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Maxime HEBRARD
Maxime HEBRARD

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Nextflow

#setup #macos #workflow #automation

If you ever wrote bash scripts for each of your task, then try to write "one script to rule them all", a gigantic master script that handle parameters, and chains all the other tasks... Then you should stop right here and look for a workflow manager ! Nextflow.io is what you are looking for.

Nextflow

Install on MacOS

Before reading this post, I suggest you follow Improved Shell (MacOS).

Install Java

At the point of writing this post, the recommanded java version to install is OpenJDK 21. See Which JDK for more info.

  • Open 'Terminal'
  • Install OpenJDK from Homebrew 
brew install openjdk@21
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  • Link it to Java 
sudo ln -sfn /opt/homebrew/opt/openjdk@21/libexec/openjdk.jdk /Library/Java/JavaVirtualMachines/openjdk-21.jdk
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  • Add it to the PATH 
echo 'export PATH="/opt/homebrew/opt/openjdk@21/bin:$PATH"' >> ~/.zshrc
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Java version

Install Nextflow

  • Download Nextflow 
curl -s https://get.nextflow.io | bash
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  • Make Nextflow executable 
chmod +x nextflow
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  • Create a new directory with write permissions to store binary 
mkdir -p $HOME/.local/bin/
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  • Move Nextflow into the directory 
mv nextflow $HOME/.local/bin/
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  • Add the directory to the PATH 
echo 'export PATH="$HOME/.local/bin:$PATH"' >> ~/.zshrc
source ~/.zshrc
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  • Confirm Nextflow is installed correctly 
nextflow info
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Nextflow info

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