From fdc4f3c0b3c6043912d0942c360c7f13588fe0dc Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 25 Sep 2024 20:19:25 +0200 Subject: [PATCH] Simplify parameter docs structure --- nextflow_schema.json | 90 ++++++++++++++++++++++---------------------- 1 file changed, 45 insertions(+), 45 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index abda2412..49c7903e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -54,49 +54,8 @@ } } }, - "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.", @@ -140,6 +99,47 @@ "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)$" }, "mirna_tools": { "type": "string", @@ -619,10 +619,10 @@ "$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"