nextflow as a galaxy module?

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Hi,

Is it possible to make a custom module in galaxy that runs a nextflow workflow, such as mymodule.nf? If so, could you please tell me a bit about how to implement this?

Thanks!

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You can run anything that can be run as a command line as a Galaxy tool. It will be bad and can’t take advantage of scheduling steps individually and tracking the progress, but it’ll work. Refer to Building Galaxy Tools Using Planemo — Planemo 0.75.11 documentation for a guide on how to write Galaxy tools.

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Hi @jdlamstein! I noticed your post about working with nextflow pipelines in Galaxy. I’m particularly interested in wrapping the nf-core/ampliseq pipeline.

I was wondering if you managed to successfully write a proper XML file with Planemo(as @mvdbeek suggested) for this or any other pipeline and if you could share your experience or any tips you might have. It would be really helpful as I work on this.

Thanks in advance!