[ONT] Remove KMC

[sage-wright]

This PR closes #203

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

🧠 Summary

This PR removes the KMC module from the TheiaCoV and TheiaProk ONT workflows. In place of the estimated genome length in TheiaProk ONT, I have added a default genome length of 5 Mb, which is around .7 Mb larger than the average genome length as estimated by calculating the mean genome length of all bacteria included in this file.

⚡ Impacted Workflows/Tasks

TheiaProk_ONT and TheiaCoV_ONT

This PR may lead to different results in pre-existing outputs: Yes, assemblies generated may be different due to differences in the use of estimated genome length in RASUSA downsampling.

This PR uses an element that could cause duplicate runs to have different results: No

🛠️ Changes

⚙️ Algorithm

• 5 Mb is default genome size in the read_qc_trim_ont subworkflow.

➡️ Inputs

No

⬅️ Outputs

KMC outputs have been removed.

🧪 Testing

Test on TheiaProk here

Test on TheiaCoV (flu) here

Suggested Scenarios for Reviewer to Test

🔬 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

[cimendes]

TheiaProk_ONT_PHB Test:

• Tested with the following data. Expected genome size corresponds to the approximate size of the reference on NCBI (rounded to the nearest Mb)
• Run: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/b5b64cf6-8187-496d-85f5-d03ab6a416ce

<style> </style>

entity:theiaprok_ont_nokmc_id	expected_length	expected_taxon	read1
ERR8958704	5700000	Klebsiella pneumoniae	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/ERR8958704_1.fastq.gz
ERR8958706	5700000	Klebsiella pneumoniae	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/ERR8958706_1.fastq.gz
ERR8958710	5700000	Klebsiella pneumoniae	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/ERR8958710_1.fastq.gz
ERR8958833	2900000	Staphylococcus aureus	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/ERR8958833_1.fastq.gz
ERR8958851	2900000	Staphylococcus aureus	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/ERR8958851_1.fastq.gz
ERR8958852	2900000	Staphylococcus aureus	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/ERR8958852_1.fastq.gz
ERR8958857	6200000	Pseudomonas aeruginosa	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/ERR8958857_1.fastq.gz
ERR8958858	6200000	Pseudomonas aeruginosa	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/ERR8958858_1.fastq.gz
SAMN04961841	5000000	Salmonella enterica	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/SRR19768527_1.fastq.gz
SAMN05250424	5000000	Salmonella enterica	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/SRR19768533_1.fastq.gz
SAMN05596277	5000000	Salmonella enterica	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/SRR19768539_1.fastq.gz
SAMN20849361	4800000	Shigella sonnei	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/SRR18254047_1.fastq.gz
SAMN22657138	4800000	Shigella sonnei	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/SRR18254048_1.fastq.gz
SAMN22962688	4800000	Shigella sonnei	gs://theiagen-large-public-files-rp/terra/phb-validation/theiaprok-ont-reads/SRR18254049_1.fastq.gz

[cimendes]

The run succeeded and I've now managed to look at the results from the assembly lengths produced versus the expected genome size. The differences are very very small except for Shigella sonnei where the assemblies were around 10% larger than expected:

<style> </style>

entity:theiaprok_ont_nokmc_id	assembly_length	expected_length	Difference (%)	expected_taxon	gambit_predicted_taxon
ERR8958704	5754162	5700000	1%	Klebsiella pneumoniae	Klebsiella pneumoniae
ERR8958706	5725948	5700000	0%	Klebsiella pneumoniae	Klebsiella pneumoniae
ERR8958710	5755096	5700000	1%	Klebsiella pneumoniae	Klebsiella pneumoniae
ERR8958833	2902609	2900000	0%	Staphylococcus aureus	Staphylococcus aureus
ERR8958851	2902596	2900000	0%	Staphylococcus aureus	Staphylococcus aureus
ERR8958852	2902610	2900000	0%	Staphylococcus aureus	Staphylococcus aureus
ERR8958857	6281842	6200000	1%	Pseudomonas aeruginosa	Pseudomonas aeruginosa
ERR8958858	6294596	6200000	2%	Pseudomonas aeruginosa	Pseudomonas aeruginosa
SAMN04961841	4833663	5000000	3%	Salmonella enterica	Salmonella enterica
SAMN05250424	4744535	5000000	5%	Salmonella enterica	Salmonella enterica
SAMN05596277	4786893	5000000	4%	Salmonella enterica	Salmonella enterica
SAMN20849361	5275674	4800000	10%	Shigella sonnei	Shigella sonnei
SAMN22657138	5356338	4800000	12%	Shigella sonnei	Shigella sonnei
SAMN22962688	5295788	4800000	10%	Shigella sonnei	Shigella sonnei

The reason why is beyond this PR . BUSCO duplication score is not awful.

The results are concordant with what was obtained with PHB v2.1.0 (https://app.terra.bio/#workspaces/theiagen-validations/PHB_Validation_v2-1-0/data)

[cimendes]

@sage-wright Can you update the documentation while I view the results from TheiaCoV ONT?

[cimendes]

TheiaCoV_ONT:

• Flu, MPXV and SC2
• Run: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/d1c22ccb-4335-4fe4-8eb7-5e690c976349

[sage-wright]

@cimendes, documentation has been updated!