FungiPhyloGen: A Nextflow pipeline for fungal genomic epidemiology

Zenodo (CERN European Organization for Nuclear Research) 2026 Open access

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Authors: Stanford Kwenda, Tshiama Mwamba, Serisha D. Naicker, Tsidiso G. Maphanga, Silondiwe P. Nzimande, Sabelle Jallow, Nelesh Premapragasan Govender
DOI: 10.5281/zenodo.18121445
Cited by: 0

Abstract

Removed hardcoded file paths for FastQC and contaminants; these are now dynamically set via nextflow.config. Replaced hardcoded CPU/Memory directives with standard process labels (process_low, process_medium, process_high). Fully refactored profiles. The pipeline now switches seamlessly between Local (standard) and HPC (Slurm) execution without modifying module code.

Publication details

Journal / source
Zenodo (CERN European Organization for Nuclear Research)
Publication date
2 January 2026