Migrate Nextflow Code

Migrate a Nextflow pipeline to new language patterns. Follow best practices from the Nextflow docs. Use nextflow lint to validate code as you go. Verify that the pipeline produces the same results before/after migration.

Requirements

Requires Nextflow 26.10 or later for the nextflow lint command with type checking.

Requires nf-core template 3.0.0 or later, if applicable. If the pipeline has a .nf-core.yml, check which version of nf-core/tools last generated its template. If nf_core_version is unspecified or less than 3.0.0, stop and tell the user to upgrade their template first. This will resolve syntax errors in the template code and provide a cleaner baseline.

Migrations

Apply each migration requested by the user, one at a time, in the following order. Each migration requires the ones before it.

Each migration links the relevant docs. Consult these docs when you aren't sure how to do something. For example, which type to use, which method to use for a given type, or how to use a specific channel operator. Don't just guess or try to work from past knowledge. The linter can guide you, but the docs provide examples and best practices.

Strict syntax

Update a pipeline to comply with nextflow lint. Pipelines written before the introduction of the strict syntax parser may contain patterns that are no longer valid.