If you want the results to be written to this directory (not to a new directory), comment out ```OUTDIR: /path/to/outdir```
- PATHS_WITH_FILES - directory that can contain subdirectories where the fastq reads are located. You can add several paths by adding ```path2: /path/to/dir``` under ```PATHS_WITH_FILES```. (The line you add has to have indentation)
The script goes through the subdirectories of the directory you choose under ```PATHS_WITH_FILES``` looking for files with **fq.gz** extension.
The script goes through the subdirectories of the directory you choose under ```PATHS_WITH_FILES``` looking for files with fastq extension.
Example: if ```path1: /lustre/nobackup/WUR/ABGC/shared/Chicken/Africa/X201SC20031230-Z01-F006_multipath```, the subdirectory structure could be:
