Freyja-NF

Automated SRA downloading, processing and Freyja analysis pipeline for SARS-CoV-2 wastewater sequencing data.

Usage

nextflow run https://github.com/andersen-lab/Freyja-nf -entry fastq --fastq_dir [fastq_dir] --output [output_dir] 

Configuration

Addtional configuration options can be found in nextflow.config