Script Style Guide

Coding style

comments are preceeded by 1 #, Where scripts are organised into sections, section headers are all CAPITALS

Script naming conventions

Job submission scripts to be numbered. Numbers should be sequential even even task aren't necessarily. Job submission scripts that "start" with batch, indicated an array job with some element of parallelisation across samples (not nesseccariy 1 job per sample).

processing scripts not numbered.

Job submission script format

SLURM scheduler

Start with a series of check to confirm variables are as expected.

use dashed line to separate checks from main body

Processing script format

`##

REQUIRES the following variables from config file

REQUIRES the following software

INPUT

OUTPUT

*

(command line) VARIABLES

#-------------------------------#

MAIN ` where MAIN is the code body of the script Start with an initiation statement End with completion statement.