unable to run script with LSF executor - error for project

[complexgenome]

Hi,
I'm new to nextflow and first time setting up the config file for an executor. I'm on a LSF system. When I request an interactive node I use following command:

bsub -L /bin/bash -Ip -n 2 -P acc_pareks02a -q premium -R rusage[mem=80GB] -R span[hosts=1] -W 56:00 /bin/bash

That is: two CPUs, project/lab - pareks02a queue premium, memory, node using hosts=1 and walltime.
In the nextflow.config I provide following:

profiles {
	minerva {
		process.executor = 'LSF'
		process.queue = 'premium'
        process.memory = '50GB'
		process.cpus = 2
		process.time = '40 h'
		clusterOptions = { " -P acc_pareks02a "}
	}
}

I use clusterOptions to mention the project for internal settings of the cluster.

I run as: nextflow run main.nf -profile minerva
It errors out as:

Caused by:
  Failed to submit process to grid scheduler for execution
Command executed:
  bsub
Command exit status:
  255
Command output:
 Project name must be specified using bsub -P.

If I look at .command.run file I see:

#!/bin/bash
#BSUB -o /sc/arion/projects/pareks02a/sanjeev/nextflow_pipeline/scripts_pipeline/test_pipeline_screen/work/8f/71f5163cd7d8c8c19eee9545c40492/.command.log
#BSUB -q premium
#BSUB -n 2
#BSUB -R "span[hosts=1]"
#BSUB -W 40:00
#BSUB -M 25600
#BSUB -R "select[mem>=51200] rusage[mem=51200]"
#BSUB -J nf-FASTP_(1)
NEXTFLOW TASK: FASTP (1)
set -e
set -u
NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x
NXF_ENTRY=${1:-nxf_main}

How do I proceed or provide necessary flag information in the nextflow.config file to incorporate -P flag?

[bentsherman]

Use the clusterOptions directive

[complexgenome]

Hi @bentsherman Thanks for your reply.
In the code above, I used clusterOptions I've tried removing {} but didn't work, also used single quote but no success.

[bentsherman]

It is a process directive so should be process.clusterOptions. Also don't think you need the curly braces here since there is no variable interpolation

[complexgenome]

@bentsherman Great, it works now. Thank you 🙏
One last question - Would each process be submitted as a job? For instance, process1 is submitted successfully . Process2 takes input as output of process1. Would process2 be also submitted as an independent job?

[bentsherman]

Yes exactly