==== Nextflow ====

[[https://www.nextflow.io/|Nextflow]]


Available versions of Nextflow:

^ Nextflow  ^
| 23.10.0   |
| 24.04.4   |
| 25.04.2   |
| 26.04.6   |

=== Job 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:

<code bash 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 "$NXF_CONTAINER" \
    --outdir "${SLURM_JOB_NAME}.${SLURM_JOB_ID}"
</code>

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:

<code>
export NXF_SYNTAX_PARSER="v1"
</code>