[RASUSA] update from 0.7.0 -> 2.1.0

[xonq]

This PR closes #461 and updates RASUSA container and documentation references to v2.1.0. Issue #461 references v2.0.0, though this PR advances to v2.1.0 as the most recent stable update hosted on StaPH-B.

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

🧠 Summary

Copy StaPH-B RASUSA v2.1.0 container to Theiagen artifacts repository, update container in task_rasusa.wdl and downstream workflows, modify task_rasusa.wdl execution of RASUSA to conform to RASUSA's new subcommand and argument formatting, and update documentation to reference new container version.

⚡ Impacted Workflows/Tasks

Immediate impacts:
task_rasusa.wdl
wf_rasusa.wdl

Immediate Downstream impacts:
wf_read_QC_trim_ONT.wdl
wf_theiaprok_ont.wdl
task_broad_terra_tools.wdl
wf_theiaeuk_illumina_pe.wdl

This PR may lead to different results in pre-existing outputs: Yes/No
No

This PR uses an element that could cause duplicate runs to have different results: Yes/No
This PR does not change the state of RASUSA output compared to previous versions, though RASUSA inherently produces different results due to random sampling in its algorithm.

🛠️ Changes

• Update RASUSA v0.7.0 -> v2.1.0
• Copy StaPH-B container to general-theiagen artifacts repo
• Set rasusa task to hard fail
• Update rasusa task to conform to new RASUSA argument formatting - no changes to argument inputs
• Update documentation to reflect new container version
  See Algorithm

⚙️ Algorithm

(task_rasusa.wdl)

• Fail hard via set -euo pipefail
• Prepend -o for each output file detected to conform to rasusa update
• Use new subcommand argument input format:

    # set single-end or paired-end outputs
    if [ -z "~{read2}" ]; then
      OUTPUT_FILES="-o ~{samplename}_subsampled_R1.fastq.gz"
    else
      OUTPUT_FILES="-o ~{samplename}_subsampled_R1.fastq.gz -o ~{samplename}_subsampled_R2.fastq.gz"
    fi

    rasusa reads \
      ${COVERAGE} \
      ~{'--seed ' + seed} \
      ~{'--bases ' + bases} \
      ~{'--frac ' + frac} \
      ~{'--num ' + num} \
      ${OUTPUT_FILES} \
      ~{read1} ~{read2}

➡️ Inputs

No input changes at the task / workflow level

⬅️ Outputs

No output changes

🧪 Testing

• RASUSA standalone wf compared with control RASUSA v0.7.0 run - test comparison yielded same sized FastQ files as expected.
• TheiaEuk PE wf compared to control PHB v2.3.0 - test succeeded as expected
• TheiaProk ONT wf compared to control PHB v2.3.0 - test succeeded as expected; failures in control and dev RASUSA version are consistent and due to input dataset error not affiliated with this update.

Suggested Scenarios for Reviewer to Test

Initial testing covers most usage scenarios

🔬 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]

some minor documentation updates needed, code changes look good so far! will test shortly

[sage-wright]

code changes look good and reads are being downsampled 🎉