Introduction

Overview

Questions

• What are the FAIR research principles?
• How do FAIR principles apply to software?
• How does folder organisation help me?

Objectives

• Explain the FAIR research principles in the context of research software
• Explain how file management helps in being FAIR
• Understand elements of good naming strategy

FAIR principles

FAIR stands for Findable, Accessible, Interoperable, and Reusable and comprises a set of principles designed to increase the visibility and usefulness of your research to others. FAIR principles have been applied for software, here is a brief concept translation:

Findable

• Create a description of your software to make it discoverable by search engines and other search tools
• Use a unique and persistent identifier (DOI) for your software (e.g. by depositing your code on Zenodo, OSF, GitHub)

Accessible

• The code and its description (metadata) has to be available even when the software is no longer actively developed (this includes earlier versions of the software)

Interoperable

• Use community-agreed standard formats for inputs and outputs of your software and its metadata

Reusable

• Document your software (including its functionality, how to install and run it) so it is both usable (can be executed) and reusable (can be understood, modified, built upon, or incorporated into other software)
• Give a licence to your software clearly stating how it can be reused

Task 1.1

Grid with the characteristics of: Reproducible; same data, same analysis. Replicable; different data, same analysis. Robust; same data, different analysis. And generalisable; different data, different analysis; Research

The Turing Way project illustration by Scriberia. Used under a CC-BY 4.0 licence. DOI: 10.5281/zenodo.3332807.

Join Menti: https://www.menti.com/alg8a76zkfgp

Menti

File Naming

There is no single way to manage file naming, but consistency is key. Here’s a couple of options, and ways you can combine approaches:

Case Convention	Example
Pascal Case	PascalCase
Camel Case	camelCase
Snake Case	snake_case
Kebab Case	kebab-case
Flat Case	flatcase
Upper Flat Case	UPPERFLATCASE
Pascal Snake Case	Pascal_Snake_Case
Camel Snake Case	camel_Snake_Case
Screaming Snake Case	SCREAMING_SNAKE_CASE

It’s good practice to mention your file naming convention in your data management plan and/or meta data.

1. Choose a convention and apply it consistently
2. Use descriptive names
3. Optional: Tap into default ordering
4. Optional: Build file naming in your workflow

Task 1.2

Before we dive into the details, let’s look at some examples of file names, and come up with suggestions to improve clarity and functionality.

🔨 Needs work	✔️ Suggestion
School123 Period1.RDS
period1_school123_A_ITER2_CONVERGED_SIM.RDS
school123_period1_I_goodness_fit.png

Show me the solution

🔨 Needs Edits	✔️ Suggestion
School123 Period1.RDS	school123_period1.RDS
period1_school123_A_ITER2_CONVERGED_SIM.RDS	school123_period1_A_ITER2_CONVERGED_SIM.RDS
school123_period1_I_goodness_fit.png	school123_period1_I_gof.png

Default ordering

To create a default ordering, we can add a number or date at the beginning of file names. This keeps our files sorted in ascending order based on file versions or in chronological order. If your file name starts with a number, we recommend left padding them with zeros, because your computer will order 003 < 004 < 020 < 100 as opposed to 100 < 20 < 3 < 4. If you need to re-order your files at a later point, you may be tempted to re-name all of your files. It is best to use a template from the start to avoid running into this mess.

There are certain conventions that apply to file naming, ex. if you need to use a date then file names can start with year-month-day (for example 2020-02-21). We recommend using something like the ISO 8601 standard: YYYY-MM-DD for dates.

Dynamically generated

Output in multiple forms can be generated as part of running a computational pipeline. Result files can contain a key identifier or label, depending on your unit of analysis. Workflow managers offer important scaffolding to support how you track the flows of inputs and outputs across multiple stages of a pipeline. The identifier may well be a pseudonym if your project works with confidential data. We can come back to this to see how we can assign handy process labels in our workflow with base functions like paste0() in R statistical software. This way we can concatenate literal words or values with ones that depend on the input flowing into a process.

Adapting a Workflow

A repository (or a “repo”) is a storage location for your research project. A repository can contain a range of digital objects and can be used to store your project by using online platforms such as GitHub. The aim of a repository is to organise your project in such a way that is both accessible to others and efficient to use.

File management system

So far, we saw the key documents that one should add when starting or setting up a project repository. If you are following along, navigate to repo-boilerplate.

Example for a Research Project

A good way to map the organisation of folders within your directory is using a file tree.

Task 1.3

Here are some suggestions on the files and folders your workflow should have, you can download the template for the folder here:

Project folder
└── 📁workflow                <- Main workflow directory
  └── 📁apptainer          <- Container definitions for Apptainer (formerly Singularity)
  └── 📁bin                 <- Executable scripts used in the workflow, ex. in R these would be functions
  └── 📁conf               <- Configuration files for different execution environments
  └── 📁data               <- Input data files for the workflow
  └── 📁docker             <- Docker container definition and dependencies
  └── 📁docs               <- Documentation, reports, and visualizations
  └── 📁modules            <- Nextflow modules for different analysis steps
  └── 📁params             <- Parameter files for the workflow
  └── 📁templates          <- Template scripts used in the workflow
  └── .dockerignore        <- Files to exclude from Docker builds
  └── .gitignore           <- Files to exclude from Git version control
  └── main.nf              <- Main Nextflow workflow definition
  └── nextflow.config      <- Main Nextflow configuration
  └── params.config        <- Parameter configuration
  └── README.md            <- Project documentation

Show me the solution

Step 1: Follow the link to repo-boilerplate to navigate to the code repository.

Step 2: Click on the code tab to download the folders for the workflow.

Workflow manager template folder build your own workflow

Alternatively, you can use git to download the code for the specific branch, with the following code:

BASH

git clone -b repo-boilerplate --single-branch https://github.com/omiridoue/sgsss-workflow.git

Example repositories

• Nextflow repository

Key Points

• Name your files consistently
• Keep it short but descriptive
• Share/establish a naming convention when working with collaborators
• Consider generating output file names dynamically
• Avoid special characters or spaces to keep it machine-compatible
• Use capitals or underscores to keep it human-readable
• Use consistent date formatting, for example ISO 8601: YYYY-MM-DD to maintain default order
• Include a version number when applicable
• Record a naming convention in your data management plan