Example Nextflow workflows for NeSI HPC system.
- simple: A very simple model which takes in lists of latitudes, longitudes and random seeds, obtains the cross-product of the lists, subsamples to a specified maximum number of models, runs all the models, filters the model runs based on a value, and then combines the model outputs into a single output file.
In addition to configuration files specific to each workflow, there is a NeSI configuration included at the top level of this repo: nextflow.config.
This configuration will set some basic parameters for running Nextflow on NeSI.
There are default working and output directories, set to /nesi/nobackup/$PROJECT/work and /nesi/project/$PROJECT/out respectively.
These settings can be changed by editing the configuration file, or by passing options in the run command.
For example, the output directory can be set in the run command as follows: nextflow run <workflow> -output-dir ./out.
For additional information, see the Configuration Options in the Nextflow documentation.
Any of these workflows can be run in an interactive Slurm session after loading the Nextflow module. Additionally, each workflow contains a simple sbatch file which will submit a Slurm job which will run the given workflow with the default settings. You will need to edit the account/pathing details in the sbatch file before submitting the job.