Core pipeline

Steps to generate data for the G-nom core analyses are bundled in the core pipeline. It currently includes the following tools:

fCat and taXaminer are not yet included pending a bioconda release.

The core pipeline is not executed by G-nom itself but designed to run in a separate HPC environment (it is generally advisable to isolate compute clusters from web-facing applications). The pipeline uses nextflow and is built on top of nf-core. Nextflow supports all major HPC schedulers, including e.g. SLURM and LSF and can be set up in a few minutes. Nf-core provides a common style for the development of nextflow pipelines. The environments required to run the various tools are set up using conda.

Further usage instructions can be found in the repository. Please report issues in the pipeline repository rather then the main G-nom repository.