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nextflow_schema.json
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nextflow_schema.json
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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/biocorecrg/ExOrthist/master/nextflow_schema.json",
"title": "biocorecrg/ExOrthist pipeline parameters",
"description": "ExOrthist is a Nextflow-based pipeline to obtain groups of exon orthologous at all evolutionary timescales.",
"type": "object",
"$defs": {
"generic_options": {
"title": "Generic Options",
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
"properties": {
"wf": {
"type": "string",
"description": "Workflow to be run, by default the main one. Alternative is plot",
"default": "main"
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"hidden": true
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
}
}
},
"input_output_options": {
"title": "Input/Output Options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": [
"annotations",
"genomes",
"cluster",
"output"
],
"properties": {
"annotations": {
"type": "string",
"description": "Path to GTF annotation files",
"format": "file-path-pattern",
"default": "${projectDir}/test/GTF/*_annot-subsetted.gtf.gz"
},
"genomes": {
"type": "string",
"description": "Path to fasta genome files",
"format": "file-path-pattern",
"default": "${projectDir}/test/GENOMES/*_gDNA-subsetted.fasta.gz"
},
"cluster": {
"type": "string",
"description": "Path to cluster file (txt files)",
"format": "file-path",
"default": "${projectDir}/test/hg38_mm10_bosTau9.tab"
},
"output": {
"type": "string",
"description": "Output folder path",
"format": "directory-path",
"default": "${projectDir}/output_test",
"fa_icon": "fas fa-folder-open"
}
}
},
"analysis_parameters": {
"title": "Analysis Parameters",
"type": "object",
"fa_icon": "fas fa-map-signs",
"required": [
"evodists",
"long_dist",
"medium_dist",
"short_dist"
],
"properties": {
"evodists": {
"type": "string",
"description": "Path to a file with pairwise evolutionary distances",
"format": "file-path",
"default": "${projectDir}/test/evodists.txt"
},
"long_dist": {
"type": "string",
"description": "Long distance parameters",
"default": "2,0.10,0.40,0.15"
},
"medium_dist": {
"type": "string",
"description": "Medium distance parameters",
"default": "2,0.30,0.60,0.20"
},
"short_dist": {
"type": "string",
"description": "Short distance parameters",
"default": "2,0.50,0.60,0.25"
},
"alignmentnum": {
"type": "integer",
"description": "Alignment number",
"default": 1000
},
"orthogroupnum": {
"type": "integer",
"description": "Orthogroup number",
"default": 500
}
}
},
"additional_data": {
"title": "Additional Data",
"type": "object",
"fa_icon": "fas fa-terminal",
"properties": {
"extraexons": {
"type": "string",
"description": "Extra exons (e.g. from VastDB)",
"format": "file-path-pattern"
},
"bonafide_pairs": {
"type": "string",
"description": "Bona fide orthologous exon pairs",
"format": "file-path"
},
"orthopairs": {
"type": "string",
"description": "Orthopairs",
"format": "file-path"
},
"prevaln": {
"type": "string",
"description": "Pre-computed alignments",
"format": "directory-path"
}
}
},
"plot_parameters": {
"title": "Plot Parameters",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Specific parameters for generating plots",
"default": "",
"properties": {
"geneID": {
"type": "string",
"description": "Gene ID",
"default": "ENSG00000159055"
},
"ordered_species": {
"type": "string",
"description": "List of ordered species, separated by commas",
"default": "hg38,mm10,bosTau9"
},
"relevant_exs": {
"type": "string",
"description": "Relevant exons",
"default": "chr21:32274830-32274896"
},
"isoformID": {
"type": "string",
"description": "Isoform ID",
"default": "ENSP00000290130"
},
"sub_orthologs": {
"type": "string",
"description": "File with sub-orthologs information",
"format": "file-path"
},
"output_plot": {
"type": "string",
"description": "Path where to store resulting plot",
"format": "directory-path",
"default": "${projectDir}/output_plot"
}
}
},
"institutional_config_options": {
"title": "Institutional config options",
"type": "object",
"fa_icon": "fas fa-university",
"description": "Parameters used to describe centralised config profiles. These should not be edited.",
"help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"properties": {
"custom_config_version": {
"type": "string",
"description": "Git commit id for Institutional configs.",
"default": "master",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"custom_config_base": {
"type": "string",
"description": "Base directory for Institutional configs.",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"hidden": true,
"help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
"fa_icon": "fas fa-users-cog"
},
"config_profile_name": {
"type": "string",
"description": "Institutional config name.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_description": {
"type": "string",
"description": "Institutional config description.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_contact": {
"type": "string",
"description": "Institutional config contact information.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_url": {
"type": "string",
"description": "Institutional config URL link.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
}
}
},
"notification_options": {
"title": "Notification Options",
"type": "object",
"properties": {
"email": {
"type": "string",
"description": "Email for notification",
"format": "email"
},
"hook_url": {
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-broadcast-tower",
"help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/generic_options"
},
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/analysis_parameters"
},
{
"$ref": "#/$defs/additional_data"
},
{
"$ref": "#/$defs/plot_parameters"
},
{
"$ref": "#/$defs/institutional_config_options"
},
{
"$ref": "#/$defs/notification_options"
}
]
}