Add neisseria subwf: ngmaster and meningotype

[kapsakcj]

Setting as a draft until testing in Terra is complete and when staphb/ngmaster:1.0.0 docker image is available

staphb docker image is available staphb/ngmaster:1.0.0, just doing one final test in Terra with new docker image

This PR:

• alters the meningotype task (for N. meningitidis):
  • by default run all typing options (except mlst which is done via ts_mlst task which uses more up-to-date dbs)
  • produce new String outputs for the serogroup and each allele number
  • runtime now uses cpu input variable
  • removed optional inputs for toggling various typing. We want all to run all the time (except mlst)
• alters ngmaster task (for N. gonnorhoeae):
  • docker default is kapsakcj/ngmaster:1.0.0, need to change this to staphb/ngmaster:1.0.0 when available
  • altered output TSV filename to be more descriptive
  • added code to parse output TSV for MLSequence Types from 2 schemes (NG-MAST and NG-STAR). Additionally parsing allele numbers that correspond w each scheme.
  • added numerous String outputs for each MLST and allele numbers
  • runtime now uses cpu input variable
• task_gambit.wdl edited to designate 2 new merlin_tag's: Neisseria gonorrhoeae and Neisseria meningitidis
• export_taxon_tables task edited to accept new inputs from ngmaster & meningotype tasks
• wf_merlin_magic.wdl edited to run:
  • ngmaster when merlin_tag is set to Neisseria gonorrhoeae
  • meningotype when merlin_tag is set to Neisseria meningitidis
  • all new outputs added to workflow outputs
• Both workflows/wf_theiaprok_illumina_pe.wdl and workflows/wf_theiaprok_illumina_se.wdl were edited to have new ngmaster & meningotype outputs
  • also added new outputs as inputs for export_taxon_tables task

Testing:

• [x] Illumina_PE on both species - Successful Terra workflow (albeit with kapsakcj/ngmaster:1.0.0); will add link to second test w staphb/ngmaster:1.0.0 docker image soon)
• [x] Illumina_PE - Successful Terra workflow N. gonnorhoeae with updated staphb/ngmster:1.0.0 docker image
• [x] Illumina_SE on both species- Successful Terra workflow

CC @cimendes

[kapsakcj]

Something is up with the CI, looks like it's failing to install dependencies before any of the miniwdl check's are run

[cimendes]

@kapsakcj a retrigger seems to have done the trick :)

[cimendes]

@kevinlibuit @kapsakcj can the branch be deleted?

[kapsakcj]

I'll delete it now. Usually wait to delete them, but since we haven't told any users about this branch I doubt anyone is using it. And if they are, they can switch to main 👍