Update Walkercreek for Nextflow 26 strict compatibility

[tives82]

Summary

This PR updates Walkercreek to run successfully with Nextflow 26.04.1 using the v2 strict syntax parser.

This makes the pipeline compliant with newer Nextflow syntax requirements while preserving existing workflow behavior across the supported Walkercreek platforms.

Major changes

• Updated pipeline manifest metadata:
  • nextflowVersion changed to >=26.04.1
  • pipeline version updated to 4.1.0
• Updated syntax for Nextflow 26 strict parser compatibility.
• Fixed strict parser issues related to:
  • top-level workflow statements
  • deprecated or invalid closure syntax
  • duplicate variable declarations
  • module/subworkflow output handling
  • process script interpolation issues
• Fixed SEQKIT_PAIR issue caused by shell variable interpolation in the gzip step.
• Updated Nextclade subworkflow version channel handling to avoid missing .versions output errors.
• Added bin/generate_summary_alerts.py.
• Updated summary report modules and workflow wiring so summary_alerts.tsv is generated consistently.
• Added missing ref/h3n2_barcode.html.

Validation performed

I tested the updated pipeline with Nextflow 26.04.1 and the v2 strict syntax parser:

• Nextflow linting completed with no errors.

I also tested all Walkercreek platforms successfully after the strict-parser updates.
Tested platforms:

• flu_illumina
• flu_nanopore
• flu_ww_illumina
• flu_ww_nanopore
• rsv_illumina

I also tested summary_alerts.tsv generation using known influenza coinfection samples and confirmed that alerts are now generated where expected.

[jwarnn]

I ran three test runs; twice with a custom samplesheet and once with the test profile. They all completed successfully. I am approving the PR but left a comment to consider about lowering the required nextflowversion in the manifest.

[jwarnn]

I tested the pipeline at a lower version using NXF_VER=24.04.2 . The run executed with no problem. I am not sure of the importance of this line of the manifest; I have had runs stop if the version is lower than what the manifest says is required but that didn't happen for this run. It might be more accessible if older versions are allowed. Maybe consider keeping nextflowVersion = '>=24.04.2'

[tives82]

I agree the manifest should show the minimum supported version. Thanks for testing it. I’ll keep nextflowVersion = '>=24.04.2' to show support for users on older versions.