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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/EBI-Metagenomics/metaviraverse/main/nextflow_schema.json",
"title": "EBI-Metagenomics/metaviraverse pipeline parameters",
"description": "Viral catalogue generation pipeline",
"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.",
"fa_icon": "fas fa-file-csv"
},
"filter_rrna": {
"type": "boolean",
"help_text": "Filter out rRNA before processing",
"default": false
},
"vitap_db": {
"type": "string",
"format": "directory-path",
"description": "Path to VITAP DB.",
"help_text": "You need to pre-download VITAP DB https://figshare.com/articles/dataset/The_database_of_VITAP_2024_03_18_/25426159/3",
"fa_icon": "fas fa-folder-open"
},
"run_vitap_taxonomy": {
"type": "boolean",
"help_text": "Additionally generate taxonomy assignment for viral_sequences representatives with VITAP tool",
"default": false
},
"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"
},
"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"
}
}
},
"clustering_options": {
"title": "Clustering thresholds for ANI and coverage",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define clustering thresholds for ANI and coverage",
"properties": {
"cluster_vclust": {
"type": "boolean",
"help_text": "Use vclust as clustering tool",
"default": true
}
}
},
"amr_options": {
"title": "Antimicrobial resistence dbs and options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define AMR databases and options",
"properties": {
"amrfinderplus_db": {
"type": "string",
"help_text": "Path to amrfinderplus database",
"fa_icon": "fas fa-users-cog"
},
"deeparg_db": {
"type": "string",
"help_text": "Path to deeparg database",
"fa_icon": "fas fa-users-cog"
},
"deeparg_db_version": {
"type": "string",
"help_text": "Version of deeparg database",
"fa_icon": "fas fa-users-cog"
},
"deeparg_model": {
"type": "string",
"help_text": "Model of deeparg",
"fa_icon": "fas fa-users-cog"
},
"deeparg_tool_version": {
"type": "string",
"help_text": "Version of deeparg tool",
"fa_icon": "fas fa-users-cog"
},
"rgi_db": {
"type": "string",
"help_text": "Path of RGI db",
"fa_icon": "fas fa-users-cog"
},
"skip_amrfinderplus": {
"type": "boolean",
"help_text": "Flag to skip amrfinderplus ",
"default": true
},
"skip_deeparg": {
"type": "boolean",
"help_text": "Flag to skip deeparg ",
"default": true
},
"skip_rgi": {
"type": "boolean",
"help_text": "Flag to skip RGI ",
"default": false
}
}
},
"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",
"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
},
"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$",
"default": "25.MB",
"fa_icon": "fas fa-file-upload",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"multiqc_config": {
"type": "string",
"format": "file-path",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"multiqc_logo": {
"type": "string",
"description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
"fa_icon": "fas fa-image",
"hidden": true
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
},
"pipelines_testdata_base_path": {
"type": "string",
"fa_icon": "far fa-check-circle",
"description": "Base URL or local path to location of pipeline test dataset files",
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"hidden": true
},
"trace_report_suffix": {
"type": "string",
"fa_icon": "far calendar",
"description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/clustering_options"
},
{
"$ref": "#/$defs/amr_options"
},
{
"$ref": "#/$defs/institutional_config_options"
},
{
"$ref": "#/$defs/generic_options"
}
]
}