Common Workflow Language

[Christopher Fields]

Just curious, but has anyone looked at integration of Common Workflow Language support (CWL, https://github.com/common-workflow-language/common-workflow-language) for Nextflow?  Or is this of general interest?  

Thanks,

chris

[Paolo Di Tommaso]

Hi Christopher,

That would be interesting but it surely is a challenging task due to the inherent differences between Nextflow and the CWL specification. For example with Nextflow we have chosen to have tasks defined simply providing a piece of code to be executed in the hosting environment, this greatly simplifies applications prototyping. Instead the CWL specification requires each single tool (including any command line options) to be wrapped by a JSON definition.  

This makes really difficult for Nextflow to be able to generate a workflow definition complaint with CWL. 

However I think that at some point, when the specification will be stable, we could take in consideration some kind of interoperability, for example having a conversion tool/produce that would allow a CWL workflow to be converted to a Nextflow script. Surely something that deserve to be investigated. 

Cheers,

Paolo

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[Christopher Fields]

Hi Paolo,

That's essentially what I was thinking (e.g. a conversion layer).  My feeling is this will be a primary, and easiest, mode of support to implement.  Peter Amstutz, one of the CWL core members, also mentioned your interest in CWL but mentioned some differences on the CWL mail list between CWL design and how nextflow is implemented:

https://groups.google.com/d/msg/common-workflow-language/qQ8-jCNkAXE/HjlQ1cDjAgAJ

Thanks!

chris

[Paolo Di Tommaso]

Hi Chris, 

I share this view and I agree that could be useful for both projects. The problem is that we are a very small team and at this time I think it's more important to focus our effort on the *computing* capabilities of the framework more than the interoperability with other workflow tools. 

This does not mean that we don't care about the portability and reproducibility of nextflow applications. Indeed, this has been the main project goal since the day zero. 

However Nextflow aims to achieve workflow reproducibility targeting different computing platforms, more than supporting multiple workflow tools.

Said that, we are more than happy to take in consideration any collaboration proposal for a Nextflow-CWL conversion layer. This could even be an interesting Google Summer of Code project in the context OBF. 

What do you think? 

Cheers,

Paolo

[Kyle Hernandez]

Hello,

I too have been interested in using nextflow as the engine for cwl. Has there been anymore discussion of this?

[Paolo Di Tommaso]

Hi Kyle, 

We have submitted a project idea for this year GSoC. However we still don't know if there will be any student working on that. 

In any case I think it would be an interesting integration and we would be eager to receive pull request for that. May you eventually be interested in contributing to it? 

Best,

Paolo

 

 

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