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nextflow_schema.json
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nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/seqeralabs/nf-aggregate/main/nextflow_schema.json",
"title": "seqeralabs/nf-aggregate pipeline parameters",
"description": "Minimal nf-core pipeline compatible with template",
"type": "object",
"definitions": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"schema": "assets/schema_input.json",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"description": "File containing Seqera Platform run identifiers one per line.",
"fa_icon": "fas fa-file-excel"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
}
}
},
"pipeline_options": {
"title": "Pipeline-specific options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Generic options for the pipeline.",
"help_text": "Generic options for the pipeline.",
"properties": {
"seqera_api_endpoint": {
"type": "string",
"default": "https://api.cloud.seqera.io",
"description": "Seqera Platform API endpoint URL.",
"fa_icon": "fas fa-question-circle"
},
"seqera_cli_extra_args": {
"type": "string",
"description": "Extra arguments to pass to the Seqera Platform CLI command in addition to defaults defined by the pipeline.",
"fa_icon": "fas fa-plus"
},
"java_truststore_path": {
"type": "string",
"description": "Path to custom cacerts Java truststore used by Seqera Platform.",
"fa_icon": "fas fa-key"
},
"java_truststore_password": {
"type": "string",
"description": "Password for custom cacerts Java truststore used by Seqera Platform.",
"fa_icon": "fas fa-key"
},
"skip_run_gantt": {
"type": "boolean",
"description": "Skip GANTT chart creation for each run.",
"fa_icon": "fas fa-fast-forward"
},
"skip_multiqc": {
"type": "boolean",
"description": "Skip MultiQC.",
"fa_icon": "fas fa-fast-forward"
}
},
"required": ["seqera_api_endpoint"]
},
"generic_options": {
"title": "Generic options",
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"help": {
"type": "boolean",
"description": "Display help text.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"multiqc_config": {
"type": "string",
"format": "file-path",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"multiqc_logo": {
"type": "string",
"description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
"fa_icon": "fas fa-image",
"hidden": true
},
"multiqc_title": {
"type": "string",
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature",
"hidden": true
},
"modules_testdata_base_path": {
"type": "string",
"description": "Base path / URL for data used in the modules",
"hidden": true
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
},
"validationShowHiddenParams": {
"type": "boolean",
"fa_icon": "far fa-eye-slash",
"description": "Show all params when using `--help`",
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
},
"validationFailUnrecognisedParams": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters fails when an unrecognised parameter is found.",
"hidden": true,
"help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
},
"validationLenientMode": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters in lenient more.",
"hidden": true,
"help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
},
"validationSkipDuplicateCheck": {
"type": "boolean",
"description": "Do not check samples are not duplicates of each other.",
"help_text": "Allows samples in the samplesheet to be duplicates of each other.",
"hidden": true,
"fa_icon": "fas fa-clone"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/pipeline_options"
},
{
"$ref": "#/definitions/generic_options"
}
]
}