Installation

Prerequisites

While you do not need to install every software used within nf-pediatric, there is two core dependencies that need to be available at runtime:

1. Nextflow (>= 24.10.5)

   To install the nextflow executable, please refer to the official nextflow documentation. While nf-pediatric has a minimal nextflow version, it is always tested against the latest version available (and oldest), so you can go ahead and install the latest version available. If you plan on running the pipeline on an HPC server, you might want to validate it is not already installed by your server’s admins.

   To validate nextflow is installed, you can run the following command:

   Command

   nextflow run helloworld

   Expected output

   Check the command’s output, you’ve been greeted in 4 different languages (english, french, italian, spanish) !

   N E X T F L O W   ~  version 24.10.4
   
   Pulling nextflow-io/helloworld ...
   downloaded from https://github.com/nextflow-io/hello.git
   Launching `https://github.com/nextflow-io/helloworld` [disturbed_mahavira] DSL2 - revision: afff16a9b4 [master]
   
   executor >  local (4)
   [59/71fa40] process > sayHello (4) [100%] 4 of 4 ✔
   Bonjour world!
   
   Hello world!
   
   Ciao world!
   
   Hola world!

2. Docker OR Apptainer

   In order to avoid users installing all software dependencies used within nf-pediatric, the pipeline relies on containers for all processing steps. Those containers can be run using two technologies: Docker or Apptainer.

   1. Docker

      When available, the pipeline should be used with Docker. It works on all OS systems, and can be installed following the official documentation. On HPC servers, for example, Docker is often not allowed or supported, in this case, you should refer to the Apptainer section.

      To validate Docker is installed and available, you can run the following command:

      Command

      docker run hello-world

      Expected output

      Unable to find image 'hello-world:latest' locally
      latest: Pulling from library/hello-world
      e6590344b1a5: Pull complete
      Digest: sha256:bfbb0cc14f13f9ed1ae86abc2b9f11181dc50d779807ed3a3c5e55a6936dbdd5
      Status: Downloaded newer image for hello-world:latest
      
      Hello from Docker!
      
      This message shows that your installation appears to be working correctly.
      To generate this message, Docker took the following steps:
      1. The Docker client contacted the Docker daemon.
      2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
          (amd64)
      3. The Docker daemon created a new container from that image which runs the
          executable that produces the output you are currently reading.
      4. The Docker daemon streamed that output to the Docker client, which sent it
          to your terminal.
      To try something more ambitious, you can run an Ubuntu container with:
      
      $ docker run -it ubuntu bash
      
      Share images, automate workflows, and more with a free Docker ID:
      https://hub.docker.com/
      For more examples and ideas, visit:
      https://docs.docker.com/get-started/

   2. Apptainer

      Apptainer (previously singularity) is an alternative container system to Docker that works solely (for now) on Linux. On HPC servers, this will the container system that will mostly be used (often times already installed by the server’s admins). If you need to install it, please refer to the official documentation.

      To validate Apptainer is installed and accessible, you can run the following command:

      Command

      apptainer --help

      Expected output

      Linux container platform optimized for High Performance Computing (HPC) and
      Enterprise Performance Computing (EPC)
      
      Usage:
      apptainer [global options...]
      
      Description:
      Apptainer containers provide an application virtualization layer enabling
      mobility of compute via both application and environment portability. With
      Apptainer one is capable of building a root file system that runs on any
      other Linux system where Apptainer is installed.
      
      Options:
          --build-config    use configuration needed for building containers
      -c, --config string   specify a configuration file (for root or
                              unprivileged installation only) (default
                              "/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/apptainer/1.2.4/etc/apptainer/apptainer.conf")
      -d, --debug           print debugging information (highest verbosity)
      -h, --help            help for apptainer
          --nocolor         print without color output (default False)
      -q, --quiet           suppress normal output
      -s, --silent          only print errors
      -v, --verbose         print additional information
          --version         version for apptainer
      
      Available Commands:
      build       Build an Apptainer image
      cache       Manage the local cache
      capability  Manage Linux capabilities for users and groups
      checkpoint  Manage container checkpoint state (experimental)
      completion  Generate the autocompletion script for the specified shell
      config      Manage various apptainer configuration (root user only)
      delete      Deletes requested image from the library
      exec        Run a command within a container
      help        Help about any command
      inspect     Show metadata for an image
      instance    Manage containers running as services
      key         Manage OpenPGP keys
      oci         Manage OCI containers
      overlay     Manage an EXT3 writable overlay image
      plugin      Manage Apptainer plugins
      pull        Pull an image from a URI
      push        Upload image to the provided URI
      remote      Manage apptainer remote endpoints, keyservers and OCI/Docker registry credentials
      run         Run the user-defined default command within a container
      run-help    Show the user-defined help for an image
      search      Search a Container Library for images
      shell       Run a shell within a container
      sif         Manipulate Singularity Image Format (SIF) images
      sign        Add digital signature(s) to an image
      test        Run the user-defined tests within a container
      verify      Verify digital signature(s) within an image
      version     Show the version for Apptainer
      
      Examples:
      $ apptainer help <command> [<subcommand>]
      $ apptainer help build
      $ apptainer help instance start
      
      
      For additional help or support, please visit https://apptainer.org/help/

Once everything installed and/or available, you can proceed to the inputs section.