Pre-requisites
Nextflow installed → If not see: 1. Getting started with Nextflow Ask for help if you need assistance.
Overview:
Create working directory folders for hands-on training exercises
Copy data and scripts for today’s session
(Optional ) run a test to verify Nextflow is properly installed and to assess the execution of the nf-core/rnaseq pipeline with example data provided by developers.
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Before we start using the HPC, let’s start an interactive session:
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qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=2:mem=8gb |
where:
‘walltime’ is amount of time requested to run the interactive session
‘cpus’ number of CPUs to be used by the interactive session
‘mem’ amount of memory assigned to the interactive session
Create working directories
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cp /work/training/2024/rnaseq/scripts/* $HOME/workshop/2024-2/session4_RNAseq/scripts ls -l $HOME/workshop/2024-2/session4_RNAseq/scripts |
Line 1: Copies all files from /work/datasets/workshop/scripts/ as noted by an asterisk to the newly created folder $HOME/workshop/2024-2/session4_RNAseq/scripts/
Line 2: List the files copied to the ‘script’ folder
Copy public data to working folder
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cp /work/training/2024/rnaseq/data/* $HOME/workshop/2024-2/session4_RNAseq/data/ ls -l $HOME/workshop/2024-2/session4_RNAseq/data |
Line 1: Copies all files from /work/datasets/workshop/scripts/ folder as noted by an asterisk to newly created folder $HOME/workshop/2024-2/session4_RNAseq/data/
Line 2: List the files copied to the ‘data’ folder
(Optional ): 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.
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mkdir -p $HOME/workshop/2024-2/session4_RNAseq/runs/run0_test cd $HOME/workshop/2024-2/session4_RNAseq/runs/run0_test |
Line 1: Create folder using the make directory “mkdir” command. We use the flap -p (parental) to create parental folders if not yet created.
Line 2: Move to the newly created folder.
Copy the launch_nf-core_RNAseq_test.pbs from the ‘scripts’ folder to the “run0_test” current folder
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cp $HOME/workshop/2024-2/session4_RNAseq/scripts/launch_nf-core_RNAseq_test.pbs . |
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cat launch_nf-core_RNAseq_test.pbs |
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#!/bin/bash -l
#PBS -N nfrnaseq_test
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
#work on current directory
cd $PBS_O_WORKDIR
#load java and set up memory settings to run nextflow
module load java
export NXF_OPTS='-Xms1g -Xmx4g'
nextflow run nf-core/rnaseq -r 3.14.0 -profile test,singularity --outdir results
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nextflow command: nextflow run
pipeline name: nf-core/rnaseq
pipeline version (revision): -r 3.14.0
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:
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