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Recent Releases of https://github.com/cfia-ncfad/nf-ionampliseq

https://github.com/cfia-ncfad/nf-ionampliseq - 2.1.0

Added

  • [test] nf-test for BCFTOOLS_FILTER and BCFTOOLS_CONSENSUS to ensure that updated multiallelic variant handling produces expected results including test data.
  • [ci] nf-test job to ci.yml
  • [feat] Better support for multiallelic variant handling in BCFTOOLS_FILTER using more comprehensive logic using Bcftools filter statements and awk. Updated BCFTOOLS_CONSENSUS to properly handle new multiallelic variant handling.

Changes

  • [docs] Updated --help message to use nextflow_schema.json.
  • [refactor] Moved workflow.onComplete code from main.nf to lib/helpers.nf

What's Changed

  • Fix handling of multiallelic variants by @peterk87 in https://github.com/CFIA-NCFAD/nf-ionampliseq/pull/5
  • Release 2.1.0 by @peterk87 in https://github.com/CFIA-NCFAD/nf-ionampliseq/pull/6

Full Changelog: https://github.com/CFIA-NCFAD/nf-ionampliseq/compare/2.0.1...2.1.0

- Nextflow
Published by peterk87 11 months ago

https://github.com/cfia-ncfad/nf-ionampliseq - 2.0.1

This release makes the potential frameshift introducing filter for variant calling results optional and off by default.

Added

  • [config] filter_frameshift_variants pipeline parameter (default: false) for optionally filtering potential frameshift introducing variants from the TVC variant calling results prior to consensus sequence generation.

Changes

  • [docs] Updated README.md and citation information.
  • [update] Use TVC Flow Evaluator calculated allele fraction (AF) for computing GT in Bcftools filtered VCF instead of observation based counts.

Fixed

  • [fix] Turned off potential frameshift variant filtering leading to inaccurate consensus sequences.
  • [fix] Removed git diff action from docker.yml since features are unsupported by GHA.

What's Changed

  • Fix aggressive frameshift variant filtering by @peterk87 in https://github.com/CFIA-NCFAD/nf-ionampliseq/pull/3
  • Release 2.0.1 by @peterk87 in https://github.com/CFIA-NCFAD/nf-ionampliseq/pull/4

Full Changelog: https://github.com/CFIA-NCFAD/nf-ionampliseq/compare/2.0.0...2.0.1

- Nextflow
Published by peterk87 11 months ago

https://github.com/cfia-ncfad/nf-ionampliseq - 2.0.0

This release modernizes nf-ionampliseq to DSL-2 standards with enhanced BLAST analysis capabilities, improved containerization, and better resource management. Key additions include BLAST database integration, enhanced variant calling options, and comprehensive process version tracking.

Added

  • [feat] BLASTN process to run blastn with consensus sequences against user-specifed DB (--blast_db).
  • [feat] BLASTN_COVERAGE process and blast_coverage.py for summarizing BLAST results and generating MultiQC tables.
  • [feat] fill-tags plugin for BCFTOOLS_FILTER and better filtering of variants for consensus sequence construction.
  • [feat] SEQTK_SUBSEQ process for extracting reference sequences based on Mash screen results.
  • [feat] CONSENSUS_MULTIQC process for enhanced consensus sequence reporting in MultiQC.
  • [feat] Enhanced container support for Docker, Singularity, Apptainer, and Podman.
  • [feat] Version tracking for all processes with versions.yml files.
  • [config] comprehensive DSL2 module configuration in conf/modules.config.
  • [config] new configuration parameters: blast_db, trim_primers, output_unmapped_reads.
  • [config] variant calling options: minor_allele_fraction, major_allele_fraction, low_coverage.
  • [config] enhanced container profiles for multiple container engines.
  • [config] proper resource management with check_max function for memory, CPU, and time limits.
  • [config] timestamped execution reports and timeline files in nextflow.config.

Changes

  • [docs] Comprehensive documentation overhaul with detailed parameter descriptions and external tool references
  • [cleanup] Removed legacy plotting module and environment.yml file for simplified architecture. Use wgscovplot instead for better and interactive plotting of coverage stats and variants.
  • [cleanup] Simplified TMAP process configuration using dynamic arguments parameter.
  • [update] Repository and container registry references updated to CFIA-NCFAD organization
  • [feat] Complete workflow modernization to DSL2 standards with proper process separation.
  • [feat] Added new Docker build workflow in .github/workflows/docker.yml for improved container publishing and CI separation.
  • [feat] Added support for building and using custom Docker images with updated samtools and TMAP/TVC binaries.
  • [feat] Enhanced process version tracking: all major processes now emit versions.yml with tool versions for reproducibility.
  • [feat] Improved error handling and retry strategies for all processes.
  • [update] MultiQC process updated to support new BLAST coverage MultiQC table.
  • [update] Bump version of workflow and dependencies for 2.0.0 release.
  • [update] Repository renamed from peterk87/nf-ionampliseq to CFIA-NCFAD/nf-ionampliseq.
  • [update] Nextflow version requirement updated to !>=22.10.1.
  • [update] All processes now use proper container definitions with conda and container specifications.
  • [update] Process resource labeling standardized (process_low, process_medium, process_high).
  • [update] Input/output patterns standardized across all processes with proper emit declarations.
  • [update] TMAP and TVC processes enhanced with better parameter handling and version tracking.
  • [update] TMAP and TVC processes now use new Docker image ghcr.io/cfia-ncfad/nf-ionampliseq:2.0.0 with updated samtools and runtime dependencies.
  • [update] MASH screen workflow restructured with separate sketching and screening processes.
  • [update] FastQC process enhanced with memory optimization and version tracking.
  • [update] Samtools processes standardized with consistent version tracking and output handling.
  • [update] Mosdepth process optimized with improved output handling and version tracking.
  • [update] Edlib processes enhanced with container support and version tracking.
  • [update] Sample sheet processing improved with better error handling and validation.
  • [docs] Documentation and help text for BLAST coverage analysis improved.
  • [docs] Updated documentation to reflect new container build and usage instructions.
  • [ci] Updated GitHub Actions CI tests.
  • [ci] Moved Docker container build to separate workflow for improved CI/CD.
  • [ci] CI now tests with multiple Nextflow versions 22.10.1 and latest stable (25.04.6 currently).

Fixed

  • [fix] Container compatibility issues across different container engines.
  • [fix] Process resource allocation and memory management.
  • [fix] Version tracking consistency across all processes.
  • [fix] Input/output file handling and validation.
  • [fix] MultiQC report generation and custom content integration.

Dependencies

  • [deps] Updated to Nextflow !>=22.10.1.
  • [deps] Enhanced container support with multiple engine options.
  • [deps] Standardized conda environment specifications across all processes.
  • [deps] Added better version tracking for all bioinformatics tools.

What's Changed

  • DSL2 modernization, BLAST analysis, and enhanced containerization by @peterk87 in https://github.com/CFIA-NCFAD/nf-ionampliseq/pull/1
  • Release 2.0.0 by @peterk87 in https://github.com/CFIA-NCFAD/nf-ionampliseq/pull/2

New Contributors

  • @peterk87 made their first contribution in https://github.com/CFIA-NCFAD/nf-ionampliseq/pull/1

Full Changelog: https://github.com/CFIA-NCFAD/nf-ionampliseq/compare/1.0.1...2.0.0

- Nextflow
Published by peterk87 11 months ago