Introduction
Nextflow will very soon be making it’s new ‘Strict Syntax’ mode default (from 26.04). This more restrictive way of writing Nextflow code is being implemented by the Nextflow team to improve error messages and more consistent code.
Representing best-practice Nextflow code, nf-core is therefore also pushing forward with requiring strict syntax compliance across the board - whether in pipelines, modules, and also now configs.
The core team, lead by Nicolas (@nvnieuwk), has done a survey of existing configs and identified 57 configs on nf-core/configs repository that are not currently Nextflow Syntax compliant. Once the users on these infrastructures update to the latest version of Nextflow, their pipelines will not be able to execute.
What are we doing?
To assist configs maintainers and users in avoiding potential problems running pipelines on their infrastructure when they update to future versions of Nextflows, we are trying a multi-pronged approach to spread awareness of the changes:
- Notify the config maintainers of soon-to-be non-compliance on a dedicated issue
- Post (this!) blog post for outside visibility, but also a cross-reference on the nf-core Slack’s #announcements channel
- For configs without fixes, the core team will update config description message displayed at the beginning of nf-core runs to make users aware and to tell them to contact us
- e.g. if the original config author no longer is responsibility
- If we do not hear from config maintainers or pipeline users, we will consider a form of deprecating the config
We have also prepared a ‘migration’ guide describing recommended fixes for common ‘patterns’ of non-compliance. Note this remains an open document, and we welcome any contributions, whether fixes, improvements, or updates!
Timeline
We do not have a fixed timeline for this roll out, except for the deadline of the release of Nextflow v26.04.
The GitHub issue has already been made, and we will monitor the speed of responses before moving onto phase 3 and 4.
Summary
The nf-core core team hopes that with these steps we will ensure continued smooth and uninterrupted execution of the communities’ exciting analysis and research!
If you have any questions, or need any help feel free to ask for help at any time on Slack, on the #configs channel.
