort we can improve and capture the existing logging outputs and save them to standardized locations in the Snakemake working directory, creating a nice record of provenance. Capturing logs when running kevlar directly will be left as an exercise for the user. :-)

I don't have much interest in going down the rabbit hole we started exploring in https://github.com/dib-lab/khmer/issues/676.