🗑️ This dev branch should be deleted after merging to main.
:brain: Aim, Context and Functionality
This PR adds the assembly_mean_coverage metrics for influenza HA and NA in the TheiaCoV_Illumina_PE_PHB workflow which was previously only available for other pathogens.
: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 (An output in assembly_mean_coverage where organism is "flu" that was previously empty)
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 (Though not as a result of this specific PR)
: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:
The workflow now calls the assembly metric task when sample HA and/or NA bam files from IRMA are available.
File processing changed:
IRMA task now also outputs HA and NA bam files.
Compute resources changed: N/A
➡️ Inputs
Not changed
⬅️ Outputs
Now when organism is "flu", instead of the workflow returning an empty output for assembly_mean_coverage, there will be a value HA:<coverage>, NA:<coverage>
:test_tube: Testing
Test Dataset
A set of four samples were used:
Influenza B Yamagata
Influenza A H3N2
Influenza A H1N1
Influenza A H1N1 with only NA subtyped, i.e. expecting HA to fail
Commandline Testing with MiniWDL or Cromwell (optional)
Local testing done for the IRMA task and works as expected.
This PR closes #313.
🗑️ This dev branch should be deleted after merging to main.
:brain: Aim, Context and Functionality
This PR adds the
assembly_mean_coveragemetrics for influenza HA and NA in theTheiaCoV_Illumina_PE_PHBworkflow which was previously only available for other pathogens.: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 (An output in
assembly_mean_coveragewhere organism is "flu" that was previously empty)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 (Though not as a result of this specific PR)
: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: The workflow now calls the assembly metric task when sample HA and/or NA bam files from IRMA are available.
File processing changed: IRMA task now also outputs HA and NA bam files.
Compute resources changed: N/A
➡️ Inputs
Not changed
⬅️ Outputs
Now when
organismis "flu", instead of the workflow returning an empty output forassembly_mean_coverage, there will be a valueHA:<coverage>, NA:<coverage>:test_tube: Testing
Test Dataset
A set of four samples were used:
Commandline Testing with MiniWDL or Cromwell (optional)
Local testing done for the IRMA task and works as expected.
Terra Testing
Testing done here: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/7189276f-f2b7-48be-b64d-3426353d087e
Suggested Scenarios for Reviewer to Test
Subtypes other than those listed here.
Theiagen Version Release Testing (optional)
:microscope: Final Developer Checklist
🎯 Reviewer Checklist
🗂️ Associated Documentation (to be completed by Theiagen developer)