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Running Sarek on O2

Installation

Assumes you are working on O2. Before installing and running Nextflow the Java module must be loaded.

module load java/jdk-11.0.11

Nextflow

Use the MCMICRO instructions to install Nextflow.

Sarek

nextflow pull nf-core/sarek

Copy o2.config from this repository to your home directory on O2.

Running Sarek

Create a sample sheet CSV file following the nf-core/sarek instructions and save it in your working directory on O2 scratch.

Create a json file with the run parameters using the nf-core Launch pipeline feature and save it as nf-params.json in your working directory on O2 scratch.

Launch the pipeline using the following command:

sbatch run_sarek.sh

To resume a previously launched pipeline:

sbatch run_sarek.sh -resume