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Quick Start Guides#

High Performance Computing at KU#

The Center for Research Computing has detailed guides to working on their research computing environments, which can be found on their website.

Accessing the cluster#

ssh Log in to a secure shell on a remote computer or server

Log on to the cluster

ssh USERNAME@hpc.crc.ku.edu

Copying files to/from the cluster#

scp Copy files between your computer and the server, or vice versa.

Copy a file from your present working directory on your computer to your home directory on the cluster

scp myfile.txt USERNAME@hpc.crc.ku.edu:/home/USERNAME

Copy a file from your home directory on the cluster to your present working directory on your computer

scp USERNAME@hpc.crc.ku.edu:/home/USERNAME/a_file.txt ./

Nextflow Quick Start#

We have prepared installed programs on the KU computing cluster to assist users in running Nextflow pipelines, which are accessible to users affiliated with the Genomic Data Science Core or with the Center for Genomics. However, Nextflow is intended to make workflows portable and can be used in many environments, and we provide some general guidance for getting started for non-KU users.

KU Genomic Data Science Core users#

Include the following lines with the job submission script to use the pre-built Nextflow modules 

module use --append /panfs/pfs.local/work/sjmac/observer/modules
module load nextflow

NXF_ANSI_SUMMARY=true
NXF_ANSI_LOG=true

An example run script to run the nf-core RNAseq pipeline

#!/bin/bash
#SBATCH --job-name=nf_core_rnaseq
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=<USERNAME>@ku.edu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task 1
#SBATCH --time=24:00:00
#SBATCH --partition=sjmac
#SBATCH --mem=10G
#SBATCH --output=%x_%A.out

module use --append /panfs/pfs.local/work/sjmac/observer/modules
module load nextflow

NXF_ANSI_SUMMARY=true
NXF_ANSI_LOG=true

nextflow run nf-core/rnaseq \
    -c /panfs/pfs.local/work/sjmac/observer/profiles/gdsc.config
    --input sample_sheet.csv \
    --genome BDGP6 \
    --outdir output \
    --aligner star_rsem \
    --pseudo_aligner salmon \
    -resume

KU Center for Genomics users#

Include the following lines with the job submission script to use the pre-built Nextflow modules 

module use --append /panfs/pfs.local/work/kucg/observer/modules
module load nextflow

NXF_ANSI_SUMMARY=true
NXF_ANSI_LOG=true

The GDSC workflows can be downloaded using Nextflow with the following command

An example run script to run the nf-core RNAseq pipeline

#!/bin/bash
#SBATCH --job-name=nf_core_rnaseq
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=<USERNAME>@ku.edu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task 1
#SBATCH --time=24:00:00
#SBATCH --partition=sjmac
#SBATCH --mem=10G
#SBATCH --output=%x_%A.out

module use --append /panfs/pfs.local/work/sjmac/observer/modules
module load nextflow

NXF_ANSI_SUMMARY=true
NXF_ANSI_LOG=true

nextflow run nf-core/rnaseq \
    -c /panfs/pfs.local/work/kucg/observer/profiles/kucg.config
    --input sample_sheet.csv \
    --genome BDGP6 \
    --outdir output \
    --aligner star_rsem \
    --pseudo_aligner salmon \
    -resume

Other users#

  1. Install Nextflow following the directions on the Nextflow website

    • Note: Nextflow can be installed in any location, but for the purposes of this documentation it is assumed to be located in the home directory (e.g. ~/nextflow)

  2. Run a small test job

To test that everything is working correctly, you can run a simple test program with the command:

~/nextflow run hello

If everything is loaded properly, you should output that resembles the following:

N E X T F L O W  ~  version 23.04.3
Launching `https://github.com/nextflow-io/hello` [confident_picasso] DSL2 - revision: 1d71f857bb [master]
executor >  local (4)
[5a/e0c8dc] process > sayHello (2) [100%] 4 of 4 ✔
Hello world!

Bonjour world!

Hola world!

Ciao world!
  1. Download the Nextflow pipeline of interest

Download the nf-core RNAseq pipeline

~/nextflow pull nf-core/rnaseq
  1. Run the Nextflow pipeline of interest

Example run command for nf-core RNAseq pipeline

~/nextflow run nf-core/rnaseq \
    --input sample_sheet.csv \
    --genome BDGP6 \
    --outdir output \
    --aligner star_rsem \
    --psudo_aligner salmon \
    --resume
Last update: January 11, 2024