[TheiaCov] wfs add percentage_mapped_reads

[fraser-combe]

This PR closes #507

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

🧠 Summary

This PR adds outputs for percentage_mapped_reads to various workflows, specifically targeting reads for flu and non-flu organisms, ensuring consistency in outputs.

⚡ Impacted Workflows/Tasks

theiacov_ont.wdl
theiacov_illumina_pe.wdl
theiacov_illumina_se.wdl
theiacov_clearlabs.wdl

This PR may lead to different results in pre-existing outputs: No
This PR uses an element that could cause duplicate runs to have different results: No

🛠️ Changes

Added unified output for percentage_mapped_reads across theiacov_ont, theiacov_illumina_pe, theiacov_illumina_se, and theiacov_clearlabs workflows.
Consolidated flu and non-flu percentage mapped reads using select_first to ensure a single output variable for mapped reads.
Refined logic for flu and non-flu workflows to ensure correct handling of percentage_mapped_reads.

⚙️ Algorithm

• No major algorithmic changes were introduced, but the logic for flu and non-flu organisms in calculating percentage_mapped_reads was updated to call different tasks.

• For iVar-based workflows (theiacov_illumina_pe, theiacov_illumina_se), the percentage is parsed from the samtools flagstat file.

• For non-iVar workflows, the assembled_reads_percent task is used to pass in BAM files and calculate mapped reads.

➡️ Inputs

No new inputs were added.

⬅️ Outputs

The following outputs were updated or added:

percentage_mapped_reads:
For non-flu organisms, calculated using either ivar_consensus.percentage_mapped_reads (for iVar-based workflows) or from stats_n_coverage.percentage_mapped_reads for ONT workflows.

🧪 Testing

Tested both flu and non-flu cases across workflows, ensuring the correct mapping of percentage_mapped_reads.

TheiaCov_ONT (non flu)
https://app.terra.bio/#workspaces/theiagen-training-workspaces/Theiagen_Combe_Sandbox/job_history/a158d7fc-aac7-4c9e-8782-e8d96afe059a

TheiaCov_ONT (flu)
https://app.terra.bio/#workspaces/theiagen-training-workspaces/Theiagen_Combe_Sandbox/job_history/fd988d1f-5a75-4b7f-b1e5-ce293a345a13

ThieaCov_illumina_pe (flu)
https://app.terra.bio/#workspaces/theiagen-training-workspaces/Theiagen_Combe_Sandbox/job_history/3ca0d049-31b4-4179-b2ce-20753946f40c/ec42f3a3-7b30-4756-aa72-39640adb92a9

TheiaCov_illumina_pe (non-flu)
https://app.terra.bio/#workspaces/theiagen-training-workspaces/Theiagen_Combe_Sandbox/job_history/cd90a924-8fe9-48c3-814e-d4fce8453632

TheiaCov_illumina_se
https://app.terra.bio/#workspaces/theiagen-training-workspaces/Theiagen_Combe_Sandbox/job_history/dcfb1141-a483-4eb3-b280-7377a1df4a4e

Suggested Scenarios for Reviewer to Test

Run workflows with flu and non-flu samples to ensure the correct assignment of percentage_mapped_reads.

Validate the unified logic correctly handles percentage_mapped_reads for both flu and non-flu workflows, particularly for iVar-based and non-iVar-based workflows.

🔬 Final Developer Checklist

• The workflow/task has been tested and results, including file contents, are as anticipated
• The CI/CD has been adjusted and tests are passing (Theiagen developers)
• Code changes follow the style guide
• Documentation and/or workflow diagrams have been updated if applicable (Theiagen developers only)

🎯 Reviewer Checklist

• All changed results have been confirmed
• You have tested the PR appropriately (see the testing guide for more information)
• All code adheres to the style guide
• MD5 sums have been updated
• The PR author has addressed all comments
• The documentation has been updated

[sage-wright]

Great start, just needs a couple changes to clean things up a bit

[fraser-combe]

confirmed mapped reads output after moving into flu track wf,

[sage-wright]

Running tests on illumina pe flu here and various ont here.

One last request: could you tidy up some of the extra newlines at the end of the tasks in the output sections?

[sage-wright]

Also I was wrong and you do need to provide a default value for the percentage_mapped_reads in case the read_screen fails (see here).

Could you coerce all of these non-optional outputs into Strings and provide "" as the default value at the end of the select_first for the workflows? That way, when the read_screen fails, there isn't a 0 populated to the column since that would be an inaccurate statement.

• in ClearLabs, remove the ? quantifier off the float
• in SE, change the Float? to a String?
• in PE, change the Float to a String and add a , "" to the end of the select_first block
• in ONT, change the Float to a String and add a , "" to the end of the select_first block
• in ivarconsensus, change change it to be a String and add , "" to the end of the select_first (like we do for meanbaseq and meanmapq, assembly_mean_coverage, etc.

Thanks!

[sage-wright]

just as a side note, do you have any examples where it's not 100%?

[fraser-combe]

just as a side note, do you have any examples where it's not 100%?

No Id have to try and find data, unless you have any potential data that may provide this kind of result

[fraser-combe]

Those updates should be passing tests now, let me know if you need me to find more testing data after your tests have completed