[Standardization] Standardizing the language behind percent identity and coverage

[awh082834]

This PR closes #557 and #558

🗑️ This dev branch should be deleted after merging to main.

🧠 Summary

Still in testing and hunting down any other variations of these inputs. Opening this now for discussion and input on any that I may have missed!

Standardizing the language of percent identity and coverage to min_percent_identity and min_coverage wherever possible.
Inputs that use decimal values for identity have been kept to min_identity to thwart confusion between percent and decimal values.

⚡ Impacted Workflows/Tasks

Tasks:

• emmtyper
• pbptyper
• abricate_vibrio
• abricate
• pasty
• kleborate
• lissero
• virulencefinder
• abricate_abaum
• kaptive
• ectyper
• amrfinder
• resfinder
• plasmidfinder
• ts_mlst
• tbprofiler
• srst2_vibrio

Workflows:

• TheiaProk
• TheiaCov
• merlin_magic

This PR may lead to different results in pre-existing outputs: No

This PR uses an element that could cause duplicate runs to have different results: No

🛠️ Changes

Instances of mincov, minident, or any variation of percent identity and coverage have been changed to min_percent_identity and min_coverage.

⚙️ Algorithm

No algorithmic changes.

➡️ Inputs

abricate_flu_minid -> abricate_flu_min_percent_identity
kaptive_min_identity -> kaptive_min_percent_identity
ectyper_opid -> ectyper_o_min_percent_identity
ectyper_hpid -> ectyper_h_min_percent_identity
virulencefinder_identity_threshold -> virulencefinder_min_percent_identity
kleborate_min_identity -> kleborate_min_percent_identity
lissero_min_id -> lissero_min_percent_identity
pasty_min_pident -> pasty_min_percent_identity
emmtyper_percid -> emmtyper_min_percent_identity
pbptyper_min_pident -> pbptyper_min_percent_identity
abricate_vibrio_minid -> abricate_vibrio_min_percent_identity
abricate_flu_minid -> abricate_flu_min_percent_identity
abricate_abaum_minid -> abricate_abaum_min_percent_identity
abricate_mincov -> abricate_min_coverage
abricate_flu_mincov -> abricate_flu_minc_coverage
ectyper_opcov -> ectyper_o_min_coverage
ectyper_hpcov -> ectyper_h_min_coverage
virulencefinder_coverage_threshold -> virulencefinder_min_coverage
lissero_min_cov -> lissero_min_coverage
tbp_parser_coverage_threshold -> tbp_parser_min_coverage
abricate_vibrio_mincov -> abricate_vibrio_min_coverage
srst2_vibrio_min_cov -> srst2_vibrio_min_coverage
amrfinderplus_mincov -> amrfinder_plus_min_coverage
amrfinderplus_minid -> amrfinder_plus_min_identity (not percent identity as the input is not a percentage. Done to prevent confusion.)
resfinder_min_cov -> resfinder_min_coverage
plasmidfinder_min_cov -> plasmid_finder_min_coverage
ts_mlst_minid -> ts_mlst_min_percent_identity
ts_mlst_mincov -> ts_mlst_min_coverage

⬅️ Outputs

No outputs have been changed.

🧪 Testing

TheiaCov:

ONT
FASTA
Illumina_PE
SE not tested as it does not contain wf_flu_track which utilizes task_abricate.

TheiaProk:

ONT
FASTA
Illumina_PE
Illumina_SE

Suggested Scenarios for Reviewer to Test

🔬 Final Developer Checklist

• The workflow/task has been tested and results, including file contents, are as anticipated
• The CI/CD has been adjusted and tests are passing (Theiagen developers)
• Code changes follow the style guide
• Documentation and/or workflow diagrams have been updated if applicable
  • You have updated the "Last Known Changes" field for any affected workflows in the respective workflow documentation page and for every entry in the three workflows_overview tables to be the tag for the next upcoming release. If you do not know the tag, please put "vX.X.X"

🎯 Reviewer Checklist

• All changed results have been confirmed
• You have tested the PR appropriately (see the testing guide for more information)
• All code adheres to the style guide
• MD5 sums have been updated
• The PR author has addressed all comments
• The documentation has been updated