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This page will guide you through the installation steps required to run nf-core/pixelator.

Installing Nextflow​

Nextflow is distributed as a self-installing package, which means that it does not require any special installation procedure. We currently support Nextflow >=22.04.5.

Download the executable package by running either one of the following commands in your terminal window:

wget -qO- https://get.nextflow.io | bash

This will create the nextflow main executable file in the current directory.

Make the binary executable on your system by running

chmod +x nextflow

Optionally, move the nextflow file to a directory defined in your $PATH variable to make the nextflow command available without having to type the full path to the executable.

Installing Docker​

We have tested extensively nf-core/pixelator with docker, so that is our recommended system to manage container images:

Installing other container management platforms​

Install any of Apptainer/Singularity, Podman, Shifter or Charliecloud for full pipeline reproducibility.

The nf-core/pixelator pipeline has been tested with docker, Apptainer/Singularity and Podman.

You can use conda both to install Nextflow itself and also to manage software within pipelines.

note

Use of conda as a configuration profile when running pipelines is discouraged due to lack of reproducibility. Please only use it as a last resort solution.

More information can be found in the configuration options.