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nf-core/configs: Icahn School of Medicine at Mount Sinai

To use, run the pipeline with -profile mssm. This will download and launch the mssm.config which has been pre-configured with a setup suitable for the Minerva HPC environment.

Running the workflow on the Minerva HPC

The latest version of Nextflow is not installed by default on the cluster. You will need to install it into a directory you have write access to.

The template script below relies on a conda install for Nextflow. Following this conda installation will add the necessary package channels, setup a new env named "nextflow", and install Nextflow.

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda create --name nextflow
conda activate nextflow
conda install nextflow

Master execution script

Nextflow manages each process as a separate job that is submitted to the cluster by using the bsub command. To do so, make a single, master script with a similar structure to the following code, and submit with bsub < my_script.lsf to orchestrate the full slate of tasks in the pipeline.

#!/bin/bash
#BSUB -J <JOB TITLE>
#BSUB -P <PROJECT NAME>
#BSUB -W 144:00
#BSUB -q premium
#BSUB -n 2
#BSUB -u <EMAIL>
#BSUB -o output_%J.stdout
#BSUB -eo error_%J.stderr
#BSUB -L /bin/bash

export http_proxy=http://172.28.7.1:3128
export https_proxy=http://172.28.7.1:3128
export all_proxy=http://172.28.7.1:3128
export no_proxy=localhost,*.chimera.hpc.mssm.edu,172.28.0.0/16

ml java
ml anaconda3
ml singularity

source $CONDA_PREFIX/etc/profile.d/conda.sh
conda init bash
conda activate nextflow

nextflow run <PIPELINE> \
	-w /sc/arion/scratch/$USER \
	-profile mssm \
	-resume