Bhattlab metagenomics workflows [nf]

Computational workflows for metagenomics tasks, packaged with Nextflow and Singularity.

This repository is modeled on the Snakemake workflows from the Bhattlab, where you might find more workflows.

Table of contents

1. Setup
2. Running a workflow
3. Available workflows
   • Preprocessing metagenomic data
   • Metagenomic Assembly
   • Metagenomic Binning
   • Metagenomic Classification
   • Sourmash read comparison
   • Viral contig prediction

Quickstart

If you're in the Bhatt lab and working on SCG, you should clone this repository to your folder:

git clone git@github.com:bhattlab/bhattlab_workflows_nf.git

You can then run a workflow like this:

module load java/18.0.2.1
module load nextflow/22.10.5

nextflow run </path/to/this/repo>/workflows/preprocessing.nf \
	-c </path/to/this/repo>/config/run.config \
	-params-file params.yml \
	-with-trace -with-report -resume

Note that you might have to modify the params.yml file according to your project. There is a template in the config folder, as a start.
Other users will need to change these options (see Running a workflow)

Important
Once everything is done and ran correctly, you should delete all the unnecessary temporary files and save us space on SCG! Just remove the work folder from wherever you called the nextflow command:

rm -r ./work

You can also remove the .nextflow folder, which contains metadata and cache from the run.

rm -rf .nextflow 

Question?

Please feel free to check out the documentation folder. Maybe your question has already been answered. Otherwise, you can open an issue in this repository. Please make sure to thorougly describe your problem and to attach any relevant output and log files.