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MetaGEAR

MetaGEAR Workflows

MetaGEAR Workflows is the Nextflow / nf-core pipeline at the core of the platform. It takes shotgun metagenomic data through four cohesive workflows that can be run independently or in sequence, with outputs in a consistent schema designed to be easy to post-process.

→ schirmer-lab/metagear-pipeline ↗ — source, releases, and the canonical pipeline reference.

What it does

Database setup. Installs the reference databases the other workflows need: Kneaddata host + contaminant genomes, MetaPhlAn marker database, HUMAnN nucleotide and protein databases.

Quality control. Read-level quality assessment, adapter trimming (TrimGalore), and host / contaminant removal (Kneaddata) for DNA and RNA inputs.

Microbial profiles. Taxonomic profiling with MetaPhlAn and functional profiling with HUMAnN, producing per-sample abundance tables for taxa, gene families, and pathways.

Gene analysis. Gene-centric analysis with optional contig catalog assembly — for downstream lab-specific work or as the foundation for searchable indexes.

How you run it

You can invoke the pipeline directly with Nextflow if you’re already a Nextflow user:

Terminal window
nextflow run schirmer-lab/metagear-pipeline \
  -profile docker \
  --input samplesheet.csv \
  --outdir results/

But the recommended path — especially if you aren’t a regular Nextflow user — is via MetaGEAR Tools, the CLI that installs the pipeline, manages reference databases, and applies sensible defaults. See the MetaGEAR Tools (CLI) page.

Inputs and outputs

The pipeline takes a CSV samplesheet pointing at paired-end FASTQ files:

sample,fastq_1,fastq_2
SAMPLE-01,/path/to/sample1_R1.fastq.gz,/path/to/sample1_R2.fastq.gz

Outputs are written to a results directory with one subdirectory per workflow and consistent file naming — easy to feed into your own downstream scripts or notebooks.

Built on nf-core

MetaGEAR Workflows uses the nf-core framework, inheriting community conventions for reproducibility, containerization, and testing. It runs with Docker, Singularity, or any nf-core-supported execution profile, on a laptop or an HPC cluster.

Where to go next