Adds VADR task and outputs for MPXV

[kapsakcj]

Setting as a draft for now, until testing in Terra is done and #171 is merged. The changes from PR 171 are included in this PR as well.

The design strategy was to alter the VADR task as little as possible and allow the user to define VADR input params to control between SARS-CoV-2 usage and MPXV. We will provide input JSONs to avoid typos.

This PR:

• task_ncbi.wdl changes:
  • adds cpu input param, default 2
  • adds --split --cpu ~{cpu} to VADR v-annotate.pl command to speed things up a little bit
  • increases default RAM allocation to 8GB from 2. VADR recommends 4GB RAM/CPU
• workflow changes, includes workflows TheiaCov_{ClearLabs, ONT, illumina_pe, illumina_se, fasta}:
  • calls VADR task if organism is set to MPXV
  • adds 4 new outputs, specific to MPXV since VADR is called for the sars-cov-2 specific tasks

VADR_Update workflow does not require changes, all that needs adjusted is the input parameters

Input parameters that must be specified:

• vadr_mpxv.maxlen=210000
• vadr_mpxv.skip_length=30000 ◀️ We can adjust higher to be more strict on when/when not to run VADR. 10000 is default for SARS-CoV-2, I just came up with 30000 with little reasoning
• vadr_mpxv="--glsearch -s -r --nomisc --mkey mpxv --r_lowsimok --r_lowsimxd 100 --r_lowsimxl 2000 --alt_pass discontn,dupregin" - This input is VERY important and may change in the future if NCBI/Eric decides to alter the suggested MPXV input params

I'm expecting CI to fail, as there are a good number of changes introduced here. Will address later after we're happy w the code

[kapsakcj]

Planning to restructure so that the call for the VADR task appears in the block where organism is set to sarscov2 or mpxv.

Please do not review for now

[kapsakcj]

I plan on closing this PR and opening another one with the branch cjk-vadr-consolidation which will include the changes from this PR (dev branch started from this dev branch cjk-vadr-mpx) and additionally consolidate to using the same task call block in all workflows, and thus only 4 VADR workflow-level outputs instead of having separate ones for sars-cov-2 and mpxv.