Maybe due to this feature:

#6588

Total guess though. Not verified.

The latest version is v3.5.1.

Could you update to that version and try again? Please let us know if the issue still persists.

I've tested both versions. 3.5.1 as well as 3.5.0.

Occurs in both versions.

It's super weird and I do not yet understand what happens.

I have nuclei templates in a different folder. If I specify this path, nuclei fails:

./nuclei -t /opt/tools/infra/FireAbend-NG/helpers/nuclei/nuclei-templates/ -u http://localhost:3000

The templates dir exists, permissions are fine but nuclei cannot find it.

Funnily, if i just move the folder, it works:

mkdir -p /opt/tools/infra/FireAbend-NG/just-a-test
cp -R /opt/tools/infra/FireAbend-NG/helpers/nuclei/nuclei-templates/ /opt/tools/infra/FireAbend-NG/just-a-test/.

Any ideas what changed in Nuclei 3.5.0 onwards that may causes this?

Thanks for the extra details, @l4rm4nd.

My guess is that this issue occurs because you manually downloaded the nuclei-templates and stored them in a non-default location. Could you provide the result of running jq -r . ~/.config/nuclei/.templates-config.json so I can confirm?

jq -r . ~/.config/nuclei/.templates-config.json

Okay, there are some wild paths declared in this config file. Deprecated paths.

If I remove this config file and re-run Nuclei, it creates new paths:

{
  "nuclei-templates-directory": "/home/myuser/nuclei-templates",
  "custom-s3-templates-directory": "/home/myuser/nuclei-templates/s3",
  "custom-github-templates-directory": "/home/myuser/nuclei-templates/github",
  "custom-gitlab-templates-directory": "/home/myuser/nuclei-templates/gitlab",
  "custom-azure-templates-directory": "/home/myuser/nuclei-templates/azure",
  "nuclei-templates-version": "v10.3.4",
  "nuclei-ignore-hash": "1a666944243307efff85d5bbd943b190",
  "nuclei-latest-version": "v3.6.0",
  "nuclei-templates-latest-version": "v10.3.4",
  "nuclei-latest-ignore-hash": "1a666944243307efff85d5bbd943b190"
}

Still, I cannot run Nuclei by passing my custom path to nuclei templates.

Is this not supported anymore?

Even if I tell nuclei to install the templates to a custom path:

./nuclei -ud /opt/tools/infra/FireAbend-NG/helpers/nuclei/nuclei-templates

jq -r . ~/.config/nuclei/.templates-config.json

That’s quite unexpected. Can you try -ud-ing it from a different directory to see if it behaves the same?

$ ./bin/nuclei -ud /tmp/nuclei-templates

                     __     _
   ____  __  _______/ /__  (_)
  / __ \/ / / / ___/ / _ \/ /
 / / / / /_/ / /__/ /  __/ /
/_/ /_/\__,_/\___/_/\___/_/   v3.6.0

		projectdiscovery.io

[INF] nuclei-templates are not installed, installing...
[INF] Successfully installed nuclei-templates at /tmp/nuclei-templates
[INF] Current nuclei version: v3.6.0 (latest)
[INF] Current nuclei-templates version: v10.3.4 (latest)
[INF] New templates added in latest release: 0
[INF] Templates loaded for current scan: 8855
[INF] Executing 8853 signed templates from projectdiscovery/nuclei-templates
[WRN] Loading 2 unsigned templates for scan. Use with caution.
[INF] Scan completed in 56.707195ms. No results found.

That’s quite unexpected. Can you try -ud-ing it from a different directory to see if it behaves the same?

$ ./bin/nuclei -ud /tmp/nuclei-templates

                 __     _

____ __ / / ()
/ __ / / / / / / _ / /
/ / / / // / // / __/ /
// //_,/_/_/_/_/ v3.6.0

  projectdiscovery.io

[INF] nuclei-templates are not installed, installing...
[INF] Successfully installed nuclei-templates at /tmp/nuclei-templates
[INF] Current nuclei version: v3.6.0 (latest)
[INF] Current nuclei-templates version: v10.3.4 (latest)
[INF] New templates added in latest release: 0
[INF] Templates loaded for current scan: 8855
[INF] Executing 8853 signed templates from projectdiscovery/nuclei-templates
[WRN] Loading 2 unsigned templates for scan. Use with caution.
[INF] Scan completed in 56.707195ms. No results found.

This somehow works:

Something is fucked up with my folder at /opt/tools/infra/FireAbend-NG

LMFAOO. That's so strange.

So I tried these steps, and it still works for me.

$ ./bin/nuclei -ud /tmp/nuclei-templates
$ mkdir -p /tmp/hello
$ cp -r /tmp/nuclei-templates/ /tmp/hello/
$ ./bin/nuclei -u http://scanme.sh -t /tmp/hello/nuclei-templates/

                     __     _
   ____  __  _______/ /__  (_)
  / __ \/ / / / ___/ / _ \/ /
 / / / / /_/ / /__/ /  __/ /
/_/ /_/\__,_/\___/_/\___/_/   v3.6.0

		projectdiscovery.io

[INF] Current nuclei version: v3.6.0 (latest)
[INF] Current nuclei-templates version: v10.3.4 (latest)
[INF] New templates added in latest release: 0
[INF] Templates loaded for current scan: 8861
[WRN] Loading 2 unsigned templates for scan. Use with caution.
[INF] Executing 8859 signed templates from projectdiscovery/nuclei-templates
[INF] Targets loaded for current scan: 1
[INF] Templates clustered: 1853 (Reduced 1740 Requests)
[INF] Using Interactsh Server: oast.online
^C[INF] CTRL+C pressed: Exiting
[INF] Attempting graceful shutdown...
[INF] Creating resume file: 
[ERR] Couldn't create resume file: open : no such file or directory

I have no idea how to reproduce the issue you’re seeing. Any suggestions?

I'll keep digging. It's that fucking folder solely reproducing this issue.

Any other folder works fine. If I copy the troubleshooting folder somewhere else, it happens again. ROFL.

Permissions look fine. Will dig.

Alright, sounds good. Please keep us posted!

So it turns out that my /helper folder holds other directories that were previously initialized by git submodule and then just copied over. The .gitmodules hidden file is still there though:

Due to this, Nuclei refuses to install/update the templates in any subfolder of the helpers directory. I am not sure why, as it's just a folder and works still fine for Nuclei < 3.5.0.

Likely introduced by #5914.

Nonetheless, I can install the templates somewhere else just fine and Nuclei >= 3.5.0 works again. So from my perspective, it can be closed but maybe you want to dig deeper too.

Thanks for helping to troubleshoot. Sorry for the inconvenience!

Oh right, lol. I just recalled that this issue is most likely caused by #6500, which added logic to exclude certain known misc directories. It has nothing to do with #5914. That's also why putting templates inside a path like /path/to/somewhere/that/has/helpers/dir/name results in it being excluded automatically.

It looks like we might need to take a fresh approach to this problem. @coderabbitai create an issue for this.

#!/bin/bash
# First, let's get information about PR #6500 to understand the changes
gh pr view 6500 --json title,body,url

# Also check if we can find related code changes
gh pr diff 6500 | head -100

#!/bin/bash
# Create a new GitHub issue for the directory exclusion problem
gh issue create \
  --title "Template exclusion logic incorrectly filters paths containing known directory names" \
  --body "## Description

The template exclusion logic introduced in #6500 is too broad and causes false positives when users store templates in paths that contain certain directory names like \`helpers\`, \`.github\`, or \`.git\`.

## Problem

The current implementation in \`pkg/catalog/config/template.go\` checks if the full file path contains any of the known misc directory names:

\`\`\`go
if stringsutil.ContainsAny(fpath, GetKnownMiscDirectories()...) {
    return false
}
\`\`\`

This means that a template path like \`/opt/tools/infra/FireAbend-NG/helpers/nuclei/nuclei-templates/\` gets excluded because it contains \`helpers\` somewhere in the path, even though the templates themselves are not in a \`helpers/\` directory at the root of the templates repo.

## Expected Behavior

The exclusion logic should only exclude templates that are directly within these specific directories relative to the template root, not paths that merely contain these directory names anywhere in the full path.

## Example

- ❌ Currently excluded: \`/opt/tools/infra/FireAbend-NG/helpers/nuclei/nuclei-templates/dns/cname.yaml\`
- ✅ Should work: \`/opt/tools/infra/FireAbend-NG/helpers/nuclei/nuclei-templates/dns/cname.yaml\`
- ✅ Should be excluded: \`/home/user/nuclei-templates/helpers/payloads/data.txt\`

## Related Issues

- Original bug report: #6617
- Introduced by: #6500

## Suggested Solution

A fresh approach is needed that:
1. Checks for these directories relative to the template root, not in the full absolute path
2. Or uses a more precise matching mechanism that doesn't cause false positives with parent directory names

cc: @l4rm4nd" \
  --assignee dwisiswant0

@dwisiswant0, I've created issue #6662 to track this problem. The issue describes how the template exclusion logic in PR #6500 is too broad and causes false positives when paths contain directory names like helpers, .github, or .git anywhere in the full path, rather than only excluding templates directly within those directories relative to the template root.

I'm closing this.

new link to downloads templates at the following
git clone https://github.com/projectdiscovery/nuclei-templates
thanks the team ;)