From the gopeaks documentation:

GoPeaks is a peak caller designed for CUT&TAG/CUT&RUN sequencing data. GoPeaks by default works best with narrow peaks such as H3K4me3 and transcription factors. However, broad epigenetic marks like H3K27Ac/H3K4me1 require different the step, slide, and minwidth parameters.

References:

• W. M. Yashar et al GoPeaks: histone modification peak calling for CUT&Tag Genome Biol. 2022 Jul 4;23(1):14

• Gopeaks on GitHub

• Module Name: gopeaks (see the modules page for more information)
• gopeaks can take advantage of more than one CPU though it does not appear to be configurable via well known environment variables or command line arguments. Based on testing an allocation of 4-6 CPUs is appropriate
• Example files in $GOPEAKS_TEST_DATA
• Reference data in /fdb/gopeaks/

Allocate an interactive session and run the program.
Sample session (user input in bold) for running the peakfinder with a control and generating a summary plot with deeptools:

[user@biowulf]$ sinteractive --cpus-per-task=6 --gres=lscratch:20 --mem=30g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load gopeaks

[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 ~]$ cp $GOPEAKS_TEST_DATA/* .
[user@cn3144 ~]$ ls -lh

[user@cn3144 ~]$ gopeaks -b GSE190793_Kasumi_cutrun.bam -c GSE190793_Kasumi_IgG.bam --mdist 1000 --prefix Kasumi_cnr
Reading chromsizes from bam header...
nTests: 431593
nzSignals: 4.5114732e+07
nzBins: 8298786
n: 7.566515e+06
p: 7.184688090883924e-07
mu: 5.962418894299423
var: 5.962414610487421

[user@cn3144 ~]$ cat Kasumi_cnr_gopeaks.json
{
        "gopeaks_version": "1.0.0",
        "date": "2023-05-12 12:40:59 PM",
        "elapsed": "7m19.045741504s",
        "prefix": "Kasumi_cnr",
        "command": "gopeaks -b GSE190793_Kasumi_cutrun.bam -c GSE190793_Kasumi_IgG.bam --mdist 1000 --verbose --prefix=Kasumi_cnr",
        "peak_counts": 29393
}

[user@cn3144 ~]$ # create a summary graph for peaks centered on the middle of the peak interval +- 1000
[user@cn3144 ~]$ # i.e. not gene annotation

[user@cn3144 ~]$ module load deeptools
[user@cn3144 ~]$ bamCoverage -p6 -b GSE190793_Kasumi_cutrun.bam -o GSE190793_Kasumi_cutrun.bw
[user@cn3144 ~]$ bamCoverage -p6 -b GSE190793_Kasumi_IgG.bam -o GSE190793_Kasumi_IgG.bw
[user@cn3144 ~]$ computeMatrix reference-point -R Kasumi_cnr_peaks.bed -a 1000 -b 1000 --referencePoint center \
                    -S GSE190793_Kasumi_cutrun.bw GSE190793_Kasumi_IgG.bw \
                    --sortRegions descend --samplesLabel 'Cut&Run' 'IgG' -p6 -o cutrun_matrix
[user@cn3144 ~]$ plotHeatmap -m cutrun_matrix -o cutrun.png --averageTypeSummaryPlot mean --colorMap GnBu
[user@cn3144 ~]$ cp Kasumi_cnr_* *.bw cutrun.png /data/$USER/my_working_directory

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. gopeaks.sh). For example:

#!/bin/bash
set -e
module load gopeaks/1.0.0
cp $GOPEAKS_TEST_DATA/* .
gopeaks -b GSE190793_Kasumi_cutrun.bam -c GSE190793_Kasumi_IgG.bam --mdist 1000 --prefix Kasumi_cnr

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=30g gopeaks.sh

Create a swarmfile (e.g. gopeaks.swarm). For example:

gopeaks -b replicate1.bam -c control.bam --mdist 1000 --prefix replicate1_gopeaks
gopeaks -b replicate2.bam -c control.bam --mdist 1000 --prefix replicate2_gopeaks

Submit this job using the swarm command.

swarm -f gopeaks.swarm -g 30 -t 6 --module gopeaks