Hello does the nf core pipelines linter not like ` ` in para nf-core #linting

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Hello, does the nf-core pipelines linter not like ...

# linting

Niklas Schandry

10/31/2024, 3:48 PM

Hello, does the nf-core pipelines linter not like

in params? I get things like this for all params that contain an underscore:

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nextflow_config: Config default value incorrect: params.flye_mode is set as "--nano-hq" in nextflow_schema.json but is null in nextflow.config.                                                                                         
nextflow_config: Config default value incorrect: params.flye_args is set as "" in nextflow_schema.json but is null in nextflow.config.

But they are correctly defined in nextflow.config?

mashehu

10/31/2024, 3:49 PM

can you post your nextflow_config and nextlfow_schema.json?

Niklas Schandry

10/31/2024, 3:50 PM

nextflow config for those two:

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params.flye_mode = "--nano-hq"
    params.flye_args = ""

schema:

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"flye_mode": {
            "type": "string",
            "description": "flye mode",
            "default": "\"--nano-hq\""
        },
        "flye_args": {
            "type": "string",
            "description": "additional args for flye",
            "default": "\"\""
        },

Niklas Schandry

10/31/2024, 3:50 PM

There are (many) other params, but this only happens for the ones with an underscore in the name and string type

mashehu

10/31/2024, 3:51 PM

"\"--nano-hq\""

should be

"--nano-hq"

mashehu

10/31/2024, 3:51 PM

(i think)

Niklas Schandry

10/31/2024, 3:52 PM

ok, this came out of

nf-core schema create

I think

Niklas Schandry

10/31/2024, 3:52 PM

sorry, build

Niklas Schandry

10/31/2024, 3:53 PM

ah, okay, I get it, I think i added the quotes when I provided the default value in the web-thing

Niklas Schandry

10/31/2024, 3:57 PM

Hm, while that was probably an issue, there is something else, a similar issue occurs now:

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nextflow_config: Config default value incorrect: params.flye_mode is set as --nano-hq in nextflow_schema.json but is null in nextflow.config. 
nextflow_config: Config default value incorrect: params.flye_args is set as `` in nextflow_schema.json but is null in nextflow.config.

config:

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params.flye_mode = "--nano-hq"
    params.flye_args = ""

schema:

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"flye_mode": {
            "type": "string",
            "description": "flye mode",
            "default": "--nano-hq"
        },
        "flye_args": {
            "type": "string",
            "description": "additional args for flye",
            "default": ""
        },

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