how to redirect the output file of a bash script to a desired folder - linux

Question

Hello I'm running this bash script here and the command "bwa index .." will generate several files, and this command doesn't have the "-o" flag for specifying output path. I want to redirect these files into a new folder. I've searched online and all the answers I came across are redirecting files generated to a specific file name, but how to generally just redirect the output files into a new folder? Thanks very much!
#!/bin/bash
### qsub file.name to run from anywhere
### first step of BMW, making indexed fasta file
#PBS -N bwa_index
#PBS -S /bin/bash
#PBS -l walltime=24:00:00
#PBS -l nodes=1:ppn=8
#PBS -l mem=64gb
#PBS -o /gpfs/data/mcnerney-lab/liuweihan/chip_seq/becker_lab/bwa_index.out
#PBS -e /gpfs/data/mcnerney-lab/liuweihan/chip_seq/becker_lab/bwa_index.err
date
module load gcc/6.2.0
module load bwa/0.7.17
bwa index -p mm10_bwa_idx -a bwtsw /gpfs/data/mcnerney-lab/liuweihan/chip_seq/becker_lab/mm10.fa
date
echo END

Answer 1

You can change to the target directory and then run the bwa command. Using pushd and popd will ensure that rest of the script runs in correct directory.
pushd some_directory
bwa index -p mm10_bwa_idx -a bwtsw /gpfs/data/mcnerney-lab/liuweihan/chip_seq/becker_lab/mm10.fa
popd

Answer 2

First
You can define a variable and use it in your script.
Second
You can pass arguments to your script and capture them via $1, $2, $3 and so on.
Third if you wanted to be fully dynamic by using option ( e.g. --output | -o ) you can use a simple parse as bellow:
#!/bin/bash
################################################################################
# main flags, both longs and shorts
################################################################################
ARGS=`getopt -o "o::" -l "output:" -- "$#"`
eval set -- "$ARGS"
declare -A _output;
_output['flag']=0;
_output['path']=0;
################################################################################
# extract options and their arguments into variables.
################################################################################
while true ; do
case "$1" in
-o | --output )
_output['flag']=1;
_output['path']=$2;
shift 2;
;;
--)
shift;
break;
;;
* )
echo "Internal error!" ; exit 1
;;
esac
done
echo "output: ${_output['path']}";
And usage is super simple, you can use --output <YOUR-PATH> or -o <YOUR-PATH>
# test
./cli.sh --output /path/to/dir
output: /path/to/dir
./cli.sh -o /path/to/dir
output: /path/to/dir