Exercise 1 - sarek test

Prior running the nf-core/sarek pipeline with real data, we will first run a test with sample data to make sure the pipeline runs properly.

Work in the HPC

Work in the HPC

Before we start using the HPC, let’s start an interactive session:

qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=1:mem=4gb

You should be in your home directory, if unsure you can run the following command:

cd ~

List the existing files and folders:

ls -l

Let’s create a folder for the workshop

Get a copy of the scripts to be used in this module

Now let’s create a ‘scripts’ folder and copy all scripts that we will using in the session:

Line 1: The -p indicates create 'parental directories as required. Thus the line 1 command creates both /workshop/ and the subfolder /workshop/sarek/scripts/
Line 2: Copies all files from /work/datasets/workshop/scripts/ as noted by an asterisk to the newly created folder $HOME/workshop/sarek/scripts/

Create folders for running the nf-core/sarek pipeline

Let’s create an “RNAseq” folder to run the nf-core/rnaseq pipeline and move into it. For example:

Lines 1-3: create sub-folders for each exercise
Line 4: change the directory to the folder “run1_test”

Exercise 1: Running a test with nf-core sample data

First, let’s assess the execution of the nf-core/rnaseq pipeline by running a test using sample data.

Copy the launch_nf-core_sarek_test.pbs to the working directory

View the content of the script as follows:

#!/bin/bash -l #PBS -N nfsarek_run1_test #PBS -l walltime=48:00:00 #PBS -l select=1:ncpus=1:mem=5gb cd $PBS_O_WORKDIR NXF_OPTS='-Xms1g -Xmx4g' module load java #specify the nextflow version to use to run the workflow export NXF_VER=23.10.1 #run the sarek pipeline nextflow run nf-core/sarek \ -r 3.3.2 \ -profile test,singularity \ --outdir ./results

#!/bin/bash -l #PBS -N nfsarek_run1_test #PBS -l walltime=48:00:00 #PBS -l select=1:ncpus=1:mem=5gb cd $PBS_O_WORKDIR NXF_OPTS='-Xms1g -Xmx4g' module load java #specify the nextflow version to use to run the workflow export NXF_VER=23.10.1 #run the sarek pipeline nextflow run nf-core/sarek \ -r 3.3.2 \ -profile test,singularity \ --outdir ./results

nextflow command: nextflow run
pipeline name: nf-core/sarek
pipeline version: -r 3.3.2
container type and sample data: -profile test,singularity
output directory: --outdir results

Submitting the job

Submit the test job to the HPC cluster as follows:

Monitoring the Run

Outputs:

The test run should take about ~14 min to complete. Find run outputs in the “results” folder:

Once the pipeline has finished running - Assess the QC report:

NOTE: To proceed, you need to be on QUT’s WiFi network or signed via VPN.

To browse the working folder in the HPC type in the file finder:

Windows PC

Mac

Evaluate the nucleotide distributions in the 5'-end and 3'-end of the sequenced reads (Read1 and Read2). Look into the “MultiQC” folder and open the provided HTML report.