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 |
|---|
mkdir -p $HOME/workshop/sarek/scripts cp /work/training/sarek/scripts/* $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
...
| Code Block |
|---|
mkdir $HOME/workshop/sarek/run1_test mkdir $HOME/workshop/sarek/run2_trio mkdir $HOME/workshop/sarek/run3_liver cd $HOME/workshop/sarek |
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_RNAseqsarek_test.pbs to the working directory
...
#!/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:
...