This repository contains a Nextflow workflow for simulating metagenomic data based on reference genomes. The workflow consists of two processes, fetch_refs and gen_reads, which fetch reference genomes using their accession numbers and generate simulated reads from the reference genomes, respectively.
This work has been developed by a group of participants at the 9th Microbes and Food Safety Bioinformatics Hackathon held in Cambridge, UK in May 2023.
- Clone this repository:
git clone https://github.com/BioWilko/simulated-metagenome-workflow.git
cd simulated_metagenome_pipefetch_refs process: This process fetches reference genomes using their accession numbers. The input is a row from the metadata manifest file, and the output is a tuple containing the row, the reference genome FASTA file, and stdout. The ref_fetch.py script is called with the accession number, email, total reads, and proportion as arguments.
gen_reads process: This process generates simulated reads from the reference genomes using the badread package. The input is a tuple containing the row from the metadata manifest file, the reference genome FASTA file, and the number of reads to generate. The output includes a tuple containing the row, the reference genome FASTA file, and taxonomic metadata, as well as a FASTQ file with the simulated reads for each taxon.
workflow: This part of the code connects the fetch_refs and gen_reads processes using the manifest_ch channel. The output FASTQ files from the gen_reads process are collected into a single file called "simulated_metagenome.fastq" and stored in the specified output directory.
- Run the Nextflow Pipeline. The following is an example
nextflow run /file/path/to/simulated-metagenome-workflow/main.nf --meta_manifest /file/path/to/manifest/file --out_dir /file/path/to/out_dir Optional arguments include --email, --error_model, --read_len, and total_reads