[Read_Screen] Comprehensively run QC checks regardless of failure status then output results

[xonq]

This PR closes #567

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

🧠 Summary

Updates task_screen (Read_screen) to run all screening checks regardless of intermittent failures. Outputs a TSV table of read screening results that propagates for both raw and clean read screening in Theia-pipelines

⚡ Impacted Workflows/Tasks

tasks/quality_control/comparisons/task_screen.wdl and all downstream workflows

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

• Run all read screening checks regardless of previous checks missing thresholds
• output each result to a single sample-level TSV
• expose output to downstream workflows
• update documentation

⚙️ Algorithm

• conditional expression for failure check moved to end of task
• create a TSV (read_screen.tsv) for read QC results
• expose TSV to downstream WDL tasks/workflows for both raw and clean read screening

➡️ Inputs

n/a

⬅️ Outputs

Added output TSV filepath and exposed to downstream workflows

File read_screen_tsv = "read_screen.tsv"

🧪 Testing

• TheiaCoV SE wf compared to control PHB main
  • read_screen.tsv is available and formatted correctly in output
  • All other outputs in table are consistent with control
• TheiaCoV PE wf compared to control PHB main
  • read_screen.tsv is available and formatted correctly in output
  • All other outputs in table are consistent with control
• TheiaCoV ONT wf compared to control PHB main
  • read_screen.tsv is available and formatted correctly in raw and clean outputs
  • All other outputs in table are consistent with control
• TheiaProk SE wf compared to control PHB main
  • read_screen.tsv is available and formatted correctly in output
  • All other outputs in table are consistent with control
• TheiaProk PE wf compared to control PHB main
  • read_screen.tsv is available and formatted correctly in output
  • All other outputs in table are consistent with control
• TheiaProk ONT wf compared control PHB main
  • read_screen.tsv is available and formatted correctly in output
  • All other outputs in table are consistent with control
• TheiaEuk PE wf compared to control PHB main
• PE failure testing
  • min_reads threshold not met, screen_reads proceeded and populated failure log
  • min_basepairs threshold not met, screen_reads proceeded and populated failure log
  • genome_length threshold not met, screen_reads proceeded and populated failure log
  • min_coverage threshold not met, screen_reads proceeded and populated failure log
  • min_proportion threshold not met, screen_reads proceeded and populated failure log
• SE/ONT failure testing
  • min_reads threshold not met, screen_reads proceeded and populated failure log
  • min_basepairs threshold not met, screen_reads proceeded and populated failure log
  • genome_length threshold not met, screen_reads proceeded and populated failure log
  • min_coverage threshold not met, screen_reads proceeded and populated failure log

Suggested Scenarios for Reviewer to Test

n/a

🔬 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