spaceranger_5XFAD.sub

#!/bin/bash

#SBATCH --job-name=sr-5XFAD     ## Name of the job.
#SBATCH -p standard          ## partition/queue name
#SBATCH -A vswarup_lab           ## partition/queue name
#SBATCH --nodes=1            ## (-N) number of nodes to use
#SBATCH --ntasks=1          ## (-n) number of tasks to launch
#SBATCH --cpus-per-task=16    ## number of cores the job needs
#SBATCH --error=slurm-%J.err ## error log file
#SBATCH --mem 64G              ## request 64GB of memory
#SBATCH --array=0-3            ## job array
#SBATCH --time=72:00:00

# set directory for fastqs and images:
fastqs="/dfs7/dfs3/swaruplab/smorabit/data/Visium_Mouse_2021/fastqs/5XFAD_samples/"
image_dir="/dfs7/dfs3/swaruplab/smorabit/data/Visium_Mouse_2021/images/5XFAD_tifs/"
align_dir="/dfs7/dfs3/swaruplab/smorabit/data/Visium_Mouse_2021/images/5XFAD_alignment/"

# list files and get all sample names
fastq_files=($(ls $fastqs))
samples=($(ls $fastqs | cut -d '_' -f 1 | uniq))

# index based on task ID
let index="$SLURM_ARRAY_TASK_ID"

# get sample based on index:
sample=${samples[$index]}

# get the image, slide, and area corresponding to this sample
image_name=$(ls $image_dir | grep $sample)
slide=$(echo $image_name | cut -d '_' -f 2)
area=$(echo $image_name | cut -d '_' -f 3 | cut -d '.' -f 1)

# get the alignment file:
align_name=$(ls $align_dir | grep $sample)

# run spaceranger
transcriptome="/dfs7/dfs3/swaruplab/smorabit/resources/spaceranger_reference/refdata-gex-mm10-2020-A"
~/swaruplab/smorabit/bin/software/spaceranger-1.2.1/spaceranger count --id=$sample \
                       --transcriptome=$transcriptome \
                       --fastqs=$fastqs \
                       --sample=$sample \
                       --colorizedimage=$image_dir$image_name \
                       --slide=$slide \
                       --area=$area \
                       --loupe-alignment=$align_dir$align_name \
                       --localcores=16 \
                       --localmem=64