Sorry, it is not clear to me how can I solve this linting issue?

╭─ [✗] 1 Module Test Failed ───────────────────────────────────────────────────╮
│                ╷                             ╷                               │
│ Module name    │ File path                   │ Test message                  │
│╶───────────────┼─────────────────────────────┼──────────────────────────────╴│
│ mirtop/export  │ modules/nf-core/mirtop/exp… │ The environment.yml of the    │
│                │                             │ module mirtop/export is not   │
│                │                             │ valid: {'name':               │
│                │                             │ 'mirtop_export', 'channels':  │
│                │                             │ ['conda-forge', 'bioconda'],  │
│                │                             │ 'dependencies':               │
│                │                             │ ['bioconda::mirtop=0.4.25',   │
│                │                             │ 'bioconda::samtools=1.15.1',  │
│                │                             │ 'conda-forge::r-base=4.1.1',  │
│                │                             │ 'conda-forge::r-data.table=1. │
│                │                             │ 14.2']} should not be valid   │
│                │                             │ under {'required': ['name']}. │
│                ╵                             ╵                               │
╰──────────────────────────────────────────────────────────────────────────────╯

This is due to a recent change that went in today. You need to remove the

name

thank you!! :)

Hi @Phil Ewels! I just came across this thread since I was experiencing the same issue when linting my pipeline. Thanks for your help! Should we also remove the 'defaults' from the channels field in our environment.yml? After removing the 'name' field, my nf-core lint is still throwing an error, saying that the defaults channel is not a part of "conda" and "bioconda."

As far as I am aware, you should remove the defaults as well as it is not part of the template anymore. Hope this helps!

@Anabella Trigila this helps thank you so much! Out of curiosity, do you know what the nf-core template is allowing for the 'dependencies' field? I currently have "YOUR-TOOL-HERE" but my nf-core lint is throwing an error saying: The environment.yml of the module genotypevariants/all is not valid: 'YOUR-TOOL-HERE' does not match '^.[^><]=[^><].$'.

You need to pin a version I think

What is the current solution for this error? I removed the name line from the environment.yml of a module and then I get

CRITICAL 'name'

• Run nf-core/tools dev version • Remove name from the conda environment yaml

Ok, passes with the dev version. But what's the proper way to pass that test without the dev version atm?

The shared #CJRH30T6V repo uses the dev version of tools at the moment for CI, so you should remove the name when contributing there from now on

Okidoki, thanks!