You know I’m all about those workflows, about those workflows, no trouble! I’m all about those workflows, about those workflows, no trouble!
Seriously, workflow managers and orchestration tools make the scientific computation world go round! Our showcase would simply not be complete without sharing Nextflow,
If you already know about NextFlow, we encourage you to contribute to the research software encyclopedia and annotate the respository:
otherwise, keep reading!
There are many good choices of workflow managers for scientific pipelines, and NextFlow is definitely one of the leaders! What makes it special?
Nextflow is a bioinformatics workflow manager that enables the development of portable and reproducible workflows. It supports deploying workflows on a variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes. Additionally, it provides support for manage your workflow dependencies through built-in support for Conda, Docker, Singularity, and Modules.
But what makes NextFlow stand out is the user community! There is an entire repository, nextflow-io/awesome-nextflow with easily ~170 community pipelines. Working on community workflows, or modules for workflows, is a great way to practice reproducible science.
One cool thing about NextFlow is that the creators created a company called Seqera, which seems to offer biomedical analyses as a service, called Tower. I haven’t tried any of the services, but it’s empowering to see that an open source project can figure out a service model to be sustainable. You can also check out Tower on GitHub. Please let me know if you try it out!
Nextflow was published in Nature Biotechnology:
Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319. doi:10.1038/nbt.3820
You can read about the publication here.
You might visit any of the following links!
You can also post questions on the GitHub issues board.
or read more about annotation here. You can clone the software repository to do bulk annotation, or annotation any repository in the software database, We want annotation to be fun, straight-forward, and easy, so we will be showcasing one repository to annotate per week. If you’d like to request annotation of a particular repository (or addition to the software database) please don’t hesitate to open an issue or even a pull request.
You might find these other resources useful:
For any resource, you are encouraged to give feedback and contribute!