how to prepare NGS analysis environment by Docker

Question

[takoyaki]

Hi, everyone.

I would like to ask how to prepare NGS analysis environment by Docker.
I was using miniconda to install tools but Docker is more suitable to reproduce analysis results.

From Docker hub, BioContainers supply each software images and we can pull them.
However we need to make several tools usable like fastp, hisat2, samtools, and so on...

Should I prepare Dockerfile to build image by using images of each software ?
but typical Dockerfile doesn't look like using several images.

Also, to reproduce results, fixing software versions are important.

These things are easy if we use miniconda, but would you tell me how you do you do by Docker ?

Thanks in advance :)

Answer 1

[ATpoint]

Building Docker images

I would pair this up by implementing your workflow with Nextflow which natively supports Docker and Singularity. Put code on GitHub then you have version control by GitHub, execution control by Nextflow and software version control by Docker. The Dockerfile can go to GitHub as well.