General Conventions

Directory structure

The scripts follow a standardised directory structure so that scripts are generalisable. This is in the format:

Config file

As far as possible, parameters and variables should be defined in config files, that processing scripts call. We want to limit how much these need to be edited. Using the standard file structure for data, bash scripts take advantage of a standard config file named config.txt, located in the config folder. The config file needs a "local"/command line variable with the project folder name to be declared prior to using the config file.

The format of the config file is

## Data filepaths
## Reference data filepaths
## Software/script filepaths
## conda filepaths
## parameters

Some modalities also have an r config file, config.r, this contains default parameters that will be used if no alternatives are provided.

Where R parameters are likely to be changed by users, those scripts will have specific configs, with distinct names. These need to be specified in the README and a description of how to populate. If a user wants to run their own parameters, they can provide an additional config file which will override the default parameters.

Messages

All updates/progress messages derived from processing scripts rather than job submission. Job submission scripts might want time stamps at start and end to set processing time.

Sample sheets

All* modalities expect a sample sheet of a specified format (see individual wikis for details). This can be used to automate the scripts and make them more generalisable...