Add option to output a new config file

[KevinSayers]

Issue #, if available:

Description of changes:
DRAFT: Need to add CWL and WDL formatting still.
Adds --config=<path> which if specified will create a configuration file formatted correctly for the workflow's engine. The below for example would be correctly formatted for NF. This would enable users to directly utilize recommended settings from the runanalyzer.

withName: TEST {
    cpu = 2
    memory = 4
}

By submitting this pull request, I confirm that you can use, modify, copy, and redistribute this contribution, under the terms of your choice.

[markjschreiber]

Added some suggestions

[markjschreiber]

specify that it is a Nextflow style config file

[markjschreiber]

or Nextflow / CWL

[markjschreiber]

Raise an error saying we don't support WDL

[markjschreiber]

Will this always work? Do we know that our engines can't produce a task name like "[my workflow task]" with spaces?

It might make this more future proof to have a constant for the task name split string because if we need to change it due to new engines, this line of code doesn't advertise it's intent. Alternatively, perhaps have a function to split the name, perhaps with an engine name as an argument if different engines do different things.

[KevinSayers]

I will add a function that can parse the base task name and enforce the format of it.

[KevinSayers]

@markjschreiber I made this Nextflow only for now. I will add in CWL and WDL once I have spent more time working out how to handle scattered tasks for those.

[markjschreiber]

Looks good. Before merging, can you update the README with information about the --config option.

Other suggestions for improvements:
docopt has a nice mechanism for separating mutually exclusive tags (see my most recent PR and docopt documentation). If --config shouldn't be logically used with some other options then you can include a new usage line such as omics-run-analyzer <runId> --config=<path>. This can also simplify the logic for the main method as conflicting options can be rejected by the arg parser before they get to the main logic.

--write-config might be a better long name? --config might suggest you can read a config file to change the behavior of the run analyzer. Not sure?

Can you see if you can split the config logic into a separate python file. I have been trying to do this for new features to declutter the __main__.py which has gotten large and confusing.

[markjschreiber]

LGTM!