Walkercreek v4.1.0 — Nextflow 26 strict parser compatibility

Walkercreek v4.1.0

This release updates Walkercreek for compatibility with the Nextflow 26 strict syntax parser while preserving support for existing workflows and platforms.

Highlights

• Added compatibility with the Nextflow 26 strict parser.
• Refactored workflow, subworkflow, module, and config syntax to remove strict-parser errors.
• Updated deprecated channel factory usage.
• Fixed closure parameter handling and version-channel aggregation issues.
• Escaped shell variables in process scripts where required by strict parsing.
• Fixed summary_alerts.tsv generation so the report includes headers and correctly reports alerts.
• Updated summary report generation across Illumina and Nanopore workflows.
• Validated successful test runs across all supported Walkercreek platforms.

Tested platforms

The following platforms were tested successfully:

• flu_illumina
• flu_ww_illumina
• flu_nanopore
• flu_ww_nanopore
• rsv_illumina

Notes

Although this release was developed and tested for Nextflow 26 strict compatibility, the manifest minimum Nextflow version remains compatible with older supported Nextflow versions where testing confirms successful execution.

Recommended action

Users are encouraged to update to this release before moving routine analyses to Nextflow 26 or enabling strict parser behavior.

walkercreek 4.0.1

What's Changed

• Clean up flu_nanopore workflow and add nonseasonal flu alerts by @tives82 in #18

Full Changelog: v.4.0...v.4.0.1

walkercreek 4.0

What's Changed

• walkercreek version 4.0 by @tives82 in #17

Full Changelog: v.3.0...v.4.0

walkercreek 3.0

Overview

This release introduces five main platforms to accommodate different sequencing technologies (Illumina or Nanopore), sample types (clinical or wastewater), and viral targets (Flu or RSV). Also, snpEff has been integrated for variant annotation and Freyja for influenza lineage abundance in wastewater analysis. Detailed documentation and usage instructions are included in the README.md and usage.md files.

New Platforms

1. flu_illumina
   Uses IRMA for assembly of influenza from Illumina paired-end reads.
2. flu_ww_illumina
   Uses Freyja to recover relative lineage abundances from influenza wastewater samples sequenced with Illumina.
3. flu_nanopore
   Uses IRMA for assembly of influenza from Nanopore reads.
4. flu_ww_nanopore
   Uses Freyja to recover relative lineage abundances from influenza wastewater samples sequenced with Nanopore.
5. rsv_illumina
   Uses IRMA for assembly of RSV from Illumina paired-end reads.

You can select any of the above with --platform <platform_name> (for example, --platform flu_illumina).

snpEff Integration

• The Variant Annotation subworkflow now includes snpEff for annotating variants.

Freyja for Wastewater Analysis

• Freyja has been added for analyzing influenza wastewater samples (both Illumina and Nanopore).
  The barcodes are automatically downloaded at runtime to retrieve the relative lineage abundances.

Documentation Updates

• README.md now includes details about the new --platform parameter and how to run each platform.
• Added references to snpEff and Freyja usage.
• usage.md updated with examples for the new platforms, including Nanopore sample sheets.

Other Enhancements

• Minor code cleanups for naming consistency and parameter management.
• Updated pipeline summary to include references to IRMA-based assembly and Freyja usage where relevant.

walkercreek 2.0.1

This release introduces improvements to the IRMA and Abricate_flu modules, enhancing file output handling and flu B lineage classification accuracy.

Added:

Abricate_flu Module Improvements

• Implemented a refined approach for flu B lineage determination, focusing on HA and NA segments.
• Added conditional logic to accurately classify flu B viruses as either Victoria or Yamagata lineage based on specific markers.

Fixed:

IRMA Module Enhancements

• Updated BAM and FASTA file outputs to be optional, preventing process failure issues in cases where these outputs are absent.

walkercreek 2.0.0

Added:

• Nextclade Modules Update:
  Updated Nextclade modules to Nextclade version 3.0 to leverage the latest enhancements and bug fixes.

• Added IRMA_SEGMENT_COVERAGE module that calculates reference length, sequence length, and percent coverage for each segment for a given sample.

• Added MERGE_COVERAGE_RESULTS module that aggregates coverage data across all samples into merged_coverage_results.tsv file.

• Added SAMTOOLS_MAPPED_READS module that calculates the number of reads mapped and mean depth for each segment for a given sample.

• Added MERGE_BAM_RESULTS module that aggregates depth analysis data across all samples into merged_bam_results.tsv file.

• Added MERGE_BAM_COVERAGE_RESULTS module that compiles a comprehensive report from the merged_bam_results.tsv and merged_coverage_results.tsv files.

Fixed:

Configuration Fixes:
Corrected the manifest version within nextflow.config to resolve the "Wrong version printed at runtime" issue.

Additional Notes:
The documentation has been updated to reflect these changes.

walkercreek 1.0.1 - 240124

Added

• Added VADR module for flu annotation. vadr wiki
• Added skip_ncbi_sra_human_scrubber and skip_vadr params to give the option of skipping those modules

Fixed

• Corrected the input for the ASSEMBLY_TYPING_CLADE_VARIABLES subworkflow, within the main workflow, to 'PREPROCESSING_READ_QC.out.clean_reads'. This is to prevent both raw and clean reads from running through IRMA.

walkercreek 1.0.0 - 231208

UPHL-BioNGS/WalkerCreek Pipeline: Initial Release

The UPHL-BioNGS/WalkerCreek pipeline, using the nf-core template, offers a streamlined approach for analyzing Illumina paired-end influenza data.

Key Features:

• Data Handling: Efficiently processes SRA sequence files, converting them into FASTQ format for easier analysis.

• Quality Control: Comprehensive QC steps include lane merging, human read data removal, adapter sequence trimming, and detailed report generation.

• Assembly & Classification: Utilizes IRMA for adaptive assembly of influenza gene segments and subtype classification, integrating Abricate and the InsaFlu database for influenza B lineage determination.

• Influenza Clade Determination: Leverages Nextclade for detailed influenza genome analysis, focusing on clade assignment, mutation identification, and quality checks.

• Comprehensive Report: Generates a consolidated summary report, merging various data and QC reports into a single, comprehensive TSV file.