bwa的pbs作业提交脚本

#!/bin/bash
#PBS -N bwa_align
#PBS -l nodes=1:ppn=4
#PBS -l walltime=24:00:00
#PBS -q batch
#PBS -o bwa_align.out
#PBS -e bwa_align.err

# Set the working directory to the directory where the job was submitted
cd $PBS_O_WORKDIR

# Load the necessary modules
module load bwa/0.7.17
module load samtools/1.10

# Define the input and output files
input_file="input.fastq"
output_file="output.sam"

# Define the reference genome file
ref_genome="reference_genome.fa"

# Align the reads to the reference genome using BWA
bwa mem -t 4 $ref_genome $input_file > $output_file

# Convert the SAM file to BAM format and sort it
samtools view -bS $output_file | samtools sort -o output.bam

# Index the sorted BAM file
samtools index output.bam

# Cleanup intermediate files
rm $output_file

echo "BWA alignment and processing finished."