Releases: UPHL-BioNGS/walkercreek
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
andskip_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.
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Quality Control: Comprehensive QC steps include lane merging, human read data removal, adapter sequence trimming, and detailed report generation.
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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.
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Influenza Clade Determination: Leverages Nextclade for detailed influenza genome analysis, focusing on clade assignment, mutation identification, and quality checks.
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Comprehensive Report: Generates a consolidated summary report, merging various data and QC reports into a single, comprehensive TSV file.