Cryptic error message when input schema file is missing

(first reported in the nf-core Slack)

When creating a pipeline schema with nf-core pipelines schema build, the schema builder assumes that you will also create a schema for your input csv.

Partial contents of nextflow_schema.json:

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  ...
  "$defs": {
    "input_output_options": {
      "title": "Input/output options",
      ...
      "properties": {
        "input": {
          "type": "string",
          "format": "file-path",
          "exists": true,
          "schema": "assets/schema_input.json",
          "mimetype": "text/csv",

If you do not then manually create assets/schema_input.json based on the input manifest, when you try to use validateParameters() in the workflow, nextflow will throw a cryptic error message:

ERROR ~ Unable to determine the current character, it is not a string, number, array, or object

The current character read is '' with an int value of 0
Unable to determine the current character, it is not a string, number, array, or object
line number 1
index number 255

The nextflow schema passes linting (nf-core pipelines schema lint) without errors, even though the input schema does not exist.

The error is fixed by deleting the line "schema": "assets/schema_input.json", from nextflow_schema.json, or by creating a valid input schema.

Versions

• nextflow: 24.10.3
• nf-core: 3.2.0

Start by tracing validateParameters() for a schema reference to missing assets/schema_input.json, then compare its behavior with nf-core pipelines schema lint. Reproduce the failure using the nextflow_schema.json example and the listed Nextflow and nf-core versions. Done means the missing input schema produces a clear diagnostic, with regression coverage for this case.