[Kraken2_Standalone] Make task compatible with uncompressed FASTQ files

[cimendes]

This PR closes #224

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

:brain: Aim, Context and Functionality

Most of our workflows in the PHB universe ™️ are meant to be compatible with both compressed and uncompressed FASTQ files. Such is the example of TheiaProk (https://theiagen.notion.site/TheiaProk-Workflow-Series-2c710e386ea74dbc828a910b6fb77fac)

Read file names should end with .fastq or .fq, with the optional addition of .gz

Unfortunatly, this is no longer true since #286 as the addition of Kraken2 module made the workflow uncompatible with uncompressed files.

TheiaMeta is another workflow that is also not currently compatible with uncompressed FASTQs due to Kraken2 standalone task incompatibility.

This PR addresses this issue by allowing uncompressed FASTQ files to be processed by Kraken2.

Additionally, the Kraken2 standalone workflows now allow for uncompressed input files.

: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 : No

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

Kraken2_standalone task has been adjusted to allow for uncompressed FASTQ file processing.

: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: N/A

File processing changed: N/A

Compute resources changed: N/A

➡️ Inputs

Nothing was altered

⬅️ Outputs

Nothing was altered

:test_tube: Testing

Test Dataset

Locally:

• 1 uncompressed metagenomic HAV sample

On Terra:

• Uncompressed SRR19880611

Commandline Testing with MiniWDL or Cromwell (optional)

Kraken2 Standalone task: miniwdl run --task kraken2_standalone /home/ines_mendes/Git/public_health_bioinformatics/tasks/taxon_id/task_kraken2.wdl read1= ~/Test/ont/ERR3772599.fastq kraken2_db="gs://theiagen-public-files-rp/terra/theiaprok-files/k2_viral_20230605.tar.gz" samplename=ERR3772599

TheiaMeta workflow: miniwdl run /home/ines_mendes/Git/public_health_bioinformatics/workflows/metagenomics/wf_theiameta_illumina_pe.wdl read1= ~/Test/HAV_Metagenomics/HAV0001_S1_L001_R1_001.fastq read2= ~/Test/HAV_Metagenomics/HAV0001_S1_L001_R2_001.fastq samplename=TEST kraken2_db="gs://theiagen-public-files-rp/terra/theiaprok-files/k2_viral_20230605.tar.gz"

Kraken2 standalone workflow: miniwdl run /home/ines_mendes/Git/public_health_bioinformatics/workflows/standalone_modules/wf_kraken2_pe.wdl samplename="TEST" kraken2_db="gs://theiagen-public-files-rp/terra/theiaprok-files/k2_viral_20230605.tar.gz" read1= /home/ines_mendes/Test/HAV_Metagenomics/HAV0001_S1_L001_R1_001.fastq read2= /home/ines_mendes/Test/HAV_Metagenomics/HAV0001_S1_L001_R2_001.fastq

TheiaProk_illumina_pe workflow: Unable to test locally

Terra Testing

• Kraken2 Standalone: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/1a1cb0cd-a269-4175-a80d-2ab5af8ca955
• TheiaMeta: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/35f3cac4-ffe4-4bb0-83ed-f30810b864e8
• TheiaProk: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/a07d8d38-284a-4de3-ad00-4edc32b92599

Suggested Scenarios for Reviewer to Test

• Workflows using Kraken2 standalone task
  • Kraken2 Standalone
  • TheiaProk
  • TheiaMeta

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
• [x] The CI/CD has been adjusted and tests are passing (to be completed by Theiagen developer)
  • Cromwell failures were not addressed, waiting for PR #327
• [x] Code changes follow the style guide

🎯 Reviewer Checklist

• [x] All impacted workflows/tasks have been tested on Terra with a different dataset than used for development
• [x] All reviewer-suggested scenarios have been tested and any additional
• [ ] All changed results have been confirmed to be accurate
• [x] All workflows/tasks impacted by change/s have been tested using a standard validation dataset to ensure no unintended change of functionality
• [x] All code adheres to the style guide
• [x] MD5 sums have been updated
• [x] The PR author has addressed all comments

🗂️ Associated Documentation (to be completed by Theiagen developer)

• [x] Relevant documentation on the Public Health Resources "PHB Main" has been updated
• [x] Workflow diagrams have been updated to reflect changes

[sage-wright]

Testing as follows:

• Kraken2_SE_PHB with one uncompressed fastq file
  • outputs as expected ✔️
• ~TheiaProk_Illumina_SE on the same sample as above~ I forgot to run Kraken2
• TheiaMeta_Illumina_PE with two DENV samples with uncompressed fastqs
  • output are as expected ✔️

Well done!