nextflow lint -exclude misses some cases when absolute paths are reported

[mahesh-panchal]

Bug report

I'm using nextflow lint to check syntax in my repo. What's strange is when I exclude nf-core it sometimes reports absolute paths which include nf-core.

Expected behavior and actual behavior

✨ Pixi task (lint): nextflow lint -exclude .pixi .                                                                                 
Warn  modules/local/dnadotplot/main.nf:20:9: Variable was declared but not used
│  20 |     def prefix = task.ext.prefix ?: "${meta.id}"
╰     |         ^^^^^^

...

Warn  subworkflows/local/prepare_input/main.nf:167:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
│ 167 |     input.hic_ch.filter { !it.isEmpty() }
╰     |                            ^^

...

Error nf-test.config:3:18: Unexpected input: ':'
│   3 |         "nf-test": "0.9.0"
╰     |                  ^

Nextflow linting complete!
 ❌ 2 files had 2 errors
 ✅ 137 files had no errors

In this version it reports only relative paths. But when I add exclude nf-core:

✨ Pixi task (lint): nextflow lint -exclude .pixi -exclude nf-core .                                                                
Warn  modules/local/dnadotplot/main.nf:20:9: Variable was declared but not used
│  20 |     def prefix = task.ext.prefix ?: "${meta.id}"
╰     |         ^^^^^^

...

Warn  modules/local/functions.nf:84:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
│  84 |             .join( join_args, rhs.map{ [ it[0].subMap(args.keySet) ] +
╰     |                                          ^^

...

Warn  /Users/mahpa906/Documents/Projects/Earth-Biogenome-Project-pilot/modules/nf-core/tabix/tabix/main.nf:33:9: Variable was declared but not used
│  33 |     def prefix = task.ext.prefix ?: "${meta.id}"
╰     |         ^^^^^^

Warn  /Users/mahpa906/Documents/Projects/Earth-Biogenome-Project-pilot/modules/nf-core/tidk/plot/main.nf:37:9: Variable was declared but not used
│  37 |     def args = task.ext.args ?: ''
╰     |         ^^^^

...

Error nf-test.config:3:18: Unexpected input: ':'
│   3 |         "nf-test": "0.9.0"
╰     |                  ^

Nextflow linting complete!
 ❌ 2 files had 2 errors
 ✅ 106 files had no errors

The paths are now a mix of relative and absolute, and still includes some with nf-core in them.

Steps to reproduce the problem

git clone https://github.com/NBISweden/Earth-Biogenome-Project-pilot.git
cd Earth-Biogenome-Project-pilot
nextflow run lint -exclude .pixi -exclude nf-core .

Program output

It's included above to show actual output.

Environment

• Nextflow version: 25.10.4
• Java version: openjdk 17.0.11 2024-04-16 LTS
• Operating system: macOS
• Bash version: zsh 5.9 (arm64-apple-darwin25.0)

Additional context

I wonder if this has anything to do with the - in nf-core. I tested by replacing nf-core with local and it still printed out absolute paths with local in them.