News and Views: S3 file names, Spack package manager support and local hackathon sites.

In this News and Views episode, Chris Hakkaart, and Marcel Ribeiro-Dantas discuss the hottest topics in the Nextflow world.

The Sarus container engine

• AWS jobs would fail to resume a job when an S3 file path contained a space.
  • The issue didn’t occur on local servers where spaces were.
• A better implementation of the S3Serializer was added and has resolved this problem.
• The Nextflow documentation was also updated to make it clear that toUriString, not toString, should be used to retain the protocol schema for path strings.
  • The protocol schema is important when using S3 paths.

The Spack package manager

• Support for the Spack package manager has been added to Nextflow.
• Spack is a package manager for supercomputers, Linux, and macOS.
  • It makes installing software easy and supports multiple versions, configurations, platforms, and compilers.
• Nextflow now has built-in support for Spack that allows the configuration of workflow dependencies using Spack recipes and environment files.
  • This allows Nextflow applications to build packages from source on the compute infrastructure whilst taking advantage of the configuration flexibility provided by Nextflow.
• It is used in a similar way to using conda environments with its own scope and directives.

Local sites for the nf-core hackathon

• Hacking with others is a lot of fun and local sites are our way of replicating the fun we had at the in-person hackathon prior to the 2022 Nextflow Summit.
• Everything will still be online in Gather so you can join from anywhere.
• There are more than 15 local sites that are being hosted by community members.
  • Thanks to funding from the Chan Zuckerberg Initiative and Seqera all sites are being supported with goodies.
  • We are especially excited to have a site hosted by Google at the Google Academy in London.
  • Just like the last hackathon, an nf-core training event is being held prior to the hackathon for new community members to upskill.

Upcoming events

• The next nf-core/bytesize talk on February 7.
  • Matthias Hörtenhuber is going to explain the use of the newly added nf-core pre-commit tool.
  • pre-commit was developed to inspect the snapshot that is about to be committed and helps to check the code before adding it to the repository.
• The Nextflow and nf-core training is being held March 13-16.
  • Training will be presented in different languages.
  • Registration is open now.
• The nf-core hackathon is being held March 27-29.
  • Registration is open now.