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Re: Google Summer of Code 2023 Inquiry

From: Spencer Skylar Chan
Subject: Re: Google Summer of Code 2023 Inquiry
Date: Thu, 30 Mar 2023 19:27:37 -0400

Hi Ricardo,

On 3/23/23 03:58, Ricardo Wurmus wrote:

Spencer Skylar Chan <> 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

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.


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