Ngless

What it does

When your agent uses it

• Mentions NGLess
• Metagenomics pipelines with NGLess
• Writing .ngl scripts
• Is working in the ngless repository (Rust source at src/)

Example prompts

• “/ngless”

Requirements

• Python 3

Workflow steps

12 steps, taken from the first numbered list in SKILL.md.

1. 1Indexing a function call's result is not supported: use xs = readlines(f) then xs[0],
2. 2Wrong version declaration: the first non-comment line must be ngless "1.6". ngless "1.5" (and
3. 3Old module import versions: import "parallel" version "1.1" still works but warns; use "1.6".
4. 4Using tabs: only spaces allowed (4-space indent)
5. 5Forgetting discard: in preprocess blocks, filtered reads must be explicitly discarded with discard
6. 6select symbols confusion: keep_if=[{mapped}] keeps mapped reads; drop_if=[{mapped}] removes them.
7. 7count annotation sources: if features != ['seqname'], you need exactly one of gff_file=,
8. 8strand= on count(): removed; use sense={sense}
9. 9Spaces in a functional_map TSV are part of the feature name: a, b means a and b
10. 10load_fastq_directory is picky about names: .fq/.fastq (after any .gz/.bz2/.xz),
11. 11Relative paths in a YAML sample list resolve against basedir, or else the current working
12. 12Parallel scripts: must run multiple NGLess processes (one per sample) — the parallel module

What it can do on your machine

Read from SKILL.md and the folder at commit cb476d2. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Shell commands in SKILL.md call:

  • conda

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Links to these hosts (documentation or services it may open):

  • eggnog-mapper.embl.de
  • pixi.sh

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Ngless loads about 7k tokens when it runs, and up to ~13k if it reads all its reference files. Until then it costs about 98 tokens; SKILL.md has 2,640 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~98

When it runs · the whole SKILL.md, loaded when a task matches

~7k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~13k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 2,640 words (~6,993 tokens).

name

ngless

version

1.0.0

Read the full SKILL.md on GitHub

Files

SKILL.md and 2 other files (references) in skills of ngless-toolkit/ngless.

• SKILL.md
• references/configuration-and-paths.md
• references/developer-guide.md

Open the folder on GitHubat commit cb476d2