Tools to use own docker image

[fmalmeida]

Adapt the pipeline so that modules use smaller docker images, preferably, one image per module.

For example, AMRFinderPlus to use the quay.io image.

Since some tools are regularly updated and others don’t, this would allow an easier manner of updating some software versions.

[fmalmeida]

So one can easily copy and change software versions, instead of having images define within the modules as it is now, all public images should be defined in a single config file, so, if desired by users, they can quickly copy the contents and update the pipeline execution by giving an additional custom conig with -c.

It is not a problem that some tools still use the custom built docker images bundled with the pipeline. The goal of this issue was to change to the public images, all the modules that could work with them. The modules, that did not work with public images, will still use the custom ones generated by us.

[fmalmeida]

Only missing to-do for release:

• Decide how to allow users to quickly customise the version of biocontainers images to use ... To it as a parameter where users could select each version tag? Or do it as a pre-built config that can be downloaded with something like --get_docker_config and then users can change the image version and pass this custom config at will?

[fmalmeida]

Done in #91