The Sheffield Bioinformatics Core suggest that you run all of your projects from the parscratch file store but you may choose to run them from elsewhere.
Whichever file store you decide to locate your project root directory in, the assumed project sub-directory structure within this guide is as follows:
/filestore/$USER/
│
└── project_root/
│
├── config
├── params
├── sample_sheet
└── script
This directory tree can be established by running the command shown below. Please ensuring that you change filestore to the actual name of the filestore you wish to locate your project within e.g., parscratch and that you change project_root to the name of the project e.g., 2023_01_01_demo_project
# setup project directory structure
mkdir -p /filestore/$USER/project_root/{config,params,sample_sheet,script}
Many nf-core pipelines require a sample sheet detailing the files you wish to analyse. You can find nf-core pipelines by visiting https://nf-co.re/pipelines. Each pipeline page has more information on how to use the pipeline as well as a full description of sample sheet requirements and formatting.
Your sample sheet should be located inside your sample_sheet sub-directory.
There are two other things you will require to run an nf-core pipeline:
The general launch command in the script template provided here assumes you have configured your specific run using an nf-core pipeline launcher. For example, the launcher for the nf-core/rnaseq pipeline that can be found here. The parameters specified for your run using the launcher should be saved in a file named nf-params.json within the params sub-directory.
To create your run script, navigate to the script sub-directory and run the following:
nano nf_submission.sh
Paste the contents of the template file linked below into the editor ensuring to change the generic information for your own where indicated in the comment lines.
Template run submission script
Now save and exit by typing “Ctrl + O” then “Return” then “Ctrl + X”.