#!/bin/bash

# Run the pipeline
srun -c 120 --mem 200G --time 30-0 -p amd_256M python ./align.py \
    ../genome/mm10.fa \
    ../annotation/mm10.ncbiRefSeq.gtf \
    ../data \
    --threads-per-star 20 \
    --total-cpus 120 \
    --output-dir ../align \
    --star-path /beegfs/datasets/home/tsoies/miniforge3/envs/rnaseq/bin/STAR