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.