README.org

#+TITLE: Emacs Nextflow Mode

This is a mode for syntax highlighting for [[https://www.nextflow.io/][Nextflow]] based on [[https://git.kyleam.com/snakemake-mode/about/][snakemake-mode]]. More features such as a popup runner, and better script editing planned in the future! Support for DSL2 is in the works also.

Two modes are provided:

• =nextflow-ts-mode= — tree-sitter based mode for Emacs 29+ (recommended)
• =nextflow-mode= — regex-based fallback for older Emacs, built on =groovy-mode=

** Tree-sitter mode (Emacs 29+) =nextflow-ts-mode= uses the built-in =treesit= support with the [[https://github.com/nextflow-io/tree-sitter-nextflow][tree-sitter-nextflow]] grammar. Install the grammar once (requires a C compiler):

#+BEGIN_SRC emacs-lisp M-x treesit-install-language-grammar RET nextflow RET #+END_SRC

Loading =nextflow-ts-mode= registers the grammar source automatically. When the grammar is installed, buffers in =nextflow-mode= are remapped to =nextflow-ts-mode= via =major-mode-remap-alist=.

** Installation In order to use the fallback =nextflow-mode= you'll need to install these packages first: - [[https://elpa.gnu.org/packages/cl-lib.html][cl-lib]] - [[https://melpa.org/#/groovy-mode][groovy-mode]]

This package is currently not on melpa yet. If you're using [[https://github.com/hlissner/doom-emacs][Doom Emacs]] you can use this snippet to install the package.

#+BEGIN_SRC emacs-lisp (package! nextflow-mode :recipe (:host github :repo "emiller88/nextflow-mode")) #+END_SRC

** Roadmap

• Bash highlighting inside =script:= blocks via tree-sitter language injection (=script_content= nodes + an embedded bash parser)
• Standalone =auto-mode-alist= entries for =nextflow-ts-mode= so it activates without =nextflow-mode=/groovy-mode installed
• Validate highlighting against real nf-core modules; feed parse failures back to [[https://github.com/nextflow-io/tree-sitter-nextflow][tree-sitter-nextflow]]
• Decide =nextflow.config= handling for the tree-sitter mode
• Emacs 30 =treesit-thing-settings= (sexp/sentence navigation) and =which-func= integration
• MELPA packaging