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Simplify parameter docs structure
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@nictru
nictru committed Sep 25, 2024
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90 changes: 45 additions & 45 deletions nextflow_schema.json
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}
}
},
"mirna_processing_options": {
"title": "miRNA options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define paths and threasholds for miRNA analysis.",
"properties": {
"mirna_expression": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/tsv",
"pattern": "^\\S+\\.tsv$",
"description": "path to tab-separated file providing the expression counts of mirnas, which are created in pipeline 'smrnaseq'. \n\nmirna \t sample1 \t sample2 \t sample3 \t\nid1\t count_sample1 \t count_sample2 \t count_sample3 \t\nid2 \t ... \t ... \t ... \t \n",
"fa_icon": "fas fa-file-tsv"
},
"mirna_min_sample_percentage": {
"type": "number",
"fa_icon": "fas fa-circle-notch",
"description": "Minimum percentage of samples, a miRNA has to be expressed in to pass filtering.",
"help_text": "The mirna_min_percentage parameter sets the minimum percentage of samples in which a miRNA must be expressed to pass filtering. The default value is 0.2, which means a miRNA must be detected in at least 20% of the samples to be included in the analysis.",
"default": 0.2,
"minimum": 0
},
"mirna_min_reads": {
"type": "integer",
"fa_icon": "fas fa-circle-notch",
"description": "Minimum number of reads, a miRNA is required to have to pass filtering.",
"help_text": "This parameter determines the minimum number of reads that a miRNA must have to pass filtering. The default is 5, meaning a miRNA must have at least 5 reads across the samples to be considered for analysis.",
"default": 5,
"minimum": 0
},
"mirna_correlation": {
"type": "string",
"fa_icon": "fas fa-wrench",
"description": "Specifies the type of correlation to be used when analyzing the relationship between miRNA and transcript expression levels. Valid options are 'pearson' or 'spearman'.",
"help_text": "Select the correlation method to be applied in the correlation analysis of miRNAs.",
"default": "pearson",
"pattern": "^(pearson|spearman)$"
}
}
},
"discovery_options": {
"title": "Discovery Options",
"circrna_options": {
"title": "circRNA Options",
"type": "object",
"fa_icon": "fas fa-circle-notch",
"description": "Parameters for circrna discovery.",
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"help_text": "Select one or a combination of circRNA quantification tools for the pipeline e.g:\n--quantification_tools 'ciriquant,psirc'",
"default": "ciriquant,psirc",
"pattern": "^((ciriquant|psirc)(,(ciriquant|psirc))*)+$"
}
}
},
"mirna_processing_options": {
"title": "miRNA options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define paths and threasholds for miRNA analysis.",
"properties": {
"mirna_expression": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/tsv",
"pattern": "^\\S+\\.tsv$",
"description": "path to tab-separated file providing the expression counts of mirnas, which are created in pipeline 'smrnaseq'. \n\nmirna \t sample1 \t sample2 \t sample3 \t\nid1\t count_sample1 \t count_sample2 \t count_sample3 \t\nid2 \t ... \t ... \t ... \t \n",
"fa_icon": "fas fa-file-tsv"
},
"mirna_min_sample_percentage": {
"type": "number",
"fa_icon": "fas fa-circle-notch",
"description": "Minimum percentage of samples, a miRNA has to be expressed in to pass filtering.",
"help_text": "The mirna_min_percentage parameter sets the minimum percentage of samples in which a miRNA must be expressed to pass filtering. The default value is 0.2, which means a miRNA must be detected in at least 20% of the samples to be included in the analysis.",
"default": 0.2,
"minimum": 0
},
"mirna_min_reads": {
"type": "integer",
"fa_icon": "fas fa-circle-notch",
"description": "Minimum number of reads, a miRNA is required to have to pass filtering.",
"help_text": "This parameter determines the minimum number of reads that a miRNA must have to pass filtering. The default is 5, meaning a miRNA must have at least 5 reads across the samples to be considered for analysis.",
"default": 5,
"minimum": 0
},
"mirna_correlation": {
"type": "string",
"fa_icon": "fas fa-wrench",
"description": "Specifies the type of correlation to be used when analyzing the relationship between miRNA and transcript expression levels. Valid options are 'pearson' or 'spearman'.",
"help_text": "Select the correlation method to be applied in the correlation analysis of miRNAs.",
"default": "pearson",
"pattern": "^(pearson|spearman)$"
},
"mirna_tools": {
"type": "string",
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"$ref": "#/definitions/alignment_options"
},
{
"$ref": "#/definitions/discovery_options"
"$ref": "#/definitions/circrna_options"
},
{
"$ref": "#/definitions/mirna_processing_options"
"$ref": "#/definitions/mirna_options"
},
{
"$ref": "#/definitions/institutional_config_options"
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