Curated Metagenomics NextFlow Pipeline

A NextFlow pipeline for processing metagenomics data, implementing the curatedMetagenomics workflow.

Overview

This pipeline processes raw sequencing data through multiple steps:

1. FASTQ extraction with fasterq-dump
2. Quality control with KneadData
3. Taxonomic profiling with MetaPhlAn
4. Functional profiling with HUMAnN (optional)

Usage

Basic usage:

nextflow run main.nf --metadata_tsv samples.tsv

With specific parameters:

nextflow run main.nf --metadata_tsv samples.tsv --skip_humann --publish_dir results

Parameters

General Pipeline Parameters

Parameter	Description	Default
metadata_tsv	Path to TSV file with sample metadata	samples.tsv
publish_dir	Directory to publish results	results
store_dir	Directory to store reference databases	databases
cmgd_version	Curated Metagenomic Data version	4

Process Control Parameters

Parameter	Description	Default
skip_humann	Skip HUMAnN functional profiling	false

MetaPhlAn Parameters

Parameter	Description	Default
metaphlan_index	MetaPhlAn index to use	latest

HUMAnN Parameters

Parameter	Description	Default
chocophlan	ChocoPhlAn database version	full
uniref	UniRef database version	uniref90_diamond

Input Format

The metadata_tsv file should be a tab-separated values file with at least the following columns:

• sample_id: Unique sample identifier
• NCBI_accession: SRA accession number(s), separated by semicolons for multiple files

Example:

sample_id    NCBI_accession
sample1      SRR1234567
sample2      SRR2345678;SRR2345679

Output

Results will be organized by sample in the publish_dir directory:

results/
├── sample1/
│   ├── fasterq_dump/
│   ├── kneaddata/
│   ├── metaphlan_lists/
│   ├── metaphlan_markers/
│   ├── strainphlan_markers/
│   └── humann/
├── sample2/
│   └── ...

Profiles

The pipeline comes with several execution profiles:

• local: For local execution
• google: For execution on Google Cloud Batch
• anvil: For execution on AnVIL
• alpine: For execution on Alpine HPC
• unitn: For execution on UNITN PBS Pro

Example:

nextflow run main.nf -profile google --metadata_tsv samples.tsv

Dependencies

This pipeline requires:

• Nextflow 22.10.0 or later
• Container support (Docker, Singularity, etc.)