Bootstrap repository with minimal working pipeline

[nwiltsie]

Description

There are a ton of things left to do, but after solving #3 the pipeline successfully runs to completion! I'm opening this draft to solicit some feedback and coordinate efforts in wrapping up the final steps.

Problems I Can't Solve

• Process / variable naming. I don't have the scientific background to generate a better process name than run_trinucleotide_context, so some help there would be appreciated.
• Process resource allocations. All of the node-specific config files are empty and I don't know how to fill them.
• README overview section. As with the variable naming, I don't know how to describe what's happening here.

Problems I Can Muddle Through

• Cleaning up publishDir directives for intermediate and output filepaths

Problems I Can Solve

• README technical documentation (flow diagram, tool versions, input parameters, etc.)
• Workflow/process commenting, log statements, etc.
• Setting up the CHANGELOG
• Setting up metadata.yaml
• The final pipeline steps just added in Build out initial pipeline #2 (comment)

Closes #2

Checklist

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• I have reviewed the Nextflow pipeline standards.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• I have set up or verified the branch protection rule following the github standards before opening this pull request.

• I have added my name to the contributors listings in the manifest block in the nextflow.config as part of this pull request, am listed
  already, or do not wish to be listed. (This acknowledgement is optional.)

• I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

• I have updated the version number in the metadata.yaml and manifest block of the nextflow.config file following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)

• I have tested the pipeline on at least one A-mini sample.

[nwiltsie]

Okay @yashpatel6, I think it makes the most sense to merge this, register the progress, and then make smaller changes from there. Seem fair to you?

[yashpatel6]

Sounds good to me!