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For more information about Nextflow, please visit Nextflow - A DSL for parallel and scalable computational pipelines
Installing Nextflow
Nextflow is meant to run from your home folder on a linux Linux machine like the HPC.
A few commands can install Nextflow
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module load java curl -s https://get.nextflow.io | bash mv nextflow $HOME/bin #verify Nextflow is installed mkdir $HOME/nftemp && cd $HOME/nftemp nextflow run hello #check for output of running the short nextflow hello pipeline cd $HOME rm -rf nftemp |
Line 1: The module load command is necessary to ensure java is available
Line 2: This command downloads and assembles the parts of nextflow - this step might take some time.
Line 3: 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.
Line 5: Make a temporary folder for Nextflow to create files when it runs.
Line 6: Verify Nextflow is working.
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Lines 7 and 8: Clean up
Nextflow’s Default Configuration
Once Nextflow is installed, there are some settings that should be applied to take advantage of the HPC environment. Nextflow has a hierarchy of configuration files, where the base configuration that is applied to every workflow you run is here:
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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
}
EOF |
Preparing Data
Typically, the pipeline you want to run will want the data prepared in a particular way. You can check the pipeline’s help or web site website for a guide. Accessing help is typically:
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Some pipelines may need file names, and others may want a CSV file with file names and , paths to raw data, and other information.
Running Nextflow
When you run Nextflow, it is a good idea to create a folder for the run - this keeps all the files separate and easy to manage.
When Nextflow runs, it creates a work folder where all the temporary and work-in-progress files are stored and a results folder where the output of the pipeline run is typically stored.
Once you have prepared your input data for the pipeline, you are ready to run the pipeline.
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What do these lines mean?
Lines 1-5 are typical PBS system commands
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here the name of the job is MyNextflowRun, 2 CPUS and 4gb of ram is selected, and the job will run for 24 hours. This is the total time for the pipeline run - it may take days or weeks depending on how much data and the pipeline.
Line 6 is to ensure the
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Java environment is available (Nextflow needs Java to run)
Line 7 tells Nextflow how much
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RAM to use
Line 8 runs Nextflow.
To see the output of Nextflow while running as a job, you can use the Nextflow Tower.
Using the Nextflow Tower
Nextflow Tower allow monitoring of Nextflow runs. To use the NFTower, please visit
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