Run PathoFact

Configuration

To run PathoFact you need to adjust some parameters in config.yaml.

sample: This is a list of sample names, e.g. sample: ["SAMPLE_A","SAMPLE_B"]
project: A unique project name which will be used as the name of the output directory in datapath path (see below).
datapath: Path to directory containing the sample data; the output directory will be created there.
workflow: Pathofact can run the complete pipeline (default) or a specific step:
- "complete": toxin + virulence + AMR + MGE prediction
- "Tox": toxin prediction
- "Vir": virulence prediction
- "AMR": antimicrobial resistance (AMR) & mobile genetic elements (MGEs) prediction

Execution

Basic command to run the pipeline using <cores> CPUs:

# activate the env
conda activate PathoFact
# run the pipeline
# set <cores> to the number of cores to use, e.g. 10
snakemake -s Snakefile --use-conda --reason --cores <cores> -p

NOTE: Add parameter -n (or --dry-run) to the command to see which steps will be executed without running them.

NOTE: Add --configfile <configfile.yaml> to use a different config file than config.yaml.

NOTE: It is advised to run the pipeline using multiple CPUs or CPUs with "higher" memory.

For more options, see the snakemake documentation.

Execution on a cluster

The pipeline can be run on a cluster using slurm. The command can be found in the script cluster.sh which can also be used to submit the jobs to the cluster.

sbatch cluster.sh