Project workspaces

We use a standardized directory structure, called workspace, where we run and store all our experiments for a given project.

Create a workspace


The system will ask you a few questions and then create the structure for you.

Directory structure

├── conf
├── data
├── logs
├── resources
├── results

The conf directory contains Nextflow config files to run a pipeline; you must define the parameters of each experiment in a config file rather than passing them on the command line.

The data directory contains data to be processed by a pipeline. This directory usually contains the raw data (e.g. data from sequencing experiments). You should take some time to organize it in a meaningful and consistent way.

The resources directory contains data retrieved from external sources/repositories, like annotation files (e.g. genome GFF) or geneset GMT files.

The logs directory contains the log of each pipeline run.

The results directory contains the result of experiments. You should take some time to organize it in a meaningful and consistent way. It is strongly recommended to results in a directory named like 2022-01-01-my-first-test.

The file contains a description of the project and how the data and results folder are organized.

Naming guidelines

The team MUST use the Google naming guidelines, specifically:

  • Make file and directory names lowercase.
  • Separate words with hyphens, not underscores.
  • Use only standard ASCII alphanumeric characters in file and directory names.

IMPORTANT: Raw data or external resources are allowed to keep their naming standard if it makes them easier to identify.