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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/genomeassembler/master/nextflow_schema.json",
"title": "nf-core/genomeassembler pipeline parameters",
"description": "Assemble genomes from long ONT or pacbio HiFi reads",
"type": "object",
"$defs": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"schema": "assets/schema_input.json",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"description": "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/genomeassembler/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",
"default": "./results"
},
"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"
}
}
},
"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"
}
}
},
"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",
"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,
"default": "copy"
},
"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"
},
"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
}
}
},
"general_parameters": {
"title": "General parameters",
"type": "object",
"description": "Options controlling pipeline behavior",
"default": "",
"properties": {
"use_ref": {
"type": "boolean",
"description": "use reference genome",
"default": true
},
"skip_assembly": {
"type": "boolean",
"description": "skip assembly steps",
"help_text": "Skip assembly and perform only qc."
},
"skip_alignments": {
"type": "boolean",
"description": "skip alignments during qc"
}
},
"fa_icon": "fas fa-bacon"
},
"ont_options": {
"title": "ONT options",
"type": "object",
"description": "Options for ONT reads",
"default": "",
"properties": {
"ont": {
"type": "boolean",
"description": "ONT reads available?"
},
"collect": {
"type": "boolean",
"description": "collect ONT reads into a single file"
},
"porechop": {
"type": "boolean",
"description": "run porechop on ONT reads"
},
"read_length": {
"type": "integer",
"description": "read length for genomescope (ONT only)",
"minimum": 1
},
"jellyfish": {
"type": "boolean",
"description": "run jellyfish on ONT reads to compute k-mer distribution and estimate genome size",
"default": true
},
"dump": {
"type": "boolean",
"description": "dump jellyfish output"
},
"kmer_length": {
"type": "integer",
"description": "kmer length to be used for jellyfish",
"default": 21,
"minimum": 1
}
}
},
"hifi_options": {
"title": "HiFi options",
"type": "object",
"description": "Options for HiFi reads",
"default": "",
"properties": {
"hifi": {
"type": "boolean",
"description": "HiFi reads available?"
},
"lima": {
"type": "boolean",
"description": "run lima on HiFi reads?"
},
"pacbio_primers": {
"type": "string",
"description": "file containing pacbio primers for trimming with lima"
}
}
},
"assembly_options": {
"title": "Assembly options",
"type": "object",
"description": "Options controlling assembly",
"default": "",
"properties": {
"assembler": {
"type": "string",
"description": "Assembler to use. Valid choices are: `'hifiasm'`, `'flye'`, or `'flye_on_hifiasm'`. `flye_on_hifiasm` will scaffold flye assembly (ont) on hifiasm (hifi) assembly using ragtag",
"enum": ["flye", "hifiasm", "flye_on_hifiasm"],
"default": "flye"
},
"genome_size": {
"type": "integer",
"description": "expected genome size, optional",
"minimum": 1
},
"flye_mode": {
"type": "string",
"description": "flye mode",
"default": "--nano-hq",
"enum": ["--pacbio-raw", "--pacbio-corr", "--pacbio-hifi", "--nano-raw", "--nano-corr", "--nano-hq"]
},
"flye_args": {
"type": "string",
"description": "additional args for flye"
},
"hifiasm_ont": {
"type": "boolean",
"description": "Use hifi and ONT reads with `hifiasm --ul`"
},
"hifiasm_args": {
"type": "string",
"description": "Extra arguments passed to `hifiasm`"
}
}
},
"short_read_options": {
"title": "Short read options",
"type": "object",
"description": "Options for short reads",
"default": "",
"properties": {
"short_reads": {
"type": "boolean",
"description": "Short reads available?"
},
"trim_short_reads": {
"type": "boolean",
"description": "trim short reads with trimgalore",
"default": true
},
"meryl_k": {
"type": "integer",
"description": "kmer length for meryl / merqury",
"default": 21,
"minimum": 1
}
}
},
"polishing_options": {
"title": "Polishing options",
"type": "object",
"description": "Polishing options",
"default": "",
"properties": {
"polish_pilon": {
"type": "boolean",
"description": "Polish assembly with pilon? Requires short reads"
},
"polish_medaka": {
"type": "boolean",
"description": "Polish assembly with medaka (ONT only)"
},
"medaka_model": {
"type": "string",
"description": "model to use with medaka"
}
}
},
"scaffolding_options": {
"title": "Scaffolding options",
"type": "object",
"description": "Scaffolding options",
"default": "",
"properties": {
"scaffold_longstitch": {
"type": "boolean",
"description": "Scaffold with longstitch?"
},
"scaffold_links": {
"type": "boolean",
"description": "Scaffolding with links?"
},
"scaffold_ragtag": {
"type": "boolean",
"description": "Scaffold with ragtag (requires reference)?"
}
}
},
"qc_options": {
"title": "QC options",
"type": "object",
"description": "Options for QC tools",
"default": "",
"properties": {
"merqury": {
"type": "boolean",
"default": true,
"description": "Run merqury"
},
"qc_reads": {
"type": "string",
"description": "Long reads that should be used for QC when both ONT and HiFi reads are provided. Options are `'ONT'` or `'HIFI'`",
"enum": ["ONT", "HIFI"],
"default": "ONT"
},
"busco": {
"type": "boolean",
"description": "Run BUSCO?",
"default": true
},
"busco_db": {
"type": "string",
"description": "Path to busco db (optional)"
},
"busco_lineage": {
"type": "string",
"description": "Busco lineage to use",
"default": "brassicales_odb10"
},
"quast": {
"type": "boolean",
"description": "Run quast",
"default": true
}
}
},
"annotations_options": {
"title": "Annotations options",
"type": "object",
"description": "Options controlling annotation liftover",
"default": "",
"properties": {
"lift_annotations": {
"type": "boolean",
"description": "Lift-over annotations (requires reference)?",
"default": true
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/institutional_config_options"
},
{
"$ref": "#/$defs/generic_options"
},
{
"$ref": "#/$defs/general_parameters"
},
{
"$ref": "#/$defs/ont_options"
},
{
"$ref": "#/$defs/hifi_options"
},
{
"$ref": "#/$defs/assembly_options"
},
{
"$ref": "#/$defs/short_read_options"
},
{
"$ref": "#/$defs/polishing_options"
},
{
"$ref": "#/$defs/scaffolding_options"
},
{
"$ref": "#/$defs/qc_options"
},
{
"$ref": "#/$defs/annotations_options"
}
]
}