theiacov_fasta_batch_PHB wf improvements

[kapsakcj]

removed required string inputs seq_method and input_assembly_method since they are not used in the workflow. They are not required.

This PR closes #320

🗑️ This dev branch should NOT be deleted after merging to main (one potential PHL user)

:brain: Aim, Context and Functionality

described in issue #320

These changes are to ease the usage of this workflow.

: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 : Yes, seq_method and input_assembly_method will no longer be updated/overwritten after running this workflow

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, results should not change if identical versions of pangolin or nextclade (and their respective databases) are used between workflow runs

:clipboard: Workflow/Task Step Changes

🔄 Data Processing

seq_method and input_assembly_method are no longer an input, they are removed entirely. This also means they are no longer output (i.e. those output columns are no longer updated/overwritten)

Docker/software or software versions changed: No

Databases or database versions changed: No

Data processing/commands changed: No

File processing changed: Yes

Compute resources changed: No

➡️ Inputs

seq_method and input_assembly_method are no longer an input, they are removed entirely.

⬅️ Outputs

seq_method and input_assembly_method are no longer output (i.e. those output columns are no longer updated/overwritten)

:test_tube: Testing

Test Dataset

I tested with a batch of ~33 SC2 genomes (Omicron and decendant lineages) downloaded from GISAID.

Commandline Testing with MiniWDL or Cromwell (optional)

only tested via Terra, since it's difficult or impossible to test locally since the workflow involves updating Terra data tables

Terra Testing

successful workflow here: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/610e9035-24d5-40a7-b22b-70668ff4a4eb

data table is called omicron_pango_validation

Suggested Scenarios for Reviewer to Test

Would be good for the reviewer to test a large batch of genomes (300+). Should run OK. I'm just curious about how many we could run at once (1000? 10000? more??)

Theiagen Version Release Testing (optional)

-Will changes require functional or validation testing (checking outputs etc) during the release? functional -Do new samples need to be added to validation datasets? If so, upload these to the appropriate validation workspace Google bucket (). Please describe the new samples here and why these have been chosen. No -Are there any output files that should be checked after running the version release testing? Check the final output TSV used to update the Terra data table

: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)

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

[kapsakcj]

Docs have been updated, I just deleted the 2 inputs from the table in the docs. No need to update workflow diagram (if it even exists for theiacov_fasta_batch?)

[sage-wright]

Code changes look great, currently testing here