Surette Lab – Suite of Microbiome Workflows

A collection of reproducible workflows developed in the Surette Lab for microbiome data analysis using best-practice tools and standardized processing steps.

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Metagenomic Profiling Pipeline (SSuite-meta)

SSuite-meta is a Nextflow-based pipeline for generating taxonomic and functional profiles from shotgun metagenomic sequencing data.

The pipeline performs:

• Quality filtering of raw reads using fastp
• Removal of host (human) DNA using Kraken2 with CHM13 T2T as the reference genome
• Taxonomic profiling using MetaPhlAn 4
• Functional profiling using HUMAnN 4

Multiple host decontamination strategies are supported, allowing users to tailor processing to their data and analysis requirements.

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Installation

Requirements

• Linux or macOS
• Java 17 or later
• Nextflow

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1. Install Java

Nextflow requires Java 17 or newer.

Using SDKMAN! (recommended)

curl -s https://get.sdkman.io | bash
source "$HOME/.sdkman/bin/sdkman-init.sh"
sdk install java 17.0.10-tem

2. Install Nextflow

Nextflow is distributed as a self-contained executable. Download and make executable.

wget -qO- https://get.nextflow.io | bash
chmod +x nextflow

Usage

Running the Pipeline

The SSuite-meta pipeline is executed using Nextflow. A typical run requires a sample sheet in CSV format, a configuration file defining pipeline parameters, and an execution profile matching the target environment.

Example command

PIPELINE_PATH=/path/to/SSuite-meta.nf
CSV_FILE=/path/to/batch_id.csv

nextflow -log "logs/batch_id_nextflow.log" \
    run ${PIPELINE_PATH} \
    -profile <profile_name> \
    --input_csv ${CSV_FILE} \
    -with-report "results/batch_id_report.html" \
    -c "/path/to/pipeline.config" \
    --outdir "results/batch_id_results" \
    --base_dir "temp/batch_id_temp" \
    -resume

Pipeline Options (Summary)

Input and Output

• --input_csv
  CSV file defining the input metagenomic FASTQ files and associated sample information.

• --outdir
  Output directory where final taxonomic and functional profiling results are written.

• --base_dir
  Temporary working directory used by Nextflow for intermediate files and execution metadata.

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Execution and Configuration

• -profile
  Nextflow execution profile specifying the computing environment (e.g. local, cluster scheduler, container backend).

• -c
  Custom Nextflow configuration file controlling resource allocation, database paths, and tool parameters.

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Reporting and Logging

• -with-report
  Generates an HTML report summarizing pipeline performance, execution time, and resource usage.

• -log
  Path to the Nextflow runtime log file for this run.

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Workflow Control

• -resume
  Allows the pipeline to resume from previously completed steps in the event of interruption.