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This JAX NGS operations Nextflow pipeline repository contains multiple analysis pipelines, tools, and scripts that can be easily pulled and utilized by an end user.
JAX users are required to have access to the Sumner cluster, and to have Nextflow installed in their home directory. The setup for external collaborators will require additional support, and those wishing to share these workflows with such collaborators are encouraged to contact the maintainers of this repository.
Nextflow is a scalable and reproducible scripting language that is used for the development and maintenance of scientific workflows using software containers. Nextflow allows you to write a computational pipeline drawn from a series of intermediate computational steps. The language supports software containers, such as Docker and Singularity, which encapsulate the programs needed to run each step in the workflow. Taken together, the Nextflow pipelines and software containers allow for self-contained immutable and easily shareable workflows.
- Pipeline Documentation
- Basic Pipeline Troubleshooting
- Benchmarking Documentation
- Pipeline Development Documentation
Reference data is provided internally to JAX users via the internal HPC environment. For users external to JAX, reference data used by the workflows is available in a Google Cloud bucket, and transfers of data can be made upon request. The --reference_cache parameter can be used to point workflows at your local reference cache location. Support for additional HPC environments beyond SLURM is also by request.