How do you make a Bash script put output files in a specific directory
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!!
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Without seeing your entire script following advice is necessarily generic. In your
bwacommand 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 setout=/path_to_dir_you_wantand then use${out}/actual.bamin your command).