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nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/labsyspharm/mcmicro/master/nextflow_schema.json",
"title": "MCMICRO pipeline parameters",
"description": "The MCMICRO pipeline uses Nextflow to transforms multi-channel whole-slide images into single-cell data. The JSON Schema was built using the nf-core pipeline schema builder.",
"type": "object",
"definitions": {
"mandatory_parameters": {
"title": "Mandatory parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"in": {
"type": "string",
"format": "directory-path",
"description": "Location of the input directory. Must contain markers.csv (comma-delimited file containing a column titled `marker_name`) and appropriate directory structure. See documentation at mcmicro.org"
}
},
"required": [
"in"
]
},
"optional_parameters": {
"title": "Optional parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"sample_name": {
"type": "string",
"description": "The name of the experiment/specimen"
},
"start-at": {
"type": "string",
"description": "Name of the first step to be executed by the pipeline.",
"enum": [
"illumination",
"registration",
"background",
"dearray",
"segmentation",
"watershed",
"quantification",
"downstream"
],
"default": "registration"
},
"stop-at": {
"type": "string",
"description": "Name of the final step to be executed by the pipeline.",
"default": "quantification",
"enum": [
"illumination",
"registration",
"background",
"dearray",
"segmentation",
"watershed",
"quantification",
"downstream"
]
},
"tma": {
"type": "boolean",
"description": "If selected, MCMICRO treats input data as a tisssue microarray and will attempt to de-array cores using `coreograph`. If omitted, the input is assumed to be a whole-slide image."
},
"background": {
"type": "boolean",
"description": "If selected, MCMICRO treats input data as if background channels should be subtracted using the `Backsub` module. See mcmicro.org documentation for details on additional `background` and `remove` columns required in the `markers.csv` file."
},
"segmentation": {
"type": "string",
"description": "A list of segmentation modules to run",
"default": "unmicst",
"enum": [
"unmicst",
"ilastik",
"cypository",
"mesmer",
"cellpose",
["unmicst", "ilastik"],
["unmicst", "cypository"],
["unmicst", "mesmer"],
["unmicst", "cellpose"],
["ilastik", "cypository"],
["ilastik", "mesmer"],
["ilastik", "cellpose"],
["cypository", "mesmer"],
["cypository", "cellpose"],
["mesmer", "cellpose"],
["unmicst", "ilastik", "cypository"],
["unmicst", "ilastik", "mesmer"],
["unmicst", "ilastik", "cellpose"],
["unmicst", "cypository", "mesmer"],
["unmicst", "cypository", "cellpose"],
["unmicst", "mesmer", "cellpose"],
["ilastik", "cypository", "mesmer"],
["ilastik", "cypository", "cellpose"],
["ilastik", "mesmer", "cellpose"],
["cypository", "mesmer", "cellpose"],
["unmicst", "ilastik", "cypository", "mesmer"],
["unmicst", "ilastik", "cypository", "cellpose"],
["unmicst", "ilastik", "mesmer", "cellpose"],
["unmicst", "cypository", "mesmer", "cellpose"],
["ilastik", "cypository", "mesmer", "cellpose"],
["unmicst", "ilastik", "cypository", "mesmer", "cellpose"]
]
},
"downstream": {
"type": "string",
"description": "A list of downstream modules to run",
"default": "scimap",
"enum": [
"naivestates",
"scimap",
"fastpg",
"scanpy",
"flowsom",
["naivestates", "scimap"],
["naivestates", "fastpg"],
["naivestates", "scanpy"],
["naivestates", "flowsom"],
["scimap", "fastpg"],
["scimap", "scanpy"],
["scimap", "flowsom"],
["fastpg", "scanpy"],
["fastpg", "flowsom"],
["scanpy", "flowsom"],
["naivestates", "scimap", "fastpg"],
["naivestates", "scimap", "scanpy"],
["naivestates", "scimap", "flowsom"],
["naivestates", "fastpg", "scanpy"],
["naivestates", "fastpg", "flowsom"],
["naivestates", "scanpy", "flowsom"],
["scimap", "fastpg", "scanpy"],
["scimap", "fastpg", "flowsom"],
["scimap", "scanpy", "flowsom"],
["naivestates", "scimap", "fastpg", "scanpy"],
["naivestates", "scimap", "fastpg", "flowsom"],
["naivestates", "scimap", "scanpy", "flowsom"],
["naivestates", "fastpg", "scanpy", "flowsom"],
["scimap", "fastpg", "scanpy", "flowsom"],
["naivestates", "scimap", "fastpg", "scanpy", "flowsom"]
]
},
"viz": {
"type": "boolean",
"description": "If selected a Minerva story will be generated in sequential groups of 4 channels using auto-Minerva"
},
"qc-files": {
"type": "string",
"description": "Should QC files should be copied, moved, hard linked, or symbolically linked from work directories to the project directory. 'inherit' may be specified to use the value of the publish_dir_mode pipeline parameter.",
"enum": [
"copy",
"move",
"link",
"symlink",
"inherit",
],
"default": "inherit"
},
"segmentation-channel": {
"type": "string",
"description": "One or more channels to use for segmentation, specified using 1-based indexing; values will be forwarded to all segmentation modules",
"default": "1"
},
"segmentation-recyze": {
"type": "boolean",
"description": "If selected the image will be reduced to the channels specified in segmentation-channel prior to being provided to the segmentation modules."
}
}
},
"parameters_for_individual_modules": {
"title": "Parameters for individual modules",
"type": "object",
"description": "Module-specific parameters can be specified using the various `opts` arguments, followed by the parameters enclosed inside single quotes `'`:",
"default": "",
"properties": {
"ashlar-opts": {
"type": "string",
"description": "Arguments to ASHLAR"
},
"unmicst-opts": {
"type": "string",
"description": "Arguments to UnMicst"
},
"ilastik-opts": {
"type": "string",
"description": "Arguments to Ilastik"
},
"s3seg-opts": {
"type": "string",
"description": "Arguments to S3Segmenter"
},
"mcquant-opts": {
"type": "string",
"description": "Arguments to MCQUANT"
},
"naievestates-opts": {
"type": "string",
"description": "Arguments to naievestates"
},
"ilastik-model": {
"type": "string",
"description": "A custom `.ilp` file to be used as the classifier model for ilastik.",
"pattern": "^.+\\.ilp$",
"format": "file-path"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/mandatory_parameters"
},
{
"$ref": "#/definitions/optional_parameters"
},
{
"$ref": "#/definitions/parameters_for_individual_modules"
}
]
}