hyphy workflow inspired by capheine, w subworkflows

[d-callan]

various notes:

• i added comparative_genomics/hyphy subdir under workflows here. let me know if wed like a different thing.
• id say its probable other hyphy heavy workflows will be introduced over time.
• at least the main capheine inspired one i think well want for brc, possibly the hyphy core one also
• i find conditional logic in galaxy frustrating. if someone has a better way to manage the 'regex or list' input for foreground sequences or the 'do we actually need to run the compare subworkflow' bits, id be happy to hear
• i found for the tests that if i simply didnt include the optional txt input for the regex then planemo did weird things that made the tests fail, so i had to explicitly say it was null. i may investigate that a bit more and then open an issue in planemo repo
• i didnt track down ppl orcid yet, can do if we feel strongly about it
• i added all the fasta ive tested this w so far, but idk if i actually used all of them in the tests file here.. can prune if needed, but if we assume other workflows in future it might not be bad to have. sometimes hyphy complains when its not passed enough data.
• there will be an iteration on the preprocessing subworkflow, hopefully soon, to make it a bit more robust. (currently fails w segmented viruses for ex).. but i kind of want to start getting some of this somewhere, see if ppl have feedback. i guess for now i can just update the readme w the current recommended use cases.

FOR CONTRIBUTOR:

• I have read the Adding workflows guidelines
• License permits unrestricted use (educational + commercial)
• Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

• .dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
• Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
• In workflow: annotation field contains short description of what the workflow does. Should start with This workflow does/runs/performs … xyz … to generate/analyze/etc …
• In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
• In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
• Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
• Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
• Changelog contains appropriate entries
• Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

[d-callan]

i think ill mark draft until i get ppl orcid, update readme, and i guess figure out tests for the subworkflows. hopefully mon. still happy for feedback otherwise in the meantime.

[d-callan]

bug report for the optional param thing: galaxyproject/galaxy#21947
after poking around a bit i think its galaxy rather than planemo