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Recent Releases of nf-virontus

nf-virontus - 2.0.2dev

What's Changed

  • Fix primerbedtoampliconbed.py parsing of BED files with extra sequence column by @peterk87 in https://github.com/CFIA-NCFAD/nf-virontus/pull/11

Full Changelog: https://github.com/CFIA-NCFAD/nf-virontus/compare/2.0.1dev...2.0.2dev

- Nextflow
Published by peterk87 about 2 years ago

nf-virontus - 2.0.1dev

This release fixes an issue where random ambiguous bases are introduced into the consensus sequence by Bcftools (#9).

- Nextflow
Published by peterk87 over 2 years ago

nf-virontus - 2.0.0dev1

Zenodo DOI generation release.

- Nextflow
Published by peterk87 over 2 years ago

nf-virontus - 2.0.0dev

This release is a major refactor using Nextflow DSL-2 modules and similar process structure and definitions to nf-core pipelines. A single reference genome is assumed for all samples unlike previous versions of nf-virontus that would perform parallel analyses on all provided reference sequences. A smart reference genome selection module is in the works.

For SARS-Cov-2 analysis, the --scov2 flag can be used to specify the MN908947.3 Wuhan-Hu-1 sequence as the reference genome. This is equivalent to specifying --genome MN908947.3. Pangolin and Nextclade analysis will automatically be performed if the reference genome is MN908947.3.

NOTE: This is a in-development release that does not have all features expected for version 2.0.0, but should provide output that is compatible with the xlavir Excel Nextflow bioinformatics pipeline report generation tool.

Changes

  • refactor into DSL-2 modules
  • Clair3 variant calling instead of Medaka/Longshot for faster more accurate variant calling esp. at lower coverage depths
  • adapted nf-core/modules processes (Bcftools, Nextclade, Nextalign, PycoQC, NanoPlot, MultiQC)
  • added SnpEff variant effect prediction
  • added SnpSift to parse SnpEff annotations into tab-delimited table like nf-core/viralrecon
  • allele fraction threshold set at 0.75 by default for major variant to be incorporated into consensus sequence
  • added bin/simpler_snpsift.py to simplify SnpEff/SnpSift table
  • updated tools and dependencies to latest versions

- Nextflow
Published by peterk87 over 2 years ago

nf-virontus - 1.1.0

Legacy nf-virontus. No longer supported.

- Nextflow
Published by peterk87 over 2 years ago