[Bio-packaging] GNU Guix and CWL

Pjotr Prins pjotr.public66 at thebird.nl
Sun Jul 12 09:59:06 UTC 2015

Correction CWL is mostly YAML. My current thought is to use
S-expressions to generate YAML...

On Sun, Jul 12, 2015 at 11:38:00AM +0200, Pjotr Prins wrote:
> The Common Workflow Language (CWL) is going to be key to rolling out
> pipelines in bioinformatics. As it is mostly a static definition of
> workflow containing input -> procedure -> output, it looks to me that
> it can work well in conjunction with Guix expressions. Basically CWL
> is like running a (distributed) gcc compile on inputs with outputs. 
> So, defining a reproducible data analysis can be a Guix expression
> with the CWL as a 'compiler'.
> The CWL specification itself is mostly JSON. To create a more conscise
> representation we could introduce S-expressions to generate this JSON.
> CWL is a bit like RDF - it is mostly a standard description of a
> typical workflow in bioinformatics. Workflow runners honour this
> standard. And docker does *not* need to be part of that solution. The
> solution can be pure Guix (and Guix does distributed builds already).
> Using Guix as a cwl-runner (on a local build farm) is an interesting
> thought for reproducible data analysis.
> Pj.


More information about the bio-packaging mailing list