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nf-cmgg / germline

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
https://nf-cmgg.github.io/germline/
MIT License
6 stars 1 forks source link

Add dockerfile #98

Closed matthdsm closed 1 year ago

matthdsm commented 1 year ago

Description of feature

Add a dockerfile containing all the requirements for the pipeline, so we can run it as a single "tool" on nomad/galaxy/whatever

nvnieuwk commented 1 year ago

Do you mean a container that contains all tools needed or just a container able to start the pipeline and download the relevant containers itself?

matthdsm commented 1 year ago

A container with all the tools installed so the pipeline can run inside the container without creating conda envs or running docker

nvnieuwk commented 1 year ago

That's gonna be a challenge, but I'll give it a go :)

nvnieuwk commented 1 year ago

I've managed to create a container without somalier and groovy (needed when adding ped headers, but that can be rewritten). Is it bad that somalier isn't part of it?

nvnieuwk commented 1 year ago

Added in #106