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For a more comprehensive nextflow.config template for usage at Pawsey, see Nextflow.

Alternative solution

In the sbatch job script, add the line unset SBATCH_EXPORT before running Nextflow. The below is an example of submitting a job script for a Nextflow main.nf script to run:

#!/bin/bash -l

#SBATCH --account=$PAWSEY_PROJECT
#SBATCH --partition=workq
#SBATCH --job-name=nextflow-example
#SBATCH --time=1:00:00
#SBATCH --export=NONE

unset SBATCH_EXPORT

module load nextflow
module load singularity

nextflow run main.nf -profile zeus

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