#CLI Reference

#Global

nyx [COMMAND]
nyx --version
nyx --help

---

#nyx scan

Run a security scan on a directory.

nyx scan [PATH] [OPTIONS]

PATH defaults to . (current directory).

#Analysis Mode

Flag	Default	Description
--mode <MODE>	full	Analysis mode: full, ast, cfg, or taint

Mode	What runs
full	AST patterns + CFG structural analysis + taint analysis
ast	AST patterns only (fastest, no CFG or taint)
cfg / taint	CFG + taint analysis only (no AST patterns)

Deprecated aliases: --ast-only (use --mode ast), --cfg-only (use --mode cfg), --all-targets (use --mode full).

#Index Control

Flag	Default	Description
--index <MODE>	auto	Index behavior: auto, off, or rebuild

Index Mode	Behavior
auto	Use existing index if available; build if missing
off	Skip indexing, scan filesystem directly
rebuild	Force rebuild index before scanning

Deprecated aliases: --no-index (use --index off), --rebuild-index (use --index rebuild).

#Output

Flag	Default	Description
-f, --format <FMT>	console	Output format: console, json, or sarif
--quiet	off	Suppress status messages (stderr), including the Preview-tier banner for C/C++ scans
--no-rank	off	Disable attack-surface ranking
--no-state	off	Disable state-model analysis (resource lifecycle + auth state). Overrides scanner.enable_state_analysis

#Profiles

Flag	Default	Description
--profile <NAME>	(none)	Apply a named scan profile. Built-ins: quick, full, ci, taint_only, conservative_large_repo. User-defined profiles override built-ins with the same name. CLI flags still take precedence over profile values

#Filtering

Flag	Default	Description
--severity <EXPR>	(none)	Filter findings by severity
--min-score <N>	(none)	Drop findings with rank score below N
--min-confidence <LEVEL>	(none)	Drop findings below this confidence level (low, medium, high)
--require-converged	off	Drop findings whose engine provenance notes indicate widening (over-report) or analysis bail. Keeps under-report findings (emitted flow is still real). Intended for strict CI gates.
--fail-on <SEV>	(none)	Exit code 1 if any finding >= this severity
--show-suppressed	off	Show inline-suppressed findings (dimmed, tagged [SUPPRESSED])
--keep-nonprod-severity	off	Don't downgrade severity for test/vendor paths
--all	off	Disable category filtering, rollups, and LOW budgets -- show everything
--include-quality	off	Include Quality-category findings (hidden by default)
--max-low <N>	20	Maximum total LOW findings to show
--max-low-per-file <N>	1	Maximum LOW findings per file
--max-low-per-rule <N>	10	Maximum LOW findings per rule
--rollup-examples <N>	5	Number of example locations in rollup findings
--show-instances <RULE>	(none)	Expand all instances of a specific rule (bypass rollup)

Severity expression formats:

--severity HIGH              # Only high
--severity "HIGH,MEDIUM"     # High or medium
--severity ">=MEDIUM"        # Medium and above (high + medium)
--severity ">= low"         # All severities (case-insensitive)

Deprecated aliases: --high-only (use --severity HIGH), --include-nonprod (use --keep-nonprod-severity).

--fail-on returns a non-zero exit code when the threshold trips, so CI jobs fail without further wiring:

Quality-category and rollup-prone Low findings are filtered down by default. The footer tells you exactly what got dropped and which knob to turn:

#Analysis Engine Toggles

Override the corresponding [analysis.engine] values in nyx.conf for a single run. All default on; pass the --no-* variant to disable.

Pair	Config field	Effect when disabled
--constraint-solving / --no-constraint-solving	constraint_solving	Skip path-constraint solving; infeasible paths no longer pruned
--abstract-interp / --no-abstract-interp	abstract_interpretation	Skip interval / string / bit abstract domains
--context-sensitive / --no-context-sensitive	context_sensitive	Treat intra-file callees insensitively (summary-only)
--symex / --no-symex	symex.enabled	Skip the symex pipeline; no symbolic verdicts or witnesses
--cross-file-symex / --no-cross-file-symex	symex.cross_file	Skip extracting / consulting cross-file SSA bodies
--symex-interproc / --no-symex-interproc	symex.interprocedural	Cap symex frame stack at the entry function
--smt / --no-smt	symex.smt	Skip the SMT backend (still a no-op without the smt feature)
--backwards-analysis / --no-backwards-analysis	backwards_analysis	Demand-driven backwards taint walk from sinks (default off)
--parse-timeout-ms <N>	parse_timeout_ms	Per-file tree-sitter parse timeout (ms); 0 disables the cap

#Lattice-width Caps

Two caps bound the width of taint origin sets and points-to sets per SSA value. When a set would exceed the cap, entries are truncated deterministically and an engine note (OriginsTruncated / PointsToTruncated) is recorded on affected findings so you can see when precision was lost.

Flag	Default	Description
--max-origins <N>	32	Max taint origins retained per lattice value. Raise on very wide codebases where truncation is observed; lower only when lattice width is a measured bottleneck. Also set via NYX_MAX_ORIGINS
--max-pointsto <N>	32	Max abstract heap objects retained per points-to set. Raise on factory-heavy codebases where truncation is observed. Also set via NYX_MAX_POINTSTO

See configuration.md for the full schema.

#Engine-Depth Profile

Individual engine toggles are fine-grained but hard to remember in combination. The --engine-profile shortcut sets the whole stack in one shot, and individual flags are layered on top after the profile is applied.

Profile	Backwards	Symex	Abstract-interp	Context-sensitive
fast	off	off	off	off
balanced (default)	off	off	on	on
deep	on	on (cross-file + interprocedural)	on	on

All three profiles build the AST, CFG, and SSA lattice and run forward taint; the columns above show which additional analyses each profile enables. SMT (symex.smt) is always off unless Nyx was built with --features smt.

Individual flags override the profile. For example, --engine-profile fast --backwards-analysis runs the fast stack but with backwards analysis on.

#Explain Effective Engine

--explain-engine prints the resolved engine configuration (profile + config + CLI overrides + env-var fallbacks) to stdout and exits without scanning. Useful for sanity-checking a CI invocation.

nyx scan --engine-profile deep --no-smt --explain-engine

#Examples

# Basic scan
nyx scan

# Scan specific path, JSON output
nyx scan ./server --format json

# CI gate: fail on medium+, SARIF output
nyx scan . --format sarif --fail-on medium > results.sarif

# Fast AST-only scan, no index
nyx scan . --mode ast --index off

# High-severity only, quiet mode
nyx scan . --severity HIGH --quiet

# Only findings scoring 50 or above
nyx scan . --min-score 50

# Only medium+ confidence findings
nyx scan . --min-confidence medium

# Show everything (no filtering, no rollups)
nyx scan . --all

# Include quality findings but keep rollups and budgets
nyx scan . --include-quality

# See all unwrap findings expanded
nyx scan . --include-quality --show-instances rs.quality.unwrap

# Allow more LOW findings
nyx scan . --max-low 50 --max-low-per-file 5

---

#nyx index

Manage the SQLite file index.

#nyx index build

nyx index build [PATH] [--force]

Build or update the index for the given path (default: .).

Flag	Description
-f, --force	Force full rebuild, ignoring cached file hashes

#nyx index status

nyx index status [PATH]

Display index statistics (file count, size, last modified) for the given path.

---

#nyx list

nyx list [-v]

List all indexed projects.

Flag	Description
-v, --verbose	Show detailed information per project

---

#nyx clean

nyx clean [PROJECT] [--all]

Remove index data.

Argument/Flag	Description
PROJECT	Project name or path to clean
--all	Clean all indexed projects

---

#nyx config

Manage configuration.

#nyx config show

Print the effective merged configuration as TOML. Useful for sanity-checking what the scanner is actually using after nyx.conf and nyx.local merge:

#nyx config path

Print the configuration directory path.

#nyx config add-rule

nyx config add-rule --lang <LANG> --matcher <MATCHER> --kind <KIND> --cap <CAP>

Add a custom taint rule. Written to nyx.local.

Flag	Values
--lang	rust, javascript, typescript, python, go, java, c, cpp, php, ruby
--matcher	Function or property name to match
--kind	source, sanitizer, sink
--cap	env_var, html_escape, shell_escape, url_encode, json_parse, file_io, fmt_string, sql_query, deserialize, ssrf, code_exec, crypto, unauthorized_id, data_exfil, ldap_injection, xpath_injection, header_injection, open_redirect, ssti, xxe, prototype_pollution, all

#nyx config add-terminator

nyx config add-terminator --lang <LANG> --name <NAME>

Add a terminator function (e.g. process.exit). Written to nyx.local.

---

#nyx rules

Browse the built-in rule registry from the terminal. Same dataset the dashboard's Rules page reads from: cap-class entries (one per Cap with a canonical rule id), per-language label rules (sink / source / sanitizer), gated sinks, and any custom rules from your config.

#nyx rules list

nyx rules list [--lang <SLUG>] [--kind <KIND>] [--class-only|--no-class] [--json]

Flag	Values
--lang	Language slug (javascript, typescript, python, java, php, go, ruby, rust, c, cpp). Cap-class entries (language = "all") still surface alongside any language filter unless --no-class is set.
--kind	class (cap-class entry), source, sink, sanitizer
--class-only	Show only the cap-class registry entries, suppressing per-language label rules and gated sinks.
--no-class	Suppress cap-class registry entries, show only per-language label rules and gated sinks. Conflicts with --class-only.
--json	Emit JSON instead of the human-readable table. Schema matches the /api/rules response.

Examples:

# Browse the seven new vulnerability classes
nyx rules list --class-only

# All Java sinks
nyx rules list --lang java --kind sink

# JSON output for scripted filtering
nyx rules list --json | jq '.[] | select(.cap == "ldap_injection")'

The enabled column reflects the analysis.disabled_rules overlay from your config, so a rule disabled in nyx.local shows up here too. Custom rules added via nyx config add-rule appear at the end with is_custom: true.

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#Exit codes

See output.md. Summary: 0 on success (including findings without --fail-on), 1 when --fail-on trips, non-zero on scan errors.

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#Environment variables

Runtime behaviour:

Variable	Description
RUST_LOG	Set tracing verbosity (e.g. RUST_LOG=debug nyx scan .)
NO_COLOR	Disable ANSI color output

Engine toggles (legacy, still honored; prefer CLI flags or [analysis.engine] config):

Variable	Matches
NYX_CONSTRAINT	--constraint-solving
NYX_ABSTRACT_INTERP	--abstract-interp
NYX_CONTEXT_SENSITIVE	--context-sensitive
NYX_SYMEX, NYX_CROSS_FILE_SYMEX, NYX_SYMEX_INTERPROC	--symex and friends
NYX_SMT	--smt (no-op without the smt feature)
NYX_BACKWARDS	--backwards-analysis
NYX_PARSE_TIMEOUT_MS	--parse-timeout-ms
NYX_MAX_ORIGINS, NYX_MAX_POINTSTO	--max-origins, --max-pointsto