Brew Conda

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Conda install nextflow We recommend using a personal installation of Nextflow where possible, instead of using a system-wide installation. This makes it easier to update. Updating nextflow is as simple as running nextflow self-update or conda update nextflow, depending on how it was installed. The fastest way to obtain conda is to install Miniconda, a mini version of Anaconda that includes only conda and its dependencies. If you prefer to have conda.

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Nextflow

All nf-core pipelines use Nextflow, so this must be present on the system where you launch your analysis.See nextflow.io for the latest installation instructions.

Brew Honda Longview Tx

Generally speaking, Nextflow runs on most POSIX systems (Linux, Mac OSX etc) and can typically be installed by running the following commands:

You can also install Nextflow using Bioconda.

First, set up Bioconda according to the Bioconda documentation, notably setting up channels:

Then install the nf-core package:

We recommend using a personal installation of Nextflow where possible, instead of using a system-wide installation. This makes it easier to update.

Updating nextflow is as simple as running nextflow self-updateor conda update nextflow, depending on how it was installed.

Conda

Once installed you will probably need to configure Nextflow to run on your system. For instructions, see Nextflow configuration.

Pipeline software

An analysis pipeline chains the execution of multiple tools together.Historically, all tools would have to be manually installed, often a source of great frustration and a key step where reproducibility between analyses is lost.nf-core pipelines utilise the built-in support for software packaging that Nextflow offers: all can work with Docker and Singularity, and most pipelines also have support for Conda.

  • Docker
    • Typically used locally / on single-user servers and the cloud.
    • Analysis runs in a container, which behaves like an isolated operating system
    • Previously required system root access, though a 'rootless mode' is available since late 2019
  • Singularity
    • Often used as an alternative to Docker on multi-user systems such as HPC systems.
    • Also runs containers and can create these from Docker images
    • Does not need root access or any daemon processes - images built from files
  • Podman
    • Often used as an alternative to Docker on multi-user systems such as HPC systems.
    • Is a daemonless container engine that can serve as a drop-in replacement for Docker.
  • Charliecloud
    • Often used as an alternative to Docker on multi-user systems such as HPC systems.
    • Uses Linux user namespaces to run containers with no privileged operations or daemons
  • Shifter
    • An experimental implementation of container system that can convert from a wide range of other images
  • Conda
    • Packaging system that manages environments instead of running analysis in containers.
    • Poorer reproducibility than Docker / Singularity
      • There can be changes in low-level package dependencies over time
      • The software still runs in your native operating system environment and so core system functions can differ

Pipeline code

Automatic

This pipeline itself needs no installation - nextflow will automatically fetch it from GitHub if nf-core/<pipeline-name> is specified as the pipeline name.

This method requires an internet connection. If you're running on a system that has no internet connection, please see the Running Offline documentation.

Development

If you would like to make changes to the pipeline, fork the GitHub repository and then clone the files. Once cloned you can run the pipeline with nextflow run <path-to-repo>.

Note that you should only do this if you intend to make significant changes to the pipeline. All configuration options can be changed without editing the pipeline code. Forking the pipeline repositories means that you cannot use stable releases and you will fall behind new updates.

Brew Conda Pip

Reference genomes

Brew Install Conda

Some pipelines come with built-in support for iGenomes references.It may be preferable for you to download a local copy of these to your system to avoid fetching the same reference many times.For more information, see Reference genomes.