Tormesbot

I created tormesbot to assist other microbiologists who are not computer savvy in manipulating the metadata and parsing arguments to a HPC environment.

The script makes the following assumptions:

All files required for the pipeline analysis are in the same folder that you run the tormesbot script from. (fastq.gz for the genome files and .fasta for the reference genome) You have SSH ability to your HPC cluster from the computer you run tormesbot from. Your HPC cluster uses Lmod for loading programs and slurm for HPC queue management.

This script will not work 'as is' for anyone who is not using the HPC cluster at the University of South Australia and will require modifications to where the script connects to.

The script is what I believe is called 'spaghetti code'. It is my first attempt at scripting after picking up Linux about 3 months ago. (big shout out to google and stack overflow)

Of course a massive shout out to the creator of tormes, Narciso M. Quijada who created a brilliant pipeline that even this noob was able to get working with relevant ease. Tormes can be found here: https://github.com/nmquijada/tormes

Feel free to hack and slash the script for your own use!