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Prerequisites

Omnifluss is developed and launched using the Nextflow workflow language and intended for Unix operating systems.

User requirements

We successfully tested the following work environments and operating systems to launch omnifluss:

Operating system: Ubuntu Linux 24.04.02 LTS; 22.04.05 LTS
Package manager/ container engine: conda, singularity or docker. We strongly recommend the container engines (singularity or docker) for stability.
Work environment: nextflow 25.04.3

These requirements suffice for running omnifluss on your data. You can install Nextflow via its official installation instructions or simply via conda:

conda create -n omnifluss -c bioconda -c conda-forge nextflow==25.04.3

Note: With Nextflow in your active working environment you don't need to install omnifluss at all! In the standard use case, Nextflow will automatically clone and use the omnifluss source code from its Github repository.

Developer requirements

Operating system: Ubuntu Linux 24.04.02 LTS, 22.04.05 LTS
Package manager/ container engine: conda, singularity or docker. We strongly recommend the container engines (singularity or docker) for stability.
Work environment: nextflow 25.04.3, nf-core 3.3.1, nf-test 0.9.2

These requirements are only for developers and people intending to contribute to omnifluss. You can recreate our developers' work environment via conda conda:

conda create -n omnifluss -c bioconda -c conda-forge \
    nextflow==25.04.3 \
    nf-core==3.3.1 \
    nf-test==0.9.2