SLURM with Docker

[mizraelson]

Hi, I am trying to create a pipeline so that every process will be sent to SLURM queue and will be run in Docker. (In SLURM script I use #SBATCH --container-image=debian and it works).

What is the proper way to do that in nextflow?

I have tried:

#!/usr/bin/env nextflow

nextflow.enable.dsl=2


process test {
    tag "$pair_id"
	
    queue 'short'
    executor 'slurm'
    memory '20 GB'
    cpus '40'
    clusterOptions '--container-image=debian'
	
    output:
        stdout emit: verbiage
    
    
    """
    echo "Hello world"
    """
}

workflow{

    test()
    test.out.verbiage.view()
}

workflow.onComplete = {
    println "Analysis complete"
}

But it fails with an error:

N E X T F L O W  ~  version 21.10.6
Launching `part2_docker.nf` [loving_koch] - revision: d295bd99dc
executor >  slurm (1)
executor >  slurm (1)
[78/df841e] process > test (null) [100%] 1 of 1, failed: 1 ✘
Error executing process > 'test (null)'

Caused by:
  Process `test (null)` terminated for an unknown reason -- Likely it has been terminated by the external system

Command executed:

  echo "Hello world"

Command exit status:
  -

Command output:
  (empty)

Command wrapper:
  pyxis: importing docker image: debian
  slurmstepd: error: Could not run slurm task_prolog [/opt/aldan3/TaskProlog.sh]: No such file or directory
  slurmstepd: error: Unable to create TMPDIR [/scratch]: Read-only file system
  slurmstepd: error: Setting TMPDIR to /tmp
  touch: cannot touch '.command.begin': No such file or directory
  /var/spool/slurmd/job10077/slurm_script: line 81: .exitcode: No such file or directory

Work dir:
  /home/mizraelson/Tutorial/PART2/work/78/df841e8c0315ccddcc36b2eac994b2

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

What am I doing wrong?