Linting automatically adds changes incompatible with Prettier

[fasterius]

Description of the bug

When running linting with the latest version of nf-core tools (2.11) it automatically changes the formatting in modules.json - changes that Prettier (version 3.1.1, the latest) fails - this is not the case with version 2.10. This is an example of the changes introduced with nf-core lint:

[...]
"fastqc": {
    "branch": "master",
    "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
    "installed_by": [
        "modules"
    ]
}
[...]

The relevant lines are the three with the intalled_by setting; Prettier wants this to be "installed_by": ["modules"], i.e. on a single line.

I was under the impression that linting wouldn't write any changes unless the --fix flag was also supplied? I tried to see where this was changed, but all I could find was a PR for sorting the modules list (https://github.com/nf-core/tools/pull/2570/files). Not too familiar with the nf-core tools code, so not sure if that's it or something else.

Command used and terminal output

$ git clone [email protected]:nf-core/spatialtranscriptomics.git
$ cd spatialtranscriptomics
$ nf-core lint
$ git diff

This problem persists for e.g. the nf-core/rnaseq/ pipeline as well - I checked just to make sure it wasn't just the pipeline I was working on.

System information

Nextflow: 23.04.4.5881
Hardware: MacBook Pro 2023
Executor: local
OS: MacOS
Version of nf-core/tools: 2.11
Python version: 3.12.1

[mirpedrol]

Thanks for reporting :) This is now fixed with v2.11.1

[fasterius]

Wow, that was quick! It does indeed work now, thanks a lot!