add agrvate to S. aureus subwf pull request

[kapsakcj]

Opened a separate branch to ease testing on Terra without disrupting anyone currently using the cjk-saureus-subwf branch.

This PR adds the tool agrvate to the merlin magic subworkflow for any samples identified as "Staphyloccus aureus" by GAMBIT.

Setting as a draft until I'm done testing in Terra Testing in Terra is complete, I'm comfortable merging this into the cjk-saureus-subwf dev branch.

Tested both TheiaProk_Illumina_SE: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/curtis_sandbox/job_history/058e88f0-df97-4094-a7e7-08a312d959a2

and TheiaProk_Illumina_PE (failures here are due to test data, not code changes): https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/curtis_sandbox/job_history/83b43378-ae76-488d-a70f-5f0b96ec9df2

Changes

• updated tasks/species_typing/task_agrvate.wdl
  • lowered disk_size input var to 50, don't need much space
  • fixed optional integer input syntax
  • removed unnecessary echo
  • added helpful comments throughout
  • adjusted agrvate command to always use mummer with -m option since usearch is not available in the container (due to strict redistribution rules)
  • added code for parsing summary TSV from agrvate
  • added 6 new outputs:

    File agrvate_summary = summary TSV
    File agrvate_results = tarball of all agrvate output files
    String agrvate_agr_group = final agr group desitnation
    String agrvate_agr_match_score = confidence in agr match, higher number the better. ranges 0-15. 15 is max
    String agrvate_agr_canonical = canonical or non-canonical agrD gene
    String agrvate_agr_multiple = number of agr groups found (expect only 1 per isolate)
    String agrvate_agr_num_frameshifts = number of frameshifts found in CDS of extracted agr operon (done during mummer step)
    String agrvate_version = version
    String agrvate_docker = docker image used

• lowered RAM to 4GB - again not a computationally intensive task
• runtime cpu now uses input variable cpu
  • added agrvate outputs to export_taxon_tables task in tasks/utilities/task_broad_terra_tools.wdl
  • added agrvate to merlin_magic workflow
• added optional input agrvate_docker_image for when new versions are released
  • added agrvate outputs to theiaprok_Illumina_pe and SE workflows

I have NOT adjusted CI, so after merging I expect to see some CI failures on the other PR. Currently the CI is setup to only run on pull requests to main branch and not to others, so we can fix the CI stuff on PR #213

[kapsakcj]

@cimendes when you get a chance can you please give the code a look over & test in Terra on some samples? I would like to get this PR merged before we merge PR #213

[cimendes]

I tested the branch on 50 S. aureus successfully on terra (https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/0c754c08-5955-49aa-83c5-2bae53ade521, one failed due to an unrelated issue), and obtained the expected output columns. :) LGTM! I think we can go ahead and merge this one.

[kapsakcj]

merge away! Thank you for testing!

[cimendes]

@kapsakcj can I delete the branch?