bw_and_bb_to_plain.sh

#!/bin/bash

# Paths to the conversion tools
BWTW_TOOL="../Packages/bigWigToWig"
BBTB_TOOL="../Packages/bigBedToBed"

parentDir="/data/user/${USER}/T2T/RawData"

# Find all subdirectories in the parent directory
for dataDir in ${parentDir}/*/; do
    # Remove trailing slash for consistency in file naming
    dataDir=${dataDir%/}

    # Convert BigWig files to Wig
    for file in ${dataDir}/*.bw; do
        jobScript="${dataDir}/convert_${file##*/}.sh"
        cat > ${jobScript} << EOF
#!/bin/bash
#SBATCH --job-name=convertBW2Wig
#SBATCH --output=convertBW2Wig_%j.out
#SBATCH --time=01:00:00
#SBATCH --mem=4G
#SBATCH --cpus-per-task=1

${BWTW_TOOL} "$file" "${file%.bw}.wig"
EOF
   	sbatch ${jobScript}
    done

    # Convert BigBed files to Bed
    for file in ${dataDir}/*.bb; do
        jobScript="${dataDir}/convert_${file##*/}.sh"
        cat > ${jobScript} << EOF
#!/bin/bash
#SBATCH --job-name=convertBB2Bed
#SBATCH --output=convertBB2Bed_%j.out
#SBATCH --time=01:00:00
#SBATCH --mem=4G
#SBATCH --cpus-per-task=1

${BBTB_TOOL} "$file" "${file%.bb}.bed"
EOF
   	sbatch ${jobScript}
    done
done