bam_to_bigwig.sub

#!/bin/bash
#SBATCH --job-name=bigwig
#SBATCH -p standard
#SBATCH -A vswarup_lab
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --error=slurm-%J.err
#SBATCH --mem 64G
#SBATCH --array=0-108
#SBATCH --time=2:00:00

# activate conda env with sinto + deeptools installed
source ~/.bashrc
conda activate scvi-env
module load samtools

# directory with merged bams
bam_dir="/dfs7/swaruplab/smorabit/collab/woodlab/cocaine_mouse_2021/Nurr2c_vs_GFP/revision/trackhubs/data/merged_bams/"

# directory where we will output bigwigs
output_dir="/dfs7/swaruplab/smorabit/collab/woodlab/cocaine_mouse_2021/Nurr2c_vs_GFP/revision/trackhubs/data/bigwigs/"
# mkdir $output_dir

# select barcodes file based on the task array:
files=($(ls $bam_dir/*.bam))

# get current sample based on the SLURM job ID
let index="$SLURM_ARRAY_TASK_ID"
file=${files[$index]}
echo $file

name=$(basename $file .bam)

# convert bam to bigwig with bamCoverage deeptools function
bamCoverage \
  -b $file \
  -o $output_dir$name.bw \
  -p 32 # number of processors