Running nfcore pipelines on Tufts HPC#

Shirley Li, Bioinformatician, TTS Research Technology xue.li37@tufts.edu

Date: 2024-11-01

You have two options for running the nf-core pipeline on Tufts HPC: through Open OnDemand or the command-line interface.

1. Open Ondemand#

Navigate to Open Ondemand, under Bioinformatics Apps, choose the appropriate application for the pipeline you wish to execute.

By using module avail, you can see the available modules. There are two ways to run the nf-core pipeline via the command-line interface:

Load the necessary modules

module load singularity/3.8.4
module load nf-core/2.13.1

Run the pipeline with this command:

nextflow run nf-core/mag -profile tufts ...

For a comprehensive list of available pipelines, visit the nf-core website. There are currently 107 pipelines available through nf-core.

Load singularity module and the specific pipeline module:

module load singularity/3.8.4
module load nf-core-mag/2.5.4

Execute the pipeline using:

mag ...

Currently, 31 pipelines have been deployed as modules on Tufts HPC for ease of use.