how to set tmp disk variable on nextflow

Question

I want to add the tmp disk value to my nextflow process.

CPU and memory requirements are setup, but how can I add the tmp disk value? The data is important for the scheduler (slurm) to select a suitable node.

The nextflow process header cloud be:

process TEST {
  echo true
  cpus '8'
  memory '40 GB'
  script:
    """
    """
}

This value is called in slurm tmp disk, viewable with squeue -o "%C %m %d", column MIN_TMP_DISK.

If any information is missing, please let me know.

Thanks

Steve Steve · Accepted Answer · 2022-05-11T01:31:10

You can use the clusterOptions process directive with the SLURM executor. From the sbatch docs, it looks like you are looking for the --tmp option:

--tmp=[units]

Specify a minimum amount of temporary disk space per node. Default units are megabytes. Different units can be specified using the suffix [K|M|G|T].

For example:

process TEST {

    debug true

    clusterOptions '--tmp=1T'

    cpus 8
    memory 40.GB

    """
    echo "Hello world"
    """
}

how to set tmp disk variable on nextflow

1 Answers