Nextflow

Available versions of Nextflow:

Example script slurm-nextflow-chipseq.sh to run nf-core/chipseq on 1 node of the cpu partition using 4 cores and at most 8 GB of memory:

slurm-sratoolkit.sh

#!/bin/bash --login
#SBATCH --job-name=nextflow_chipseq
#SBATCH --output=%x.%j.out
#SBATCH --error=%x.%j.err
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=8G
#SBATCH --partition=cpu
#SBATCH --qos=cpu
#SBATCH --time=0-03:00:00
##SBATCH --account=<account>
 
shopt -q login_shell || exit 1
 
module load nextflow/26.04.6
 
# chipseq
nextflow run nf-core/chipseq \
    -r 2.0.0 \
    -profile test,singularity \
    -with-singularity "$NFX_CONTAINER" \
    --outdir "${SLURM_JOB_NAME}.${SLURM_JOB_ID}"

In the event of errors occurring only with version 26.04.6 and the nf-core/sarek pipeline, it may be necessary to define the following environment variable:

export NXF_SYNTAX_PARSER="v1"