= Run Cellranger-ARC on Cypress =
See [https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/using/mkfastq Generating FASTQs with cellranger-arc mkfastq]. This page to show how to run Cellranger-ARC with [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/cluster-mode the cluster mode] on Cypress.

Example SLURM script:
{{{
#!/bin/bash
#SBATCH --partition=centos7     # Partition
#SBATCH --qos=normal            # Quality of Service
#SBATCH --job-name=mkFASTQ # Job Name
#SBATCH --time=24:00:00 # WallTime
#SBATCH --nodes=1               # Number of Nodes
#SBATCH --ntasks-per-node=1     # Number of tasks (MPI presseces)
#SBATCH --cpus-per-task=20      # Number of processors per task OpenMP threads()
#SBATCH --gres=mic:0            # Number of Co-Processors
#SBATCH --export=ALL
#SBATCH --mem=256000
#SBATCH --mail-type=ALL
#SBATCH --mail-user=YOUR_USER_ID@tulane.edu # YOUR EMAIL ADDRESS


module load cellranger-arc/2.2.0

cellranger-arc mkfastq --id=tiny-bcl-atac \
                 --run=./cellranger-arc-tiny-bcl-atac-1.0.0 \
                 --csv=./cellranger-arc-tiny-bcl-atac-simple-1.0.0.csv \
                 --jobmode=slurm \
                 --localmem=240 \
                 --localcores=20 \
                 --maxjobs=4 \
                 --jobinterval=1000
}}}
With this script, 'cellranger-arc' submits at most 4 sub-jobs. You can set the maximum number of jobs by changing:

{{{
          	 --maxjobs=25 \
}}}