snaptools is a python application to work with snap (Single Nucleus Accessibility Profile) files. From the authors:

A snap file is a hierarchically structured hdf5 file that is specially designed for storing single nucleus ATAC-seq datasets. A snap file (version 4) contains the following sessions: header (HD), cell-by-bin accessibility matrix (AM), cell-by-peak matrix (PM), cell-by-gene matrix (GM), barcode (BD) and fragment (FM).

• snaptools github

• Module Name: snaptools (see the modules page for more information)
• Multithreaded application. Please request appropriate number of CPUs to match the threads.
• Example files is in $SNAPTOOLS_TEST_DATA
• snaptools can use aligners like bwa. Load these modules as needed.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --gres=lscratach:5 --cpus-per-task=4 --mem=8G
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 snaptools bwa

[user@cn3144 ~]$ tar -zxf $SNAPTOOLS_TEST_DATA/snaptools_test.tar.gz

[user@cn3144 ~]$ gunzip mm10.fa.gz

[user@cn3144 ~]$ snaptools index-genome
                            --input-fasta=mm10.fa \
                            --output-prefix=mm10. \ sdx
                            --aligner=bwa \
                            --num-threads=4

[user@cn3144 ~]$ snaptools align-paired-end
                            --input-reference=mm10.fa \
                            --input-fastq1=demo.R1.fastq.gz \
                            --input-fastq2=demo.R2.fastq.gz \
                            --output-bam=demo.bam \
                            --aligner=bwa \
                            --read-fastq-command=zcat \
                            --min-cov=0 \
                            --num-threads=4 \
                            --if-sort=True \
                            --tmp-folder=/lscratch/$SLURM_JOB_ID \
                            --overwrite=TRUE

[user@cn3144 ~]$ snaptools snap-pre  \
                            --input-file=demo.bam  \
                            --output-snap=demo.snap  \
                            --genome-name=mm10  \
                            --genome-size=mm10.chrom.size  \
                            --min-mapq=30  \
                            --min-flen=0  \
                            --max-flen=1000  \
                            --keep-chrm=TRUE  \
                            --keep-single=TRUE  \
                            --keep-secondary=False  \
                            --overwrite=True  \
                            --max-num=1000000  \
                            --min-cov=100  \
                            --verbose=True

[user@cn3144 ~]$ $ snaptools snap-add-bmat  \
                            --snap-file=demo.snap  \
                            --bin-size-list 5000 10000  \
                            --verbose=True

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

[user@biowulf ~]$

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

#!/bin/bash
set -e
module load snaptools
snaptools snap-pre --input-file=example.bam --genome-name=refgenome --genome-size=refgenome.size --output=example.snap

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] snaptools.sh

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

snaptools snap-add-bmat --snap-file=example1.snap
snaptools snap-add-bmat --snap-file=example2.snap
snaptools snap-add-bmat --snap-file=example3.snap
snaptools snap-add-bmat --snap-file=example4.snap

Submit this job using the swarm command.

swarm -f snaptools.swarm [-g #] [-t #] --module snaptools