adding optional arguments to freyja boot and demix calls

This PR closes #350.

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

:brain: Aim, Context and Functionality

This PR adds additional optional inputs depth_cutoff to the Freyja_FASTQ_PHB workflow. This gives the user the option to exclude sites with coverage depth below this value and group identical barcodes.

:hammer_and_wrench: Impacted Workflows/Tasks & Changes Being Made

Freyja_FASTQ_PHB task_freyja_one sample.wdl

This will affect the behavior of the workflow(s) even if users don’t change any workflow inputs relative to the last version : No

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 : Yes, but has nothing to do with this PR

:clipboard: Workflow/Task Step Changes

🔄 Data Processing

Docker/software or software versions changed: No

Databases or database versions changed: No

Data processing/commands changed: Yes

File processing changed: No

Compute resources changed: No

➡️ Inputs

we have added a new output depth_coverage

⬅️ Outputs

No outputs changed

:test_tube: Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

Not undertaken

Terra Testing

The dataset used is the validation dataset labelled freyja_sc2

Note, there are two expected sample failures, i.e. ERR9829562 and SRR3982099

No optional inputs changed: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/9aaca3c6-5ab7-49c9-a4ea-c89b916be573

depth_cutoff set to 5: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/d1a51258-324e-42e5-b1d4-39f89bbcd878

depth_cutoff set to 1000000: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/1604eb8f-0e25-4d89-a1b9-5934ee3f0f1a

Suggested Scenarios for Reviewer to Test

Theiagen Version Release Testing (optional)

:microscope: Final Developer Checklist

[ ] 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

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

theiagen / public_health_bioinformatics