v1.6.0 - [04/21/2025]

Added

• Added the "Pre-MycoSNP" workflow for quick fungal taxonomic classification and Candida auris clade typing (using de novo assemblies)
  • Base workflow development by Jared Johnson @DOH-JDJ0303 (#119)
  • Original sourmash subtyping subworkflow by Charlotte Royer @royercj (#114)
  • Co-development, validation, testing, and documentation by Zack Mudge @zmudge3
• Added the "Genome Fraction" metric to the main MycoSNP workflow's QC report, by CJ Jossart @cjjossart (#123, #128)
• Nextflow Tower / Seqera Cloud functionality, by Jared Johnson @DOH-JDJ0303 (#104)
• Added FKS1 coordinates for a third hotspot region (single amino acid) associated with echinocandin resistance in Candida auris (for the snpeffr report - results/snpeff/combined_cauris_refB11205_fks1.csv)

Changed

• Bumped GATK version to 4.5.0.0
• Changed SnpEff-related config to work with cloud, by Jared Johnson @DOH-JDJ0303 (#103)
• Updated samplesheet and reference genome links in test.config
• Changed filename of results/snpeff/combined.csv to results/snpeff/combined_cauris_refB11205_fks1.csv
• Bumped snpeffr version to v1.1.1. The "mutation" column in the snpeffr report (results/snpeff/combined_cauris_refB11205_fks1.csv) can now contain a value of "undetermined". This occurs when GATK identifies a variant in the individual VCF file for an isolate, but then the identified variant is lost in the subsequent step when GATK creates a merged VCF file that includes all isolates.
  • Snpeffr v1.1.1 updates by Mal Rajeev @mrajeev08

Removed

• Removed --tmpdir parameter and associated config in nextflow.config

Fixed

• Fixed Candida auris FKS1 hotspot 1 coordinates in nextflow.config, to include the first nucleotide of F635, and remove two extra nucleotides at the end

Deprecated

• Nextflow -entry parameter to run specific workflow is deprecated. Use MycoSNP's --workflow parameter instead.