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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/ampliconpipeline/master/nextflow_schema.json",
"title": "ebi-metagenomics/ampliconpipeline pipeline parameters",
"description": "MGnify amplicon 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,
"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/ampliconpipeline/usage#samplesheet-input).",
"fa_icon": "fas fa-file-csv",
"schema": "assets/schema_input.json"
},
"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"
}
}
},
"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
},
"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
},
"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)."
},
"save_trimmed_fail": {
"type": "boolean",
"default": true,
"description": "For fastp, specify true to save files that failed to pass trimming thresholds"
},
"mpt_version": {
"type": "string",
"default": "0.1.3--pyhdfd78af_0",
"description": "Version of the mgnify-pipelines-toolkit to use."
}
}
},
"ref_dbs": {
"title": "Ref DBs",
"type": "object",
"description": "Paths to the different reference databases needed for the pipeline",
"default": "",
"properties": {
"ssu_db_fasta": {
"type": "string",
"format": "file-path",
"description": "Path to SILVA-SSU processed fasta file"
},
"ssu_db_tax": {
"type": "string",
"format": "file-path",
"description": "Path to SILVA-SSU processed tax file"
},
"ssu_db_otu": {
"type": "string",
"format": "file-path",
"description": "Path to SILVA-SSU processed otu file"
},
"ssu_db_mscluster": {
"type": "string",
"format": "file-path",
"description": "Path to SILVA-SSU processed mscluster file"
},
"ssu_label": {
"type": "string",
"default": "SILVA-SSU",
"description": "SILVA SU Label"
},
"lsu_db_fasta": {
"type": "string",
"format": "file-path",
"description": "Path to SILVA-LSU processed fasta file"
},
"lsu_db_tax": {
"type": "string",
"format": "file-path",
"description": "Path to SILVA-LSU processed tax file"
},
"lsu_db_otu": {
"type": "string",
"format": "file-path",
"description": "Path to SILVA-LSU processed otu file"
},
"lsu_db_mscluster": {
"type": "string",
"format": "file-path",
"description": "Path to SILVA-LSU processed mscluster file"
},
"lsu_label": {
"type": "string",
"default": "SILVA-LSU",
"description": "SILVA LSU Label"
},
"dada2_silva_label": {
"type": "string",
"default": "DADA2-SILVA",
"description": "DADA2 SILVA label"
},
"dada2_pr2_label": {
"type": "string",
"default": "DADA2-PR2",
"description": "DADA2 PR2 label"
},
"unite_db_fasta": {
"type": "string",
"format": "file-path",
"description": "Path to UNITE processed fasta file"
},
"unite_db_tax": {
"type": "string",
"format": "file-path",
"description": "Path to UNITE processed tax file"
},
"unite_db_otu": {
"type": "string",
"format": "file-path",
"description": "Path to UNITE processed otu file"
},
"unite_db_mscluster": {
"type": "string",
"format": "file-path",
"description": "Path to UNITE processed mscluster file"
},
"unite_label": {
"type": "string",
"default": "UNITE",
"description": "UNITE label"
},
"itsone_db_fasta": {
"type": "string",
"description": "Path to ITSoneDB processed fasta file"
},
"itsone_db_tax": {
"type": "string",
"format": "file-path",
"description": "Path to ITSoneDB processed tax file"
},
"itsone_db_otu": {
"type": "string",
"format": "file-path",
"description": "Path to ITSoneDB processed otu file"
},
"itsone_db_mscluster": {
"type": "string",
"format": "file-path",
"description": "Path to ITSoneDB processed mscluster file"
},
"itsone_label": {
"type": "string",
"default": "ITSoneDB",
"description": "ITSoneDB label"
},
"pr2_db_fasta": {
"type": "string",
"format": "file-path",
"description": "Path to PR2 processed fasta file"
},
"pr2_db_tax": {
"type": "string",
"format": "file-path",
"description": "Path to PR2 processed tax file"
},
"pr2_db_otu": {
"type": "string",
"format": "file-path",
"description": "Path to PR2 processed otu file"
},
"pr2_db_mscluster": {
"type": "string",
"format": "file-path",
"description": "Path to PR2 processed mscluster file"
},
"pr2_label": {
"type": "string",
"default": "PR2",
"description": "PR2 label"
},
"rfam": {
"type": "string",
"format": "file-path",
"description": "Path to Rfam processed covariance model file"
},
"claninfo": {
"type": "string",
"format": "file-path",
"description": "Path to Rfam processed claninfo subset"
},
"std_primer_library": {
"type": "string",
"format": "directory-path",
"description": "Path to standard primer library"
}
}
},
"max_job_request_options": {
"title": "Max job request options",
"type": "object",
"fa_icon": "fab fa-acquisitions-incorporated",
"description": "Set the top limit for requested resources for any single job.",
"help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
"properties": {
"max_cpus": {
"type": "integer",
"description": "Maximum number of CPUs that can be requested for any single job.",
"default": 16,
"fa_icon": "fas fa-microchip",
"hidden": true,
"help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
},
"max_memory": {
"type": "string",
"description": "Maximum amount of memory that can be requested for any single job.",
"default": "128.GB",
"fa_icon": "fas fa-memory",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"hidden": true,
"help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
},
"max_time": {
"type": "string",
"description": "Maximum amount of time that can be requested for any single job.",
"default": "240.h",
"fa_icon": "far fa-clock",
"pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
"hidden": true,
"help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
}
}
}
},
"allOf": [
{
"$ref": "#/defs/input_output_options"
},
{
"$ref": "#/defs/generic_options"
},
{
"$ref": "#/defs/ref_dbs"
},
{
"$ref": "#/defs/max_job_request_options"
}
]
}