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nextflow_schema.json
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nextflow_schema.json
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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/nf-core/demultiplex/master/nextflow_schema.json",
"title": "nf-core/demultiplex pipeline parameters",
"description": "Demultiplexing pipeline for Illumina sequencing data",
"type": "object",
"$defs": {
"workflow_options": {
"title": "Workflow options",
"type": "object",
"description": "",
"default": "",
"properties": {
"trim_fastq": {
"type": "boolean",
"default": true,
"description": "Whether or not to skip trimming"
},
"skip_tools": {
"type": "string",
"default": "[]",
"description": "Comma-separated list of tools to skip (fastp,fastqc,kraken,multiqc,checkqc,falco,md5sum,samshee)"
},
"sample_size": {
"type": "integer",
"default": 100000,
"description": "Number of reads to subsample for contamination detection."
},
"kraken_db": {
"type": "string",
"format": "path",
"description": "Path to Kraken2 DB to use for screening"
},
"json_schema_validator": {
"type": "string",
"description": "String in JSON format to be passed to samshee module for samplesheet validation"
},
"name_schema_validator": {
"type": "string",
"description": "Schema name to be passed to samshee module for samplesheet validation"
},
"file_schema_validator": {
"type": "string",
"format": "file-path",
"description": "Local JSON file to be passed to samshee module for samplesheet validation"
},
"v1_schema": {
"type": "boolean",
"description": "Whether or not illumina samplesheet is v1 "
}
}
},
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"schema": "assets/schema_input.json",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/demultiplex/usage#samplesheet-input).",
"fa_icon": "fas fa-file-csv"
},
"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"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"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"
}
}
},
"demultiplex_options": {
"title": "Demultiplexing options",
"type": "object",
"fa_icon": "fas fa-microscope",
"description": "Options for demultiplexing.",
"required": ["demultiplexer"],
"properties": {
"demultiplexer": {
"type": "string",
"enum": ["bases2fastq", "bcl2fastq", "bclconvert", "fqtk", "sgdemux", "mkfastq"],
"description": "Demultiplexer to use.",
"fa_icon": "fas fa-microscope",
"default": "bclconvert"
}
}
},
"downstream_csv_options": {
"title": "Downstream CSV options",
"type": "object",
"description": "Options to customize downstream csv creation",
"default": "",
"properties": {
"strandedness": {
"type": "string",
"enum": ["unstranded", "auto", "reverse", "forward"],
"default": "auto",
"description": "Specifies the strandedness of RNA-Seq data for downstream sample sheet generation. This parameter does not affect the demultiplexing process but is used to generate the appropriate field in the nf-core/rnaseq samplesheet",
"fa_icon": "fas fa-arrows-alt-v"
}
}
},
"institutional_config_options": {
"title": "Institutional config options",
"type": "object",
"fa_icon": "fas fa-university",
"description": "Parameters used to describe centralised config profiles. These should not be edited.",
"help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"properties": {
"custom_config_version": {
"type": "string",
"description": "Git commit id for Institutional configs.",
"default": "master",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"custom_config_base": {
"type": "string",
"description": "Base directory for Institutional configs.",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"hidden": true,
"help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
"fa_icon": "fas fa-users-cog"
},
"config_profile_name": {
"type": "string",
"description": "Institutional config name.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_description": {
"type": "string",
"description": "Institutional config description.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_contact": {
"type": "string",
"description": "Institutional config contact information.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_url": {
"type": "string",
"description": "Institutional config URL link.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
}
}
},
"checkqc_options": {
"title": "CheckQC options",
"type": "object",
"description": "",
"default": "",
"properties": {
"checkqc_config": {
"type": "string",
"default": "[]",
"description": "Path to the checkqc config yml file.",
"fa_icon": "far fa-check-square"
}
}
},
"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": {
"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
},
"email_on_fail": {
"type": "string",
"description": "Email address for completion summary, only when pipeline fails.",
"fa_icon": "fas fa-exclamation-triangle",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
"help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
"hidden": true
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true
},
"max_multiqc_email_size": {
"type": "string",
"description": "File size limit when attaching MultiQC reports to summary emails.",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"default": "25.MB",
"fa_icon": "fas fa-file-upload",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"hook_url": {
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-people-group",
"help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
"hidden": true
},
"multiqc_config": {
"type": "string",
"format": "file-path",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"multiqc_logo": {
"type": "string",
"description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
"fa_icon": "fas fa-image",
"hidden": true
},
"multiqc_methods_description": {
"type": "string",
"description": "Custom MultiQC yaml file containing HTML including a methods description.",
"fa_icon": "fas fa-cog"
},
"remove_adapter": {
"type": "boolean",
"description": "Boolean whether to remove adapter information from Illumina samplesheet. If adapter information is present, the various bcl conversion tools will perform adapter trimming already at the demultiplexing step.",
"default": true
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
},
"pipelines_testdata_base_path": {
"type": "string",
"fa_icon": "far fa-check-circle",
"description": "Base URL or local path to location of pipeline test dataset files",
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/workflow_options"
},
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/demultiplex_options"
},
{
"$ref": "#/$defs/downstream_csv_options"
},
{
"$ref": "#/$defs/institutional_config_options"
},
{
"$ref": "#/$defs/checkqc_options"
},
{
"$ref": "#/$defs/generic_options"
}
]
}