nf-amrseq

This Page is under construction and not up to date

nf-amrseq is a nextflow pipeline to process sequencing data of Antimicrobial Multi-Resistance bacteria.

The pipeline:

1. Detect the organism by comparing the assembly to a reference species database with orgfinder.

2. Run ResFinder, amrfinder+, mobtyper, PlasmidFinder.

3. Run MLST with the schema automatically selected from detected species.

4. Generate HTML reports.

Usage

Local computer

Running the pipeline on a local computer requires docker (to run containerized software) and nextflow. nextflow is however optional as containerized version exists (see section Nextflow container below).

Note: The pipeline cannot be run directly on a NAS but only on a local folder of your hard-drive.

If the FASTA files to process are in subfolder 'data/' of your working directory

nextflow run BioinfoSupport/nf-amr -resume --input_assembly=data/*.fasta

Nextflow container

Nextflow installation is optional as containerized versions of nextflow exists. For example, on MacOS, to run a nextflow container with access to docker daemon of the host, we use:

docker run --rm -it \
  -v /var/run/docker.sock:/var/run/docker.sock \
  -v $(pwd):$(pwd) \
  --platform linux/amd64 \
  --workdir $(pwd) \
  --env NXF_HOME=$(pwd)/.nextflow_home \
  nextflow/nextflow:25.04.2 bash

HPC

To run the pipeline on a HPC cluster with slurm and singularity use -profile=hpc:

nextflow run BioinfoSupport/nf-amr -profile hpc -bg -resume --input_assembly=data/*.fasta

If nextflow is not installed on your HPC, it can be installed with:

curl -s https://get.nextflow.io | bash && chmod +x nextflow

And if you need to update the pipeline latest version, use:

nextflow pull BioinfoSupport/nf-amr

Or run a specific version:

nextflow run BioinfoSupport/nf-amr -r v0.4.12 -profile hpc -bg -resume --input_assembly=data/*.fasta

Input

• --input_assembly: FASTA files with assembled genomes to annotated

Output

By default, pipeline outputs are stored in results/ but it can controlled with option -output-dir