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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 - those that did not attend Session 3) run a test to verify Nextflow is properly installed and to test 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:
| Code Block |
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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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| Code Block |
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cp /work/training/2024/rnaseq/scripts/* $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/
Copy public data to your $HOME
| Code Block |
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cp /work/training/2024/rnaseq/data/* $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/
TBA
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| title | Solution |
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Create a folder for running the nf-RNA-seq pipeline
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mkdir -p $HOME/workshop/2024/rnaseq/runs mkdir $HOME/workshop/2024/rnaseq/runs/run1_test mkdir $HOME/workshop/2024/rnaseq/runs/run2_QC mkdir $HOME/workshop/2024/rnaseq/runs/run3_RNAseq cd $HOME/workshop/2024/rnaseq/runs |
Lines 1-4: create sub-folders for each exercise
Line 5: change the directory to the folder “run1_test”
Line 6: print the current working directory
(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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#!/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: -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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