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nf-core

Hey! I I use `nf-core pipeline schema build`  and the webserver says: `Error: Could not load schema JSON! Substituted for a blank schema.` Where do I see the error. The schema itself 'looks valid' according to the tool.

could you post the schema here, so i can test it locally?

I tried to open this one: <https://github.com/bigbio/quantms/blob/dev/nextflow_schema.json>

I see in Seqera that for one of the inputs the data file explorer icon is not shown - and wanted to figure out why.

I tried both to make the adjustments suggested and also to directly skip to the webtool using `nf-core pipelines schema build --web-only`

The `root_folder` (and it would also be nice to be able to select a `outdir` using the 'Browse' option. But after all, I would like to edit the schema using the webbrowser eventually.

So maybe folders are not supported, only `format:"file-path"`  with a `mime_type`?

```...
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/tsv",
                    "pattern": "^\\S+\\.(?:tsv|sdrf)$",
                     ...
                    "fa_icon": "fas fa-file-csv"
                },
                "outdir": {
                    "type": "string",
                    "description": "The output directory where the results will be saved.",
                    "default": "./results",
                    "fa_icon": "fas fa-folder-open"
                },
...```

Screenshot 2025-10-13 at 15.20.09.png

the problem is <https://github.com/bigbio/quantms/blob/dev/nextflow_schema.json#L1141> this crashes the current version of the website builder because it expects a string

image.png

thanks! I guessed it is some stupid mistake, but I could just not figure out how to see on which line it crashes. Is it supported in the standard tool-kit.

Regarding Seqera: What does lead to a browse button to appear?

Now that I can edit the schema is the recommended way (thanks a lot!) I will try to figure out if setting `"format": "directory-path"` will do the trick!
```                "outdir": {
                    "type": "string",
                    "description": "The output directory where the results will be saved.",
                    "default": "./results",
                    "fa_icon": "fas fa-folder-open",
                    "format": "directory-path"
                },```

sorry, no idea about what the seqera interface is looking for

Just to write it down here once: I noticed that when you switch from format type file to folder, previously set file paramters, e.g.

```"schema": "assets/schema_input.json",
"mimetype": "text/csv",```
are not deleted using the web builder (`nf-core pipelines schema build` ). That is unexpected behaviour to me. i stared building a custom workflow from the nf-core template.

we are in the middle of a rebuild of this interface, i will make sure this doesn't happen in the new interface.

but a folder can't have a mimetype or a schema, right?

I don't believe so. I was under the impression we don't actually use mimetype anyway and it was deprecated? 