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nextflow_schema.json
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209 lines (209 loc) · 8.86 KB
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/ScaleBio/ScaleTagToolkit/main/nextflow_schema.json",
"title": "ScaleBio Tag Toolkit pipeline parameters",
"description": "See Readme.md for further documentation.",
"type": "object",
"definitions": {
"help_options":{
"title":"Help options",
"type":"object",
"fa_icon": "fas fa-terminal",
"properties": {
"help": {
"type":"boolean",
"description":"Print params description to console?",
"hidden":true,
"default":false
},
"show_hidden_params":{
"type":"boolean",
"description":"Show parameters marked as hidden when invoking --help?",
"hidden":true,
"default":false
}
}
},
"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.",
"properties": {
"samples": {
"type": "string",
"format": "file-path",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"description": "Csv file describing all samples in the analysis run (required!)",
"fa_icon": "fas fa-file-csv"
},
"runFolder": {
"type": "string",
"description": "Top-level sequencer run directory (or null when using fastq input)",
"format": "directory-path",
"default": null
},
"fastqSamplesheet": {
"description": "bcl-convert samplesheet.csv when running from BCL; If null, will be auto-generated based on samples.csv",
"hidden": true,
"type": "string",
"format": "file-path",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"default": null
},
"fastqDir": {
"type": "string",
"description":"Directory containing pre-generated FASTQs files (or null when using runFolder input)",
"format": "directory-path",
"default": null
},
"libStructure": {
"type": "string",
"format": "file-path",
"mimetype": "text/json",
"pattern": "^\\S+\\.json$",
"description": "Json file describing library structure and index/barcode sequences",
"fa_icon": "fas fa-file-json",
"default": "lib-atacUniversal-a.json"
},
"outDir": {
"type": "string",
"description": "Name of the output directory for workflow results",
"format": "directory-path",
"default": "out"
}
},
"required": [
"samples", "outDir"
]
},
"reference_genome_options": {
"title": "Reference genome options",
"type": "object",
"fa_icon": "fas fa-dna",
"description": "Reference genome related files and options required for the workflow.",
"properties": {
"genome": {
"type": "string",
"description": "json file with paths and parameters for the reference genome (required!)",
"format": "file-path",
"mimetype": "text/json",
"pattern": "^\\S+\\.json$"
},
"peaks": {
"type": "string",
"description": "Pre-defined peaks (bed / narrowPeaks) to use for quantification (count matrix output) instead of de-novo peak calls",
"format": "file-path",
"default": null
}
},
"required": [
"genome"
]
},
"analysis_options": {
"title": "Analysis options",
"type": "object",
"fa_icon": "fas fa-sliders-h",
"description": "Configure analysis steps and options",
"properties": {
"fastqc": {
"type": "boolean",
"description": "Enable fastqc on all input fastq files",
"default": true
},
"trimFastq": {
"type": "boolean",
"description":"Enable adapter trimming (if running from Fastq input)",
"default": true
},
"adapter": {
"type": "string",
"description": "Adapter sequence (3')",
"default": "CTGTCTCTTATACACATCT"
},
"subsample": {
"type": "boolean",
"description": "Enable sub-sampling of reads (fastq files) to a fixed depth. Target depth per-sample set in samples.csv",
"hidden": true
},
"splitMerge": {
"type": "boolean",
"hidden": true
},
"qcAndArchRParams": {
"type": "string",
"description": "yml file containing parameters for QC and ArchR analysis",
"default": "${projectDir}/references/parameters/qcAndArchR.yml"
},
"generateReport": {
"type": "boolean",
"description": "Generate an interactive HTML report of results?",
"default": true
},
"runArchR": {
"type": "boolean",
"description": "Attempt to run automated ArchR analysis?",
"default": true
},
"archrCondaEnv": {
"type": "string",
"description": "Path to created conda environment with ArchR installed",
"hidden": true
}
}
},
"max_job_request_options": {
"title": "Max job request options",
"type": "object",
"fa_icon": "fab fa-acquisitions-incorporated",
"description": "Set the top limit for requested resources for any single job.",
"help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
"properties": {
"max_cpus": {
"type": "integer",
"description": "Maximum number of CPUs that can be requested for any single job.",
"default": 32,
"fa_icon": "fas fa-microchip",
"hidden": true
},
"max_memory": {
"type": "string",
"description": "Maximum amount of memory that can be requested for any single job.",
"default": "30.GB",
"fa_icon": "fas fa-memory",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"hidden": true
},
"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|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": "#/definitions/help_options"
},
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/reference_genome_options"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/analysis_options"
}
]
}