How do you make a Bash script put output files in a specific directory

Question

[tmrhyd]

So I have a script for bwa to align a chloroplast to a genome I have.(of a plant) It's a bash script and I have "#SBATCH -o output_file" before the script. I want this output file to go into an already existing directory. How do I do this?

Thank you guys so much!!

[GenoMax]

Without seeing your entire script following advice is necessarily generic. In your bwa command you could add full path before the output file name (e.g. bwa mem genome.fa reads.fastq | samtools sort -o /path_to_directory_you_want/alignment.bam). If you are using private variables then set out=/path_to_dir_you_want and then use ${out}/actual.bam in your command).