Profiles

Local profiles

OrthoGarden comes with simple local profiles two, four, and eight, invoked in the pipeline run using:

-profile local,four

Local config

.
└── conf
    └── local.config

The file local.config defines the parameters to use for the various processes in the local pipeline. Modify this file to limit or expand the computational capacity of the pipeline for your system.

Slurm profile

It may also be possible to run OrthoGarden using slurm-based system using the following profile when running the pipeline:

-profile slurm,custom

OrthoGarden has been tested on the UTK High Performance and Scientific Computing cluster ISAAC-NG.

Slurm config

.
└── conf
    ├── slurm.config
    └── slurm_custom.config

The file slurm.config defines the slurm parameters to use for the various processes in the pipeline. Each imports the clusterOptions from the slurm_custom.config file.

Modifying slurm_custom.config to meet the account, qos, and partition settings of your HPC will be necessary before running OrthoGarden on slurm-based servers.

Slurm example run

The following sbatch script might be modified for other slurm-based HPC systems, but it will be highly dependent on the limitations of the account, partition, and qos of the server.

#!/bin/bash
#SBATCH -J orthogarden_test
#SBATCH -A acf-utk0032
#SBATCH --partition=long
#SBATCH --qos=long
#SBATCH --nodes=1
#SBATCH --cpus-per-task=2
#SBATCH --mem=4G
#SBATCH --time=5-00:00:00
#SBATCH --error=job.e%J
#SBATCH --output=job.o%J

# Now list your executable command/commands.

module load nextflow/23.10.0

export NXF_OPTS="-Xms500M -Xmx2G"
export NXF_ANSI_LOG=false

nextflow run main.nf \
    --input tests/anopheles_pseudoref/pseudo_refs/metadata_test.csv \
    --threshold_val 0.9 \
    --publish_dir ~/orthogarden_test \
    -profile slurm,custom \
    -resume

[!NOTE] This is a simplified usage script and likely won't reflect the server behavior of all HPCs. This job uses a pre-existing Nextflow module, but regardless of package source, the NXF options are highly recommended.