[Freyja] Expose additional outputs and parse demixed output file for easy downstream concatenation

[cimendes]

This PR closes #

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

🧠 Summary

This PR exposes several new outputs from Freyja parsed from the freyja_demixed.tsv output file, namely:

• freyja_resid (String)
• freyja_summarized (String)
• freyja_lineages (String)
• freyja_abundances (String)

Additionally, the freyja_demixed.tsv output file is wrangled into freyja_demixed_parsed file for easy downstream concatenation, resulting in a new output file:

• freyja_demixed_parsed (File)

This file looks like this:

LIMS_ID	summarized	lineages	abundances	resid	coverage
PTB	[('Delta', 0.997513322334662)]	AY.1 AY.34	0.53921400 0.45829932	4.409106631109497	50.15884693843427

⚡ Impacted Workflows/Tasks

• Freyja_FASTQ_PHB

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

⚙️ Algorithm

The python block has been expanded to expose the new outputs and perform file wrangling with pandas to create the new parsed demixed file.

➡️ Inputs

Nothing changed

⬅️ Outputs

New outputs:

• freyja_resid (String)
• freyja_summarized (String)
• freyja_lineages (String)
• freyja_abundances (String)
• freyja_demixed_parsed (File)

🧪 Testing

Local testing of task:
miniwdl run --task freyja_one_sample /home/ines_mendes/Git/public_health_bioinformatics/tasks/taxon_id/freyja/task_freyja.wdl samplename="PTB" primer_trimmed_bam= PTB.primertrim.sorted.bam reference_genome= nCoV-2019.reference.fasta

Test on Terra:
https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/8cf1e2b6-5fc9-40af-a0c2-19c78b967ea7

Suggested Scenarios for Reviewer to Test

Test Freyja on an alternative organism! Only tested on SC2.

🔬 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
  • You have updated the "Last Known Changes" field for any affected workflows in the respective workflow documentation page and for every entry in the three workflows_overview tables to be the tag for the next upcoming release. If you do not know the tag, please put "vX.X.X"

🎯 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]

a few documentation and style changes requested.

testing here

[sage-wright]

outputs on terra look good! ⭐ once those changes are in and i run a verification test i'll merge!

[sage-wright]

final confirmation test here

[cimendes]

Test with non-SC2 (MPXV): https://app.terra.bio/#workspaces/theiagen-validations/ines_sandbox/job_history/02f791f0-6503-4e7f-b636-79010bf0a69e

[sage-wright]

⭐ fabulous