Episode 12 S3 file names, Spack package manager support and local hackathon sites.

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

  • News and Views
  • 01 February 2023

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

Improved handling of S3 paths with spaces

  • 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.
Episode coming soon..

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