Purdue University

Commands

• check_modules.py
• compile_stan_model.py
• consensus.py
• renamer.py
• retag.py
• shared_samples.py
• souporcell.py
• souporcell_pipeline.py

Module

You can load the modules by:

module load biocontainers
module load souporcell

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 souporcell on our clusters:

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

module --force purge
ml biocontainers souporcell

souporcell_pipeline.py -i A.merged.bam \
    -b GSM2560245_barcodes.tsv \
    -f refdata-cellranger-GRCh38-3.0.0/fasta/genome.fa \
    -t 8 -o demux_data_test -k 4