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Configuration

The plugin can be configured using several configuration options. These options have to be in the validation scope which means you can write them in two ways:

validation.<option> = <value>

OR

validation {
    <option1> = <value1>
    <option2> = <value2>
}

parametersSchema

This option can be used to set the parameters JSON schema to be used by the plugin. This will affect parameter validation (validateParameters()), the summary logs (paramsSummaryLog() and paramsSummaryMap()) and the creation of the help messages.

validation.parametersSchema = "path/to/schema.json" // default "nextflow_schema.json"

This option can either be a path relative to the root of the pipeline directory or a full path to the JSON schema (Be wary to not use hardcoded local paths to ensure your pipeline will keep working on other systems)

monochromeLogs

This option can be used to turn of the colored logs from nf-schema. This can be useful if you run a Nextflow pipeline in an environment that doesn't support colored logging. This option will automatically be set to true when ANSI logging is disabled in Nextflow.

validation.monochromeLogs = <true|false> // default: false

lenientMode

This option can be used to make the type validation more lenient. In normal cases a value of "12" will fail if the type is an integer. This will succeed in lenient mode since that string can be cast to an integer.

validation.lenientMode = <true|false> // default: false

showHiddenParams

Deprecated

This configuration option has been deprecated since v2.1.0. Please use validation.help.showHidden instead.

By default the parameters, that have the "hidden": true annotation in the JSON schema, will not be shown in the help message. Turning on this option will make sure the hidden parameters are also shown.

validation.showHiddenParams = <true|false> // default: false

ignoreParams

This option can be used to turn off the validation for certain parameters. It takes a list of parameter names as input. Currently, the parameter nf_test_output is added to ignoreParams by default.

validation.ignoreParams = ["param1", "param2"] // default: []

defaultIgnoreParams

Warning

This option should only be used by pipeline developers

This option does exactly the same as validation.ignoreParams, but provides pipeline developers with a way to set the default parameters that should be ignored. This way the pipeline users don't have to re-specify the default ignored parameters when using the validation.ignoreParams option.

validation.defaultIgnoreParams = ["param1", "param2"] // default: []

maxErrValSize

Configure the maximum characters of a value that may be shown in an error message. It takes a whole number above or equal to 1. A value will be truncated when it goes over the maximum amount of characters.

Setting this option to -1 will allow any amount of characters for values.

See the below example where the limit is to 20 characters:

* --test (abcdefghij...qrstuvwxyz): Value is [string] but should be [integer]

validation.maxErrValSize = 100 // default: 150

help

The validation.help config scope can be used to configure the creation of the help message.

This scope contains the following options:

enabled

This option is used to enable the creation of the help message when the help parameters are used in the nextflow run command.

validation.help.enabled = true // default: false

shortParameter

This option can be used to change the --help parameter to another parameter. This parameter will print out the help message with all top level parameters.

validation.help.shortParameter = "giveMeHelp" // default: "help"

--giveMeHelp will now display the help message instead of --help for this example. This parameter will print out the help message.

fullParameter

This option can be used to change the --helpFull parameter to another parameter.

validation.help.shortParameter = "giveMeHelpFull" // default: "helpFull"

--giveMeHelpFull will now display the expanded help message instead of --helpFull for this example.

showHiddenParameter

This option can be used to change the --showHidden parameter to another parameter. This parameter tells the plugin to also include the hidden parameters into the help message.

validation.help.showHiddenParameter = "showMeThoseHiddenParams" // default: "showHidden"

--showMeThoseHiddenParams will now make sure hidden parameters will be shown instead of --showHidden for this example.

showHidden

By default the parameters, that have the "hidden": true annotation in the JSON schema, will not be shown in the help message. Turning on this option will make sure the hidden parameters are also shown.

validation.help.showHidden = <true|false> // default: false

beforeText

This option does not affect the help message created by the paramsHelp() function

Any string provided to this option will printed before the help message.

validation.help.beforeText = "Running pipeline version 1.0" // default: ""

Info

All color values (like \033[0;31m, which means the color red) will be filtered out when validation.monochromeLogs is set to true

command

This option does not affect the help message created by the paramsHelp() function

This option can be used to add an example command to the help message. This will be printed after the beforeText and before the help message.

validation.help.command = "nextflow run main.nf --input samplesheet.csv --outdir output" // default: ""

This example will print the following message:

Typical pipeline command:

  nextflow run main.nf --input samplesheet.csv --outdir output

Info

All color values (like \033[0;31m, which means the color red) will be filtered out when validation.monochromeLogs is set to true

afterText

This option does not affect the help message created by the paramsHelp() function

Any string provided to this option will be printed after the help message.

validation.help.afterText = "Please cite the pipeline owners when using this pipeline" // default: ""

Info

All color values (like \033[0;31m, which means the color red) will be filtered out when validation.monochromeLogs is set to true

enumLength

This option can be used to set the maximum length of enum values in the help message. This is useful when the enum values are very long and would make the help message hard to read.

The default value is set to the value in the COLUMNS environment variable or 100 characters if that variable isn't set. Set this option to -1 to disable the length limit.

validation.help.enumLength = <integer>

Summary

The validation.summary config scope can be used to configure the output of the paramsSummaryLog() function.

This scope contains the following options:

beforeText

Any string provided to this option will printed before the parameters log message.

validation.summary.beforeText = "Running pipeline version 1.0" // default: ""

Info

All color values (like \033[0;31m, which means the color red) will be filtered out when validation.monochromeLogs is set to true

afterText

Any string provided to this option will be printed after the parameters log message.

validation.summary.afterText = "Please cite the pipeline owners when using this pipeline" // default: ""

Info

All color values (like \033[0;31m, which means the color red) will be filtered out when validation.monochromeLogs is set to true

hideParams

Takes a list of parameter names to exclude from the parameters summary created by paramsSummaryMap() and paramsSummaryLog()

validation.summary.hideParams = ["param1", "nested.param"] // default: []

Logging

The validation.logging config scope can be used to configure the logging of the plugin. These config options can receive the following values:

  • skip: Skip logging
  • debug: Log debug messages (only printed in the .nextflow.log file)
  • info: Log info messages (also printed in the terminal)
  • warn: Log warning messages (also printed in the terminal, but in yellow)
  • error: Fail the pipeline and print the error message

This scope contains the following options:

unrecognisedParams

This option can be used to configure the logging of unrecognised parameters.

validation.logging.unrecognisedParams = "warn" // default: "warn"

unrecognisedHeaders

This option can be used to configure the logging of unrecognised headers in samplesheets.

validation.logging.unrecognisedHeaders = "warn" // default: "warn"