You may be interested in the http://nucleotid.es/ & http://bioboxes.org/ efforts. Bonus, the harmonized interface can be described using the Common Workflow Language (whose 1.0 release just occurred); it is likely that you could represent the conversion using CWL itself.
On Wed, Jul 13, 2016 at 11:46 AM, Afif Elghraoui <[email protected]> wrote: > Hi, all, > > Another thought that has been floating around in my head: we have many > read aligners, variant/consensus callers, genome assemblers, and other > such tools that do the same job with different algorithms. I think it > makes sense to try to manage them as alternatives[1] and work towards > standardizing their interfaces. > > I also think that the variation in interfaces for these similar tools is > not because of any developer's attachment to them, but because there's > no real guideline for what to do (like, how to pass the reference > sequence-- some say -r while others might say --referenceFile). > > On the other hand, besides better organization and potentially more > intuitive interfaces, I'm not sure whether undertaking this is worth the > effort. Are there any strong feelings about this? > > regards > Afif > > > 1. https://wiki.debian.org/DebianAlternatives > > > -- > Afif Elghraoui | عفيف الغراوي > http://afif.ghraoui.name > > -- Michael R. Crusoe Community Engineer & Co-founder Common Workflow Language project https://impactstory.org/u/0000-0002-2961-9670 [email protected] +32 (0) 2 808 25 58 +1 480 627 9108
