Chris Hakkaart
Marcel Ribeiro-Dantas
Chris Hakkaart & Marcel Ribeiro-DantasFeb 01, 2023

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

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.