v0.8.0

Changed

• Visualizer created entirely in MultiQC (#46)
• nf-core template updated to v1.4.0 (#46)
• Consensus sequences now called using the variant callers for Illumina/Nanopore
  reads

v0.7.1

Fixed

• No visualizer output for Nanopore reads (#41)

v0.7.0

Changed

• Visualizer changed to single, static page (#40)

v0.6.5-alpha

Fixed

• Bug that prevented external genome tables again

v0.6.4-alpha

Fixed

• Kraken2 memory allocates based on the database size again

v0.6.3-alpha

Fixed

• Bug introduced for internal genome table files in v0.6.2

v0.6.0-alpha

This is a major overhaul of YAVSAP to make it use nf-core's DSL2 modules.

Added

• Interleaved and Single-end Illumina read support (#34)
• nf-core compliance
• SARS-CoV2 genome preset
• Support for tarballed and/or remote Kraken2 database

Changed

• Multiple sequence alignments and phylogenetic trees now include all samples collectively

Removed

• --pe and --ont parameters (#34)
• de novo assembly steps and parameters

v0.5.0-alpha

Added

• Samplesheet compatability (#21/#31)
• Ability to use user-created genome lists (#23)
• Nanopore read QC via NanoStat and MultiQC (#33)

Fixed

• Oversubscription error in RAxML-NG process
• Reroot functionality in phylogenetic tree viewer (#12/#29)

v0.4.0-alpha

Added

• VCF output for Illumina reads via CliqueSNV (#18)
• Parameter schema in Nextflow schema format (#19)
• Phylogenetic tree quality cutoff parameter (#20)

Changes

• HapLink.jl updated to 0.4 (#16)
• ONT reads now simulated using https://github.com/yukiteruono/pbsim2 (#17)
• Docs now stay in sync with docstrings/nextflow_schema.json (#10)

Fixed

• It is now nearly impossible to receive cooldown timeouts from NCBI (#15)

v0.3.3-alpha

Fixed

• Container for realigning reads fixed (#9)