Fix docker containers & bind mounts

[kelly-sovacool]

Changes

• Adds docker containers to process definitions, using parameters for shared containers.
• Uses --mount type=bind instead of --bind (singularity) for compatibility with docker.
• Instead of mounting the chromosomes dir for gem, passes it as an input -- similar to the reference files for alignment processes.
• Fixes output files from the gem stub.

Issues

• Resolves docker doesn't recognize --bind flag #58
• Resolves specify containers in process definitions #67
• Resolves 'default' container sometimes overrides other withName/withLabel containers #68

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• [ ] Write unit tests for any new features, bug fixes, or other code changes. testing framework not yet implemented
• [ ] Update docs if there are any API changes.
• [ ] If a new nextflow process is implemented:
  • [ ] docker container is set in conf/modules.config.
  • [ ] stub is defined.
• Update CHANGELOG.md with a one-line description of these changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

[kelly-sovacool]

Can't get past this error on GitHub Actions with Docker. It works fine with singularity on biowulf.

docker: Error response from daemon: invalid mount config for type "bind": bind source path does not exist:

[kelly-sovacool]

Actions is still not running process stubs past fastq_screen. Seems like something is up with the reference files paths. Going to merge this as-is since it does fix the issues linked above, and will circle back to the stubs problem later.