Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add Nextflow schema #511

Merged
merged 14 commits into from
Jun 28, 2023
Merged

Add Nextflow schema #511

Changes from all commits
Commits
Show all changes
14 commits
Select commit Hold shift + click to select a range
3cc616f
Add initial Nextflow schema for input parameters
adamjtaylor Feb 2, 2023
bfa60a0
Update nextflow_schema.json
adamjtaylor Feb 2, 2023
28036b7
Update nextflow schema w cache id 1680544409_a7171b6f8d1a
adamjtaylor Apr 3, 2023
bda1594
Merge branch 'labsyspharm:master' into add-schema
adamjtaylor Apr 3, 2023
d5fd67a
Update schema valid values
adamjtaylor Apr 3, 2023
870dc9b
Missing comma in schema
adamjtaylor Apr 3, 2023
5391268
Add segmentation combinations
adamjtaylor Apr 3, 2023
13e3085
Add downstream combinations
adamjtaylor Apr 3, 2023
395f943
Merge branch 'labsyspharm:master' into add-schema
adamjtaylor Apr 8, 2023
9d25354
Merge branch 'labsyspharm:master' into add-schema
adamjtaylor May 17, 2023
c7ac3b5
Merge branch 'labsyspharm:master' into add-schema
adamjtaylor Jun 28, 2023
d9fd6ca
Refinements to schema
adamjtaylor Jun 28, 2023
477b80b
Refine start-at and stop-at descriptions
adamjtaylor Jun 28, 2023
213b047
Refine background option description
adamjtaylor Jun 28, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
222 changes: 222 additions & 0 deletions nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,222 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"$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 or symbolically linked from work directories to the project directory",
"enum": [
"copy",
"move",
"symlink"
],
"default": "copy"
},
"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"
}
]
}