In this News and Views episode, Chris Hakkaart and Marcel Ribeiro-Dantas discuss the hottest topics in the Nextflow world.
The Sarus container engine
- Recently Sarus was added to Nextflow as a container engine.
- Sarus is an OCI-compatible container engine for HPC.
- Sarus is an alternative container runtime to Docker.
- Sarus works by converting Docker images to a common format that can then be distributed and launched on HPC systems.
- Similar deployment options to other container engines using Nextflow.
New stageOutMode options
- Two new
stageOutMode options (
fcp) have been added to Nextflow.
stageOutMode directive defines how output files are staged-out from the scratch directory to the process work directory.
- Has been described as "The Swiss army knife of cloud storage".
- A command-line program to manage files on cloud storage.
- Over 40 cloud storage products support
- A significantly faster alternative to the classic Unix
- Handle the most common use cases of cp with much higher performance.
fcp is optimized for systems with an SSD.
- The new options will improve file management as there are new ways for the files to be staged from the scratch directory in different circumstances.
- Git has become the de-facto standard for source code version control systems.
- Nextflow provides built-in support for Git and the most popular Git hosting platforms.
- Nextflow does not require any special configuration to access public repositories but requires repository credentials to access private repositories.
- The recent Nextflow commit adds the ability to use the
GITHUB_TOKEN environment variable.
- The environment variable is used when no credentials are found in the source code management configuration file (
- It is especially useful when accessing pipeline code from a GitHub action. Read more about the token authentication in the GitHub documentation.
- There's a nf-core/bytesize talk on January 31 by Franziska Bonath about her work to generate transcripts of bytesize talks and what these might be used for in the future.
- The Nextflow / nf-core training is being held March 13-16.
- Training will be presented in different languages.
- Registration is now open - head over to the nf-core event page to sign up.
- The nf-core hackathon is being held March 27-29.
- Hackathon 27-29 March.
- We will also support local hubs where local community members are hosting other community members.
- Watch out on Slack and Twitter for an announcement that registration is open.
Episode coming soon..