mcmicro-nf: Nextflow prototype for mcmicro

Prerequisites: Java (v8 or later), MATLAB, Docker (if running locally)

Setup

1. Install Nextflow: curl -s https://get.nextflow.io | bash
2. Pull individual modules: nextflow run ArtemSokolov/mcmicro-nf/setup.nf
3. Get model files from Clarence

Running the pipeline

Local: nextflow run ArtemSokolov/mcmicro-nf --in path/to/exemplar002

On O2:

• module load {gcc, ashlar, matlab}
• nextflow run ArtemSokolov/mcmicro-nf --in test/exemplar-002/ --tools /n/groups/lsp/mcmicro/ -profile O2