Purdue University

Commands

• cellranger-atac

Module

You can load the modules by:

module load biocontainers
module load cellranger-atac

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Cellranger-atac on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --mem=64G
#SBATCH --job-name=cellranger-atac
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers cellranger-atac

cellranger-atac count --id=sample345 \
                    --reference=refdata-cellranger-arc-GRCh38-2020-A-2.0.0 \
                    --fastqs=runs/HAWT7ADXX/outs/fastq_path \
                    --sample=mysample \
                    --localcores=8 \
                    --localmem=64