AMAP

Docs / Getting started

Installation

AMAP needs two things on your machine: Nextflow, which runs the pipeline, and a container engine, which supplies every tool the pipeline calls. You do not install Bakta, Miniprot, eggNOG-mapper or any of the rest yourself; they all live inside the AMAP image.

You also do not need to clone this repository. Nextflow pulls the pipeline straight from GitHub.

What you install

  • Nextflow 24.04 or newer, on Java 17 or newer
  • Docker, or Singularity or Apptainer on a cluster

What the first run builds

  • The eggNOG database, in the folder --eggnog_db names, kept for every run after

paururo/amaplinux/amd64

Tools

Bakta 1.12.0miniprot 0.18Diamond 2.1.24eggNOG-mapper 2.1.13pangene 1.1pathotypr 1.0.0gfatools

Runtimes

Python 3.9R 4.4

Data

Bakta database light/reference/ 9 files: the H37Rv genome, proteome and GenBank, Bakta's false positives on it, Mycobrowser's table and the lineage markers
Two things to install; everything AMAP runs comes in one image, its versions read off docker/Dockerfile. Only the eggNOG database stays outside: too large to ship, it is built on the first run that needs it.

1. Nextflow#

Nextflow needs Java 17 or newer, and Conda brings both:

conda create -n nextflow-env
conda activate nextflow-env
conda install -c bioconda nextflow

If you do not have Conda, Miniconda is a lightweight installer. Any other Nextflow installation works equally well, see the Nextflow documentation.

AMAP requires Nextflow 24.04 or newer, which is enforced by the pipeline manifest.

2. A container engine#

Pick whichever your machine allows.

Docker

Best on a laptop or workstation where you have root. Follow the Docker installation guide for your platform.

Singularity / Apptainer

The usual choice on an HPC cluster, where Docker is normally not permitted. Follow the Apptainer installation guide. Many clusters already provide it as a module:

module load singularity   # or: module load apptainer

3. Check the installation#

nextflow -version
docker --version        # or: singularity --version

4. Run the test profile#

Before pointing AMAP at real data, confirm the whole chain works. The test profile annotates the reference genome bundled in the container, so it needs no data of your own and nothing to download beyond the image:

nextflow run PathoGenOmics-Lab/AMAP -profile docker,test

The first run downloads the AMAP image, which is several gigabytes because it bundles the Bakta database and the H37Rv reference files. Expect that to take a while. Later runs reuse the cached image.

Check inputs before a long run

Once you have your own samples, --validate_only checks every FASTA and database path without executing anything:

nextflow run PathoGenOmics-Lab/AMAP -profile docker \
    --tsv samples.tsv --validate_only

See inputs for what it looks for.

Running without a container#

Possible but not recommended: you take on installing Bakta, Miniprot, eggNOG-mapper, Diamond, pangene, pathotypr, R and the report packages yourself, and pointing AMAP at each reference file with the reference arguments.

The repository ships an environment.yml that reproduces the software stack under Conda:

conda env create -f environment.yml
conda activate amap

You will still need to supply the Bakta database and the reference files, which the container would otherwise provide. See containers for what the image contains.

Next steps#

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