#!/bin/bash
#SBATCH -p cpu_medium
#SBATCH --job-name=spaceranger_01
#SBATCH --tasks=16
#SBATCH --cpus-per-task=1
#SBATCH --mem=200G
#SBATCH --time=72:00:00
#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=db3562@nyulangone.org

#set path
export PATH=/gpfs/data/yanailab/projects/db3562/10x/spaceranger-1.1.0:$PATH

ulimit -u 40960
spaceranger count --id=OVCAPDX1 \
                --transcriptome=/gpfs/data/yanailab/refs/homo_sapiens/hg38_mm10_10X/hg38_and_mm10 \
                --fastqs=/gpfs/data/yanailab/runs/2021-07-28/Sample_BS12277A/ \
		--sample=BS12277A \
                --image=/gpfs/data/yanailab/projects/db3562/data/PDX/Visium/OVCA/OVCAPDX1/OVCAPDX1.jpg  \
                --loupe-alignment=/gpfs/data/yanailab/projects/db3562/data/PDX/Visium/OVCA/OVCAPDX1/OVCAPDX1.json \
		--slide=V10L27-352 \
                --area=B1 \
		--nosecondary \
