Re: Google Summer of Code 2023 Inquiry

[Spencer Skylar Chan <schan12@terpmail.umd.edu>]

Hi Ricardo,

On 3/23/23 03:58, Ricardo Wurmus wrote:
> Hi,
> 
> Spencer Skylar Chan <schan12@terpmail.umd.edu> writes:
> 
>> One approach could be to add CWL import/export capabilities to
>> GWL. Then Snakemake/GWL conversion would be a 2 step process, using
>> CWL as an intermediate step:
>>
>> 1. Snakemake -> CWL
>> 2. CWL -> GWL
> 
> This seems doable.

Great! I've been reading the chapter in Evolutionary Genomics on 
different scalable workflows to understand this process better.

>> However, CWL is not as expressive as Snakemake. There may be some
>> details that are lost from Snakemake workflows.
>>
>> So a 1-step Snakemake/GWL transpiler could be interesting, as both
>> Snakemake/GWL use a domain-specific language inside a general purpose
>> language (Python/Guile respectively). There may be a possibility to
>> achieve more "accurate" translations between workflows.
> 
> Compared to the previous approach this seems vastly more complex.  It’s
> one thing to *execute* Snakemake code without running it through Python,
> but quite a bit more challenging to transpile Python to Scheme.
> 
> Personally, I wouldn’t know where to start.  Do you have an idea
> already?
> 

Actually I was hoping you might have some ideas :)
I do think that if the execution of the pipeline is more important than 
its representation (Snakemake or otherwise), then it would make more 
sense to focus efforts on increasing GWL's capabilities.

Thanks,
Skylar