snakemake.nvim

A Neovim plugin with keymaps for working with Snakemake workflows: quickly add --forcerun arguments to your run.sh, and jump from any input file to the rule that produces it.

Features

1. Add rule to forcerun (open_and_insert)

Place your cursor anywhere inside a Snakemake rule definition, press the keymap, and the plugin will:

1. Scan upward from the cursor to find the enclosing rule my_rule: line and extract the rule name
2. Open run.sh in Neovim's current working directory
3. Insert or update the --forcerun argument in the file
4. Save the file

First use: a --forcerun rule_name \ line is inserted directly after the snakemake command.

Subsequent uses: if a --forcerun line is already present, the new rule name is appended to it (space-separated) — so you can build up a list of rules to force-rerun without editing run.sh by hand.

2. Go to producer rule (goto_producer)

Place your cursor on a quoted input filename inside any rule's input: block and press the keymap. The plugin will:

1. Extract the file string under the cursor
2. Scan all Snakemake* and Snakefile* files under the current working directory, collecting every rule and checkpoint's output: patterns
3. Match the filename against each output pattern — including wildcard patterns like results/{sample}.bam
4. Open the file containing the matching rule (if different from the current buffer) and jump to it

Both exact matches (pattern equals pattern) and concrete-to-wildcard matches are supported. For example, with cursor on "results/sampleA.bam" in an input block, the plugin will jump to a rule with output: "results/{sample}.bam". The rule name and source file are shown in a notification.

Note: Only static quoted strings in output: blocks are indexed. expand() results, lambdas, and function callbacks are not evaluated.

Requirements

• Neovim
• A run.sh file in Neovim's current working directory containing a snakemake command

Installation

lazy.nvim

{
  "samesense/snakemake.nvim",
  config = function()
    require("snakemake").setup()
    -- add current rule to --forcerun in run.sh
    vim.keymap.set("n", "<Leader>o", function()
      require("snakemake").open_and_insert()
    end)
    -- jump to the rule that produces the file under cursor
    vim.keymap.set("n", "<Leader>g", function()
      require("snakemake").goto_producer()
    end)
  end,
},

Usage

Adding a rule to forcerun

1. Open a Snakefile in Neovim
2. Place your cursor anywhere inside a rule — on the rule line itself or any line within the rule body:

   rule my_rule:
       input: "data.txt"   # cursor can be here too
       output: "result.txt"
   

3. Press <Leader>o
4. Your run.sh will be updated — the rule is inserted after the snakemake line on the first use, or appended to the existing --forcerun line on subsequent uses

For example, after pressing <Leader>o three times on different rules:

snakemake \
  --forcerun rule_a rule_b rule_c \
  --cores 4

Note: An error is raised if no rule definition is found above the cursor, or if run.sh does not contain a snakemake line and no --forcerun lines are present.

Jumping to a producer rule

1. Open a Snakefile in Neovim
2. Place your cursor on a quoted filename inside an input: block:

   rule final:
       input: "results/sampleA.bam"   # cursor here
   

3. Press <Leader>g
4. The cursor jumps to the rule whose output: produces that file

Wildcard patterns are matched automatically — a concrete filename like results/sampleA.bam will match an output pattern results/{sample}.bam. The rule name is shown in a notification on successful navigation.