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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 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=12:mem=4gb |
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
Let’s create the working directories for today’s session:
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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/datalocal mkdir -p $HOME/workshop/2024-2/session4_RNAseq/runsdata mkdir -p $HOME/workshop/2024-2/session4_RNAseq/runsdata/run1_QCmouse mkdir -p $HOME/workshop/2024-2/session4_RNAseq/runs/run2_RNAseq/data/human mkdir -p $HOME/workshop/2024-2/session4_RNAseq/data/mydata mkdir -p $HOME/workshop/2024-2/session4_RNAseq/runs/run3_RNAseq_T2T |
The folder structure will look like this:
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mkdir -p $HOME/workshop/2024-2/session4_RNAseq/ ├── data ├── runs │ ├── 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 └── scripts |
The above code creates the following folder structure:
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Get a copy of the scripts
Now let’s copy the scripts necessary for today’s session:
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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 your $HOMEworking 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/ |
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mouse cp /work/training/ |
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2024/rnaseq/ |
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data/ |
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human/* $HOME/workshop/2024-2/session4_RNAseq/data/ |
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Using the usage and parameters sections, search how many aligner options are available for the nf-core rnaseq pipeline version 3.15.1.
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ls human ls -l $HOME/workshop/2024-2/session4_RNAseq/data |
Create a folder for running the nf-RNA-seq pipeline
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/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 . For exampleby running a test using sample data.
Create a folder for running the pipeline test:
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mkdir -p $HOME/workshop/2024-2/rnaseqsession4_RNAseq/runs mkdir $HOME/workshop/2024/rnaseq/runs/run1/run0_test mkdircd $HOME/workshop/2024-2/rnaseqsession4_RNAseq/runs/run2_QC mkdirrun0_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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cp $HOME/workshop/2024-2/rnaseqsession4_RNAseq/runs/run3scripts/launch_nf-core_RNAseq cd $HOME/workshop/2024/rnaseq/runs |
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Lines 1-4: create sub-folders for each exercise
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Line 5: change the directory to the folder “run1_test”
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_test.pbs . |
View the content of the script as follows:
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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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qsub launch_nf-core_RNAseq_test.pbs |
Monitoring the Run
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qjobs |