Content Comparison

...

4. Finally make sure you are in your home directory, if unsure you can run the following commandwe will create a folder which will contain all the exercises and code from today:

cd ~mkdir -p $HOME/workshop/2024-2/session3

Installing Nextflow for the first time

...

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.

...

Updating Nextflow

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

...

We will also run locally your first Nextflow pipeline, which is called Hello:

mkdir -p $HOME/workshop/2024-2/session3/nftemp && cd $HOME/workshop/2024-2/session3/nftemp
nextflow run hello

• Line 12: 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 23: Verify Nextflow is working.

You should see something like this:

...

Now that you have managed to run the hello pipeline, go back to your home directory and clean the test folder.

cd $HOME  rm -rf $HOME/workshop/2024-2/session3/nftemp

Nextflow’s base configuration

...

[[ -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

...