[Style Guide] Semantic adjustments throughout the PHB universe

[cimendes]

This PR closes #365 and closes #366 and closes #367 and closes #368.

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

:brain: Aim, Context and Functionality

This PR aims to harmonize a few inputs in workflows and sub-workflows to better adhere to our style-guide!

:hammer_and_wrench: Impacted Workflows/Tasks & Changes Being Made

This will affect the behavior of the workflow(s) even if users don’t change any workflow inputs relative to the last version : No, it changes only input parameters. Default JSON inputs will need to be updated

Running this workflow on different occasions could result in different results, e.g. due to use of a live database, "latest" docker image, or stochastic data processing : No

Please see Files changed for an exhaustive list of all the inputs that were adjusted!

:clipboard: Workflow/Task Step Changes

🔄 Data Processing

Docker/software or software versions changed: None

Databases or database versions changed: None

Data processing/commands changed: None

File processing changed: None

Compute resources changed: None

➡️ Inputs

• minlen -> min_length
• maxlen -> max_length
• min_contig_len -> min_contig_length
• fastp_minlen -> fastp_min_length
• trimmomatic_minlen -> trimmomatic_min_length
• trim_quality_trim_score -> trim_quality_min_score
• min_contig_len -> min_contig_length

⬅️ Outputs

None

:test_tube: Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

Skipped in favour if testing in Terra!

Terra Testing

In the comments below!

Suggested Scenarios for Reviewer to Test

• All the theiacovs except for theiacov_fasta_batch
• Freyja
• TheiaMeta
• TheiaEuk
• TheiaProk_illumina SE and PE

Theiagen Version Release Testing (optional)

:microscope: Final Developer Checklist

• [x] The workflow/task has been tested locally and results, including file contents, are as anticipated
• [x] The workflow/task has been tested on Terra and results, including file contents, are as anticipated
• [x] The CI/CD has been adjusted and tests are passing (to be completed by Theiagen developer)
• [x] Code changes follow the style guide

🎯 Reviewer Checklist

• [x] All impacted workflows/tasks have been tested on Terra with a different dataset than used for development
• [x] All reviewer-suggested scenarios have been tested and any additional
• [x] All changed results have been confirmed to be accurate
• [x] All workflows/tasks impacted by change/s have been tested using a standard validation dataset to ensure no unintended change of functionality
• [x] All code adheres to the style guide
• [x] MD5 sums have been updated
• [x] The PR author has addressed all comments

🗂️ Associated Documentation (to be completed by Theiagen developer)

• [ ] Relevant documentation on the Public Health Resources "PHB Main" has been updated
• [x] Workflow diagrams have been updated to reflect changes

[cimendes]

@sage-wright I'm setting this as ready to review as I could use the help in testing it!

[cimendes]

Propagation of new input parameters check and validation!

• Freyja_FASTQ

  • 
  • https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/91cf4f50-ad60-485d-8f69-7c322770883c

• TheiaCoV_FASTA

  • 
  • https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/19b328f8-b052-44e4-87bc-ee9f91ad2784

• TheiaCoV_Illumina_PE

  • 
  • https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/c7e03fbe-a50b-4f96-a9a9-7311b71620f7

• TheiaCoV_Illumina_SE

  • 
  • https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/1c079d2d-a871-482b-87f7-1f75764482cf

• TheiaCoV_ONT

  • No exposed inputs changed!
  • https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/78421021-9749-47f8-b269-4303e5700f88 (Some failures expected for, I believe, monkeypox virus)

[cimendes]

Propagation of new input parameters check and validation! (Continued)

• TheiaEuk_Illumina_PE

  • 
  • To be tested

• TheiaMeta_Illumina_PE

  • No exposed input parameters altered
  • https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/6ac7a91b-14a1-43a1-a46e-7efc814abe99

• TheiaProk_Illumina_PE

  • 
  • https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/2f69cd18-6d4d-46d1-a615-163fe9835a6a

• TheiaProk_Illumina_SE -

  • https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/88e43055-0c27-4b12-a4a5-70b14d0a09ac (some failures expected due to missing reads (where did they go!?))

[sage-wright]

@cimendes when we have _minlength do you think it makes sense to change that to _min_length; same for maxlength -> max_length

[cimendes]

@cimendes when we have _minlength do you think it makes sense to change that to _min_length; same for maxlength -> max_length

Ops, sorry I missed this message! It is now done!

[sage-wright]

• [x] TheiaProk PE default params here
• [x] TheiaProk SE skip screen otherwise default params here
• [x] TheiaCoV ONT ~here here~ here
• [x] TheiaCoV FASTA here

[sage-wright]

Yay! Good job.