Content Comparison

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2. Before we start using the HPC, let’s start an interactive session:

qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=1:mem=4gb

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To install Nextflow for the first time, copy and paste the following block of code into your terminal (i.e., PuTTy that is already connected to the terminal) and hit 'enter':

curl -s https://get.nextflow.io | bash
mv nextflow $HOME/bin

• Line 1: This command downloads and assembles the parts of nextflow - this step might take some time.

• Line 2: When finished, the nextflow binary will be in the current folder so it should be moved to your “bin” folder” so it can be found later.

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Updating Nextflow

If you have installed Nextflow before on the HPC then you will have to run:

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mkdir $HOME/nftemp && cd $HOME/nftemp
nextflow run hello

• Line 1: Make a temporary folder called nftemp for Nextflow to create files when it runs the hello pipeline; change directory to this newly created folder.

• Line 2: Verify Nextflow is working.

You should see something like this:

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You can also configure Nextflow to run on a cluster such as a PBS Pro resource manager and this is how we will specify when using manage, which is the setting we will use on the HPC:

process {
  executor = 'pbspro'
}

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[[ -d $HOME/.nextflow ]] || mkdir -p $HOME/.nextflow

cat <<EOF > $HOME/.nextflow/config
singularity {
    cacheDir = '$HOME/.nextflow/NXF_SINGULARITY_CACHEDIR'
    autoMounts = true
}
conda {
    cacheDir = '$HOME/.nextflow/NXF_CONDA_CACHEDIR'
}
process {
  executor = 'pbspro'
  scratch = false
  cleanup = false
}
includeConfig '/work/datasets/reference/nextflow/qutgenome.config'
EOF

• Line 1: Check if a .nextflow/config file already exists in your home directory. Create it if it does not exist

• Line 2-15: Using the cat command, paste text in the newly created .nextflow/config file which specifies the cache location for your singularity and conda.

• What are the parameters you are setting?

• Line 4-7 set the directory where remote Singularity images are stored and direct Nextflow to automatically mount host paths in the executed container.

• Line 8-10 set the directory where Conda environments are stored.

• Line 11-15 sets default directives for processes in your pipeline. Note that the executor is set to pbspro on line 12.

• Line 16 provides the local path to genome files required for pipelines such as nf-core/rnaseq

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