#! /bin/bash

# This script checks if f is a directory. If it is, f is entered, and MacroBam analysis is carried out in that directory.
# The loop finishes by going back to preceding directory. 
# This allows for MacroBam analysis of all barcode folders with one execution. 
# Pre-requisites: at least about 650 GB free space and MacroBam_v3.2.sh needs to be copied to each folder which is to be analysed.

for f in *;  do 
        if [ -d $f ];  
        then  
            cd -- "$f";  
            echo "Executing script in folder `pwd`"; 
            bash MacroBam_v3.2.sh;
            cd ..; 
        fi;  
    done;