FungiPhyloGen: A Nextflow pipeline for fungal genomic epidemiology

Description: This release updates the default variant calling parameters in the cauris_batch and cauris_small profiles to improve sensitivity for drug resistance markers in Candida auris. Key Changes: Refined Allele Frequency (AF) Threshold: Lowered the INFO/AF filter from < 0.75 to < 0.25. Rationale: Previous stringent filtering (0.75) inadvertently removed valid heterozygous variants, particularly those associated with gene duplication events (CNVs) common in azole-resistant strains (e.g., ERG11 F126L). Outcome: This adjustment rescues these critical resistance signals while maintaining a high Mapping Quality (MQ < 40) threshold to preserve phylogenetic backbone resolution. Impact: Phylogeny: Slight increase in retained heterozygous SNPs (~200–600 additional variants) but retains valid clade topology. Resistance Profiling: Significantly improved detection of potential heteroresistance and CNV-driven mutation events.