adding software survey with nextflow

Signed-off-by: vsoch <vsochat@stanford.edu>

_posts/software/2020-08-23-nextflow.md

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+---
+layout: post
+title: "Nextflow"
+date: 2020-08-23 08:30:46
+author: "@vsoch"
+annotate_criteria: https://rseng.github.io/software/repository/github/nextflow-io/nextflow/annotate-criteria/
+annotate_taxonomy: https://rseng.github.io/software/repository/github/nextflow-io/nextflow/annotate-taxonomy/
+categories:
+- Software
+---
+
+> 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 <a href="https://www.nextflow.io" target="_blank">Nextflow</a>,
+
+<br>
+
+![{{ site.baseurl }}/assets/img/posts/showcase/nextflow.png]({{ site.baseurl }}/assets/img/posts/showcase/nextflow.png)
+
+<br>
+
+If you already know about NextFlow, we encourage you to contribute to the [research software encyclopedia](https://rseng.github.io/rse/tutorials/annotation/) and annotate the respository:
+
+<ul>
+<li><a href="{{ page.annotate_criteria }}" target="_blank">Annotate the software criteria</a></li>
+<li><a href="{{ page.annotate_taxonomy }}" target="_blank">Annotate the software taxonomy</a></li>
+</ul>
+
+otherwise, keep reading!
+
+<!--more--> 
+
+ - [What is Nextflow?](#what-is)
+ - [How do I cite it?](#cite)
+ - [How do I contribute to the software survey](#contribute)
+ - [Where can I learn more?](#learn-more)
+
+
+<a id="what-is">
+## What is Nextflow?
+
+There are many good choices of <a href="https://github.com/pditommaso/awesome-pipeline" target="_blank">workflow managers</a> 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, <a href="https://github.com/nextflow-io/awesome-nextflow" target="_blank">nextflow-io/awesome-nextflow</a> with easily ~170 community pipelines. Working on community workflows, or modules
+for workflows, is a great way to practice reproducible science. Keep in mind if you need to re-distribution your
+software that Nextflow is <a href="https://www.nextflow.io/blog/2018/clarification-about-nextflow-license.html" target="_blank">licensed under GPLv3</a>.
+
+One cool thing about NextFlow is that the creators created a company called <a href="https://seqera.io/" target="_blank">Sequera</a>,
+which seems to offer biomedical analyses as a service, called <a href="https://seqera.io/#section-tower" target="_blank">Tower</a>.
+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 <a href="https://github.com/seqeralabs/nf-tower" target="_blank">Tower on GitHub</a>.
+Please let me know if you try it out! 
+
+<a id="cite">
+## How do I cite it?
+
+Nextflow was published in [Nature Biotechnology](http://www.nature.com/nbt/journal/v35/n4/full/nbt.3820.html):
+
+```
+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](https://www.nextflow.io/blog/2017/nextflow-nature-biotech-paper.html).
+
+<a id="getting-started">
+## How do I get started?
+
+You might visit any of the following links!
+
+ - [The GitHub Repository](https://github.com/nextflow.io/nextflow) is always a good place to start.
+ - [Community Pipelines](https://github.com/nextflow-io/awesome-nextflow) on GitHub
+ - [Getting Started](https://www.nextflow.io/index.html#GetStarted)
+ - [NextFlow on Gitter](https://gitter.im/nextflow-io/nextflow)
+
+You can also post questions on the [GitHub issues board](https://github.com/nextflow-io/nextflow/issues).
+
+<a id="contribute">
+## How do I contribute to the software survey?
+
+<ul>
+  <li><a href="{{ page.annotate_criteria }}" target="_blank">Annotate the software criteria</a></li>
+  <li><a href="{{ page.annotate_taxonomy }}" target="_blank">Annotate the software taxonomy</a></li>
+</ul>
+
+or read more about annotation [here]({{ site.baseurl }}/tutorials/annotate-your-software). You can clone the software repository to do
+bulk annotation, or annotation any repository in the <a href="https://rseng.github.io/software/" target="_blank">software database</a>,
+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](https://github.com/rseng/software/issues) or even a pull request.
+
+<a id="learn-more">
+## Where can I learn more?
+
+You might find these other resources useful:
+
+ - [The Research Software Database](https://github.com/rseng/software) on GitHub
+ - [RSEpedia Documentation](https://rseng.github.io/rse)
+ - [Google Docs Manuscript](https://docs.google.com/document/d/1wDb0udH9OrFWrMBsAVb8RrUMCKKRHoyEep7yveJ1d0k/edit) you are invited to contribute to.
+ - [Annotation Documentation for RSEpedia](https://rseng.github.io/rse/tutorials/annotation/)
+ - [Annotation Tutorial in RSEng docs](https://rseng.github.io/rse/tutorials/annotation/)
+
+For any resource, you are encouraged to give feedback and contribute!