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.
...
| Code Block |
|---|
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:
| Code Block |
|---|
cd ~ |
List the existing files and folders:
| Code Block |
|---|
ls -l |
Let’s create a folder for the workshop
| Code Block |
|---|
mkdir -p $HOME/workshop/sarek |
Get a copy of the scripts to be used in this module
Use the terminal to log into the HPC and Now let’s create a /RNAseq/ folder to run the nf-core/rnaseq pipeline. For example‘scripts’ folder and copy all scripts that we will using in the session:
| Code Block |
|---|
mkdir -p $HOME/workshop/sarek/scripts cp /work/training/sarek/scripts/* $HOME/workshop/sarek/scripts/ ls -l $HOME/workshop/sarek/scripts/ |
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:
| Code Block |
|---|
mkdir -p $HOME/workshop/sarek mkdir $HOME/workshop/sarek/run1_test mkdir $HOME/workshop/sarek/run2_trio mkdir $HOME/workshop/sarek/run3_liver cd $HOME/workshop/sarek |
Lines 1-43: create sub-folders for each exercise
Line 54: change the directory to the folder “run1_test”Line 6: print the current working directory
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.
...
#!/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:
...
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:
...