sam_sort.sh

#!/bin/bash

#SBATCH --job-name=sort_bam # you can give your job a name
#SBATCH --ntasks=24 # the number of processors or tasks
#SBATCH --account=itcga # our account
#SBATCH --reservation=ITCGA2025 # this gives us special access during the workshop
#SBATCH --time=10:00:00 # the maximum time for the job
#SBATCH --mem=32gb # the amount of RAM
#SBATCH --partition=itcga # the specific server in chimera we are using
#SBATCH --error=log/%x-%A.err   # a filename to save error messages into
#SBATCH --output=log/%x-%A.out  # a filename to save any printed output into

module load samtools-1.10-gcc-9.3.0-flukja5

# Define the input directory and output directory
input_dir=$1

# Loop through .bam files in the input directory
for file in "$input_dir"/*.bam; do

 # Extract the base name without the suffix (e.g., "C1_S4_L001")
  base=$(basename "$file" .bam)

  # Sort the BAM file and output to a new sorted BAM file
  samtools sort "$file" -o "$input_dir/${base}_sorted.bam"
done

echo "Finish Run"
echo "End time: $(date)"