Container

[vmurigneu]

Hi @rhysnewell

We would like to include Aviary in a nextflow pipeline. Is there a docker container recipe available for Aviary please?

Thank you
Valentine

[rhysnewell]

Hi Valentine,

There isn't a docker container yet, but it's something we've been meaning to create. The idea was to attempt to have a docker container for each rule in aviary's workflow also have a docker container but that is potentially a lot of work.

I do wonder how aviary would interact with a nextflow pipeline, as it it is essentially wrapping around a snakemake pipeline. I'm not sure how compatible the snakemake package management is with nextflow.

Rhys

[vmurigneu]

Thanks Rhys, yes that is our concern as well.
Actually we only used aviary recover so far as the assembly/polishing was already done outside of Aviary.