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
toString, should be used to retain the protocol schema for path strings.
- The protocol schema is important when using
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.
- 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 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..