NF-Core @ HPC

Executors
SLURM custom config

This is part 3 of 14 of a Introduction to NextFlow.

Executors

A key feature of Nextflow is the ability to decouple the workflow implementation from the actual execution platform.
This allows deployment of a workflow on any execution platform supported by Nextflow.

drawing

The executor defines the underlying system where processes are executed. By default, a process uses the executor defined globally in the nextflow.config file.
The process.executor directive allows you to configure which executor should be used by the process, overriding the default configuration.

See the full list of executors here.

SLURM custom config

Log in to the HPC cluster and request an interactive node.
Navigate to your nextflow_tutorial directory and make sure you have downloaded the nf-core/viralintegration pipeline (nf-core download nf-core/viralintegration -r 0.1.0)

cd /workspace/nextflow_tutorial/nf-core-viralintegration-0.1.0/workflow/

Let’s create a nfcore_custom_config profile to submit jobs to an HPC cluster that uses the slurm scheduler.

mkdir conf/nf-core-slurm
nano conf/nf-core-slurm/nfcore_custom.config

Copy and paste the following into the nfcore_custom.config file and save on exit.

/*
========================================================================================
    NF-CORE Custom Config File
========================================================================================
    Default config options for HPC compute environments
----------------------------------------------------------------------------------------
*/

//Profile config names for nf-core/configs

params {

  config_profile_description = ''
  config_profile_contact     = ''
  config_profile_url         = ''

  // Output options
  outdir                     = "results"
}

/*
========================================================================================
    Nextflow Metrics & Reports
========================================================================================
*/

timeline {
  enabled = true
  file    = "${params.outdir}/timeline.html"
}

report {
  enabled = true
  file    = "${params.outdir}/report.html"
}
trace {
  enabled = true
  fields  = 'task_id,name,status,exit,realtime,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar'
  file    = "${params.outdir}/trace.txt"
}

/*
========================================================================================
    Base Executor config
========================================================================================
*/

executor {
  queueSize = 2
}

/*
========================================================================================
    Profiles - slurm,singularity,conda,docker
========================================================================================
*/

profiles {
  slurm {
    process {
      executor     = 'slurm'
      queue        = ''
    }
    executor {
      queueSize    = 100
      pollInterval = '15 sec'
    }
  }

  singularity {
    singularity.enabled = true
  }

  conda {
    conda.enabled = true
  }

  docker {
    docker.enabled = true
  }

}

Now run the pipeline with the following options to submit the Nextflow job to the cluster.

nextflow run main.nf --custom_config_base conf/nf-core-slurm -profile test,docker --outdir results

You should see output similar to below in the directory results-slurm.
Notice the change of executor > slurm. Nextflow will now handle the submission and execution of the rest of the jobs on the cluster.

Executors

SLURM custom config

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