Introduction
Pixelgen Technologies provides software solutions that empower MPX in both data processing and analysis. We refer to our software collectively as Pixelator.
There are two modes of usage for Pixelator: as a data processing pipeline, which we refer to as nf-core/pixelator, and as a program library called pixelator. The capabilities of Pixelator as a program library are better covered in our data analysis section.
Our pipeline consists of several steps, as illustrated below. After a successful run, you will have ready-to-analyze outputs from your initial FASTQ sequencing libraries.
To build the pipeline, we used Nextflow - a workflow tool that enables task execution across multiple computing infrastructures. The use of containers makes installation effortless, and results are highly reproducible. We have packed all program logic in a Python library and all necessary executables to run on virtual machines, making it very portable.
Pixelator Architecture
The nf-core/pixelator performs a series of steps by using the pixelator command from a container image.
Pixelgen Technologies has created and is maintaining a software, commonly known as Pixelator, which is hosted in both the nf-core project and PyPI community projects. By doing so, customers can use our pipeline simply by using the nextflow command-line. The programmatic logic of the nf-core/pixelator pipeline is implemented in a Python library and command-line tool that is distributed in PyPI, biocontainers and quay.io.
Pixelator is developed using various open source projects and platforms, including nextflow, nf-core, PyPI, biocontainers, docker, quay.io and github. This enables us to create software that is compatible with various infrastructures, clouds, and highly available for our customers. nf-core is particularly useful as it works on a wide range of institutional HPC infrastructures, making it likely to be a good fit for your needs.
When using nf-core/pixelator on your platform, nextflow will download the pipeline from nf-core the first time it is run. If the pipeline has already been run, a local copy will be reused. After the initial download, the nf-core/pixelator pipeline will download a lightweight container from quay.io. This container provides a command-line oriented library of stages that contains all the execution logic required to process MPX assay raw FASTQ reads into analysis-ready results. Our pipeline, nf-core/pixelator, coordinates the execution of these stages in nextflow and also provides useful monitoring and debugging logs, as well as restarting utilities.
The implementation of nf-core/pixelator using Nextflow DSL2 involves utilizing one container for each process. This approach makes it easier to maintain and update software dependencies. Whenever possible, these processes have been submitted to and installed from nf-core/modules, which makes them available to all nf-core pipelines as well as the Nextflow community.