nf-rMAP: Nextflow-powered microbial genomics pipeline for rapid antimicrobial resistance analysis. Implements rMAP's core functionality with cloud-native scalability, enhanced QC, & modular workflows. Processes Illumina data through assembly, annotation, AMR detection & phylogenetics.
A scalable microbial genomics pipeline for comprehensive bacterial chracterization, virulence & antimicrobial resistance profiling
nf-rMAP is a Nextflow implementation of the original rMAP pipeline, offering:
- Cloud-native microbial genome analysis
- Comprehensive AMR/Virulence factor detection
- Production-grade variant calling & phylogeny
- 10x faster processing through parallelization
Key features
✔️ Full-stack analysis from raw reads to clinical reports
✔️ Supports Illumina data
✔️ Automated QC & MultiQC reporting
✔️ One-click Azure/AWS/GCP deployment
# Install Nextflow (requires Java 11+)
curl -s https://get.nextflow.io | bash
# Install dependencies via Conda (optional)
conda env create -f nf-rMAP.yml
nextflow run nf-rMAP/main.nf \
--input "data/*_{1,2}.fastq.gz" \
--outdir results \
-profile docker- Nextflow 21.10.3+
- Docker 20.10+ or Singularity 3.7+
- Conda/Mamba (Optional)
curl -s https://get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
sudo apt-get install docker.io
sudo systemctl start docker
sudo usermod -aG docker $USER
**Re-login to apply changes**
git clone https://github.com/gmboowa/nf-rMAP.git
cd nf-rMAP
Basic analysis
nextflow run main.nf \
--input "samples/*_R{1,2}.fastq.gz" \
--outdir final_results \
--amr \
--cpus 16 \
-with-report execution.htmlnextflow run main.nf \
--input "s3://my-bucket/reads/*.fastq" \
--reference data/ESKAPE_ref.gbk \
--assembly shovill \
--amr \
--phylogeny \
--pangenome \
--outdir s3://results-bucket/ \
-profile awsbatch \
-resumeParameter default description
| Parameter | Default | Description |
|-----------------|--------------|------------------------------------------|
| `--input` | **Required** | Input FASTQ path/pattern |
| `--outdir` | `results` | Output directory |
| `--reference` | `None` | Reference genome (`.gbk`/`.fasta`) |
| `--assembly` | `megahit` | Assembler: `megahit` or `shovill` |
| `--cpus` | `4` | Total CPUs to use |
| `--memory` | `32.GB` | Per-job memory allocation |
| `--amr` | `false` | Enable AMR detection |
| `--phylogeny` | `false` | Build phylogenetic trees |
**View all parameters with** --help
results/
├── reports/ # Quality control reports
├── assembly/ # Draft genomes (FASTA)
├── annotation/ # Prokka annotations (GBK)
├── variant_calling/ # VCFs & SNP tables
├── resistance_genes/ # AMR/Virulence factors
├── phylogeny/ # Newick trees & alignments
└── multiqc_report.html # Consolidated QCFor nf-rMAP (Nextflow implementation of rMAP), you'll need to download and configure these essential biological databases.
### Antimicrobial resistance (AMR) databases
| Database | Purpose | Download Command/URL |
|------------|--------------------------------------------- |----------------------------------------|
| ResFinder | Antibiotic resistance genes | `abricate --setupdb --db resfinder` |
| CARD | Comprehensive Antibiotic Resistance Database | `abricate --setupdb --db card` |
| ARG-ANNOT | Antibiotic Resistance Gene Annotation | `abricate --setupdb --db argannot` |
| MEGARES | Antibiotic resistance hierarchy | `MEGARES` *(manual download required)* |
| NCBI AMR | NCBI's curated AMR database | `amrfinder --update` |
chmod +x databases_setup_script.sh && ./databases_setup_script.sh
chmod +x MLST_schemes.sh && ./MLST_schemes.sh
### Virulence & Mobile elements
| Database | Purpose | Download Command/URL |
|-----------------|-----------------------|-------------------------------------------|
| VFDB | Virulence Factors | `abricate --setupdb --db vfdb` |
| PlasmidFinder | Plasmid replicons | `abricate --setupdb --db plasmidfinder` |
| ISfinder | Insertion Sequences | `ISfinder` *(manual download required)* |
### Taxonomic classification
| Database | Purpose | Installation Command |
|-----------|-----------------------|---------------------------------------------------------------|
| GTDB-Tk | Genome Taxonomy | `gtdbtk download --data_dir /databases/gtdbtk` |
| Kraken2 | Standard Kraken2 DB | `kraken2-build --standard --db /databases/kraken2` 'bacterial'|
### Annotation databases
| Database | Purpose | Command |
|----------|-------------------------|----------------------------------------------------------------------|
| Prokka | Prokaryotic Annotation | Automatically included |
| EggNOG | Functional Annotation | `download_eggnog_data.py -y -f --data_dir /databases/eggnog` |
### Directory structure recommendation
```bash
/databases
├── amr
│ ├── card
│ ├── resfinder
│ └── megares
├── virulence
│ ├── vfdb
│ └── plasmidfinder
├── references
│ └── species_name
├── mlst
├── kraken2
└── gtdbtk
amrfinder --update
abricate --update --datadir /databases/amr
mlst --update
- We welcome contributions!
- Open an issue to discuss proposed changes
- Fork repository and create feature branch
- Submit PR with detailed description
- Follow original rMAP repository here https://github.com/GunzIvan28/rMAP
If you use nf-rMAP, please cite:
Sserwadda, I. & Mboowa, G. (2021).
rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data.
Microbial Genomics, 7(6):000583. https://doi.org/10.1099/mgen.0.000583
PMID: 34110280 · PMCID: PMC8461470