CI
096d01f274
Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-kj8js
Source commit: 491efceaaf
Source message: deploy: 7f820d2607f3e1fabc0183915d1bb427715e18ae
238 lines
8.7 KiB
JSON
238 lines
8.7 KiB
JSON
{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "spaceranger_count",
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"description": "Count gene expression and protein expression reads from a single capture area.",
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"type": "object",
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"$defs": {
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"inputs": {
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"title": "Inputs",
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"type": "object",
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"description": "No description",
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"properties": {
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"gex_reference": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "Path of folder containing 10x-compatible reference",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"/path/to/refdata-gex-GRCh38-2020-A\"`. "
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},
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"input": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "Path to a directory containing input FASTQ data",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"/path/to/fastq_folder\"`. "
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},
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"probe_set": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "CSV file specifying the probe set used",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv\"`. "
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},
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"cytaimage": {
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"type": "string",
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"format": "path",
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"description": "Brightfield image generated by the CytAssist instrument",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"cyta_image.tif\"`. "
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},
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"image": {
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"type": "string",
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"format": "path",
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"description": "H&E or fluorescence microscope image in TIFF or JPG format",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"brightfield.tif\"`. "
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}
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}
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},
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"outputs": {
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"title": "Outputs",
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"type": "object",
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"description": "No description",
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"properties": {
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"output": {
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"type": "string",
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"format": "path",
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"description": "The folder to store the alignment results",
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"help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`, example: `\"/path/to/output\"`. ",
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"default": "$id.$key.output"
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}
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}
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},
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"slide information": {
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"title": "Slide Information",
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"type": "object",
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"description": "No description",
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"properties": {
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"slide": {
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"type": "string",
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"description": "Visium slide serial number (e.g., 'V10J25-015')",
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"help_text": "Type: `string`, multiple: `False`, example: `\"V10J25-015\"`. "
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},
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"area": {
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"type": "string",
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"description": "Visium capture area identifier (e.g., 'A1')",
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"help_text": "Type: `string`, multiple: `False`, example: `\"A1\"`. "
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},
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"unknown_slide": {
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"type": "string",
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"description": "Use this option if the slide serial number and area were entered incorrectly on the CytAssist \ninstrument and the correct values are unknown",
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"help_text": "Type: `string`, multiple: `False`, choices: ``visium-1`, `visium-2`, `visium-2-large`, `visium-hd``. ",
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"enum": [
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"visium-1",
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"visium-2",
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"visium-2-large",
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"visium-hd"
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]
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},
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"slidefile": {
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"type": "string",
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"format": "path",
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"description": "Slide design file for offline use",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"slide_design.gpr\"`. "
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},
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"override_id": {
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"type": "boolean",
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"description": "Overrides the slide serial number and capture area provided in the Cytassist image metadata",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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}
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}
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},
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"image options": {
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"title": "Image Options",
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"type": "object",
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"description": "No description",
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"properties": {
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"darkimage": {
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"type": "string",
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"format": "path",
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"description": "Multi-channel, dark-background fluorescence image",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"fluorescence.tif\"`. "
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},
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"colorizedimage": {
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"type": "string",
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"format": "path",
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"description": "Color image representing pre-colored dark-background fluorescence images",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"colored_fluorescence.tif\"`. "
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},
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"dapi_index": {
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"type": "integer",
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"description": "Index of DAPI channel (1-indexed) of fluorescence image",
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"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
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},
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"image_scale": {
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"type": "number",
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"description": "Microns per microscope image pixel",
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"help_text": "Type: `double`, multiple: `False`, example: `0.65`. "
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},
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"reorient_images": {
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"type": "boolean",
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"description": "Whether to rotate and mirror image to align fiducial pattern",
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"help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
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"default": true
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}
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}
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},
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"processing options": {
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"title": "Processing Options",
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"type": "object",
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"description": "No description",
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"properties": {
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"create_bam": {
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"type": "boolean",
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"description": "Enable or disable BAM file generation",
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"help_text": "Type: `boolean`, multiple: `False`, required, default: `true`. ",
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"default": true
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},
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"nosecondary": {
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"type": "boolean",
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"description": "Disable secondary analysis (e.g., clustering)",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"r1_length": {
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"type": "integer",
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"description": "Hard trim the input Read 1 to this length before analysis",
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"help_text": "Type: `integer`, multiple: `False`. "
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},
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"r2_length": {
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"type": "integer",
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"description": "Hard trim the input Read 2 to this length before analysis",
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"help_text": "Type: `integer`, multiple: `False`. "
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},
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"filter_probes": {
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"type": "boolean",
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"description": "Whether to filter the probe set using the \"included\" column",
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"help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
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"default": true
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},
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"custom_bin_size": {
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"type": "integer",
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"description": "Bin Visium HD data to specified size in microns (4-100, even values only) in addition to the standard binning size (2 µm, 8 µm, 16 µm)",
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"help_text": "Type: `integer`, multiple: `False`. "
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}
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}
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},
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"input selection": {
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"title": "Input Selection",
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"type": "object",
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"description": "No description",
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"properties": {
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"project": {
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"type": "string",
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"description": "Project folder name within mkfastq output",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"sample": {
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"type": "string",
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"description": "Prefix of FASTQ filenames to select",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"lanes": {
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"type": "array",
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"items": {
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"type": "integer"
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},
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"description": "Only use FASTQs from selected lanes",
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"help_text": "Type: `integer`, multiple: `True`, example: `[1;2;3]`. "
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}
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}
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},
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"nextflow input-output arguments": {
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"title": "Nextflow input-output arguments",
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"type": "object",
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"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
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"properties": {
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"publish_dir": {
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"type": "string",
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"description": "Path to an output directory.",
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"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
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}
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}
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}
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},
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"allOf": [
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{
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"$ref": "#/$defs/inputs"
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},
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{
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"$ref": "#/$defs/outputs"
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},
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{
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"$ref": "#/$defs/slide information"
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},
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{
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"$ref": "#/$defs/image options"
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},
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{
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"$ref": "#/$defs/processing options"
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},
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{
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"$ref": "#/$defs/input selection"
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},
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{
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"$ref": "#/$defs/nextflow input-output arguments"
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}
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]
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}
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