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=8gb4gb |
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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mkdir -p $HOME/workshop/2024-2/session4_RNAseq mkdir -p $HOME/workshop/2024-2/session4_RNAseq/scripts mkdir -p $HOME/workshop/2024-2/session4_RNAseq/scripts/local mkdir -p $HOME/workshop/2024-2/session4_RNAseq/data mkdir -p $HOME/workshop/2024-2/session4_RNAseq/data/mouse mkdir -p $HOME/workshop/2024-2/session4_RNAseq/data/human mkdir -p $HOME/workshop/2024-2/session4_RNAseq/data/mydata mkdir -p $HOME/workshop/2024-2/session4_RNAseq/runs mkdir -p $HOME/workshop/2024-2/session4_RNAseq/runs/run1_QC mkdir -p $HOME/workshop/2024-2/session4_RNAseq/runs/run2_RNAseq mkdir -p $HOME/workshop/2024-2/session4_RNAseq/runs/run3_RNAseq_T2T |
The above code creates the following folder structure will look like this (do not run the block of code below):
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Get a copy of the scripts
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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 cp /work/training/2024/rnaseq/scripts/local/* $HOME/workshop/2024-2/session4_RNAseq/scripts/local ls -l $HOME/workshop/2024-2/session4_RNAseq/scripts/local |
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
Line 3: Copies all files from /work/datasets/workshop/scripts/local as noted by an asterisk to the newly created folder $HOME/workshop/2024-2/session4_RNAseq/scripts/local
Line 4: List the files copied to the ‘script’ folder
Copy public data to working folder
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cp /work/training/2024/rnaseq/data/mouse/* $HOME/workshop/2024-2/session4_RNAseq/data/mouse
ls -l $HOME/workshop/2024-2/session4_RNAseq/data/mouse |
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cp /work |
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/training/2024/rnaseq/data/human/* $HOME/workshop/2024-2/session4_RNAseq/data/human ls -l $HOME/workshop/2024-2/session4_RNAseq/data/human |
Line 1: Copies mouse RNAseq folder to created ~/data/mouse folder
Line 2: List the files copied to the ‘data’ folder
Line 3: Copies human RNAseq folder to created ~/data/human folder
Line 4: 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 current folder
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cat launch_nf-core_RNAseq_test.pbs |
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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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