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Add extra_args to modules meta-schema.json #7783

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Jun 19, 2025
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Add extra_args to modules meta-schema.json #7783

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13 changes: 13 additions & 0 deletions modules/meta-schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,19 @@
"type": "string"
}
},
"extra_args": {
"type": "array",
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The current implementation in tools that I used was an object/map:

extra_args:
  args:
    description: 'samtools index'

I found this reduced the duplication/nesting of the fields and felt more intuitive to write.

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oh ok, I missed that. But maybe we should make it an array, to be consistent with the other sections: tools, input, output.

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I would be pro consistency, I don't think it makes a huge amount of difference.

To copy @mirpedrol 's example on slack:

for a map we would write

extra_args:
  args:
    description: 'samtools index'

a list would be

extra_args:
  - args:
        description: 'samtools index'

Given the rest of the meta.yaml is using teh - bullet notation then I should already be able to intuite it I think.

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I agree with @awgymer that a key-val pair would be easier to use, but a list is more consistent with the rest of the tools. I'd prefer consistency here, so would go with an array.

"description": "Extra arguments for the module",
"items": {
"type" : "object",
"properties": {
"description": {
"type": "string",
"description": "Description of the argument"
}
}
}
},
"input": {
"type": "array",
"description": "Input channels for the module",
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