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Re: Google Summer of Code 2023 Inquiry

From: Spencer Skylar Chan
Subject: Re: Google Summer of Code 2023 Inquiry
Date: Wed, 22 Mar 2023 17:44:52 -0400

Hi Ricardo,

On 3/22/23 14:19, Ricardo Wurmus wrote:

- Translating Snakemake to Guix Workflow Language (GWL)

Ricardo, maybe you would have some suggestions. :-)

Oh, this looks interesting.  Could you please elaborate on the idea?

My idea is to take as input a Snakemake workflow file and eventually output an equivalent GWL workflow file.

Currently, Snakemake workflows can be exported to CWL (Common Workflow Language):

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

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.

Is this topic something that could fit into a summer project?

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