Installation¶

Requirements¶

Software¶

Nextflow (installation guide here)
Conda or Mamba (installation guide for Mamba (recommended) here)
Optional: A container runtime engine like Docker or Apptainer.

Hardware¶

A POSIX-compatible operating system (e.g., Linux, macOS) or Windows with WSL. We strongly recommend using a Unix-based OS for best compatibility with all tools.
At least 32 GB of RAM for MEGAHIT, or 128 GB if you plan to use metaSPAdes for assembly.
At least 256 GB of disk space.

ℹ️ Storage Estimates (based on shallow shotgun metagenomics)

Nextflow installation: ~150 MB
Databases: ~120 GB
Environment folder: ~20 GB
Intermediate/cache files: 20–50 GB (varies with sample size and quality)
Output per sample: ~9 GB

Optional: Some steps in assembly-based analysis (for example, COMEBin in the binning step) will run faster if your system is equipped with a GPU.

Install MicrocosM¶

via Nextflow portal (recommended)¶

nextflow pull tnmquann/metaflow

# Check pipeline info
nextflow info tnmquann/metaflow

by cloning the repository (dev versions available)¶

git clone https://github.com/tnmquann/metaflow.git
cd metaflow
nextflow run main.nf

Database Preparation¶

Minimal
Extended