Check Organism Abundance From The Kraken report for TheiaCoV Workflows

This PR closes #230.

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

:brain: Aim, Context and Functionality

This PR checks for the abundance of the organism input in the TheiaCoV workflows using Kraken2. The organism input is passed onto the readQC_trim workflows that call the Kraken2 task. As the readQC_trim workflows are also called by the TheiaProk workflows, the organism input is optional for the readQC_trim workflows and the Kraken2 task.

For the TheiaProk workflows that do not have an organism input, the workflows will produce the most abundant organism from the Kraken report.

The organism abundance estimation will be performed pre and post human reads removal (dehosting). The pre-host reads removal abundance could be useful in estimating the target organism amplification process and contamination, while the post-host reads removal could be useful in understanding the efficiency and impact of the human read removal process.

: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. There will be new outputs.

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

:clipboard: Workflow/Task Step Changes

🔄 Data Processing

Docker/software or software versions changed: N/A

Databases or database versions changed: N/A

Data processing/commands changed: Yes. Additional steps in the Kraken2 task to extract organism abundance estimates.

File processing changed: N/A

Compute resources changed: N/A

➡️ Inputs

⬅️ Outputs

Kraken2 task most_abundant_organism percent_most_abundant_organism

TheiaCoV_illumina_PE kraken_most_abundant_organism_raw kraken_percent_most_abundant_organism_raw kraken_most_abundant_organism_dehosted kraken_percent_most_abundant_organism_dehosted

TheiaCoV_ONT kraken_most_abundant_organism_raw kraken_percent_most_abundant_organism_raw kraken_most_abundant_organism_dehosted kraken_percent_most_abundant_organism_dehosted

readQC_trim_PE kraken_most_abundant_organism_raw kraken_percent_most_abundant_organism_raw kraken_most_abundant_organism_dehosted kraken_percent_most_abundant_organism_dehosted

readQC_trim_ONT kraken_most_abundant_organism_raw kraken_percent_most_abundant_organism_raw kraken_most_abundant_organism_dehosted kraken_percent_most_abundant_organism_dehosted

TheiaProk_illumina_PE kraken_most_abundant_organism_raw kraken_percent_most_abundant_organism_raw kraken_most_abundant_organism_dehosted kraken_percent_most_abundant_organism_dehosted

:test_tube: Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

Terra Testing

TheiaProk_illumina_PE: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/87c7c951-9f58-43ee-95a4-4e65b90deaf6

TheiaCoV_illumina_PE: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/9d4da382-51eb-4209-b177-b514445ff2b0

TheiaCoV_ONT: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/8ca43601-f9b6-4d43-9e0e-8823acb0902c

Additional testing with kraken_target_org input

Organism input is sars-cov-2 and target organism is sars-cov-2, with the latter not being a proper taxonomic name expected to fail
Organism input is sars-cov-2 and target organism is influenza, for an all human reads sample
Organism input is sars-cov-2 and target organism is Severe acute respiratory syndrome coronavirus 2, input reads all SARS-CoV-2, expected to pass
Organism input is WNV and target organism is Influenza, input reads are a mixed sample of flu, WNV, HIV and SARS-CoV-2, expected to pass

https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/3787e23b-2b52-4b94-9a2d-b0d90f3e5a1d

Suggested Scenarios for Reviewer to Test

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
[ ] 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
[ ] Workflow diagrams have been updated to reflect changes

theiagen / public_health_bioinformatics