CI
93f55cc2ee
Build pipeline: viash-hub.biobox.main-dkgvl
Source commit: ad89f43726
Source message: Add authors to package config and update author information (#180)
* Add authors to package config and update author information
* update changelog
* add linkedin
335 lines
12 KiB
JSON
335 lines
12 KiB
JSON
{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "multiqc",
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"description": "MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n",
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"type": "object",
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"$defs": {
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"input": {
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"title": "Input",
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"type": "object",
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"description": "No description",
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"properties": {
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"input": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"format": "path",
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"exists": true,
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"description": "File paths to be searched for analysis results to be included in the report.\n",
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"help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"data/results\"]`. "
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}
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}
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},
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"ouput": {
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"title": "Ouput",
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"type": "object",
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"description": "No description",
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"properties": {
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"output_report": {
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"type": "string",
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"format": "path",
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"description": "Filepath of the generated report.\n",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_report.html\"`, direction: `output`, example: `\"multiqc_report.html\"`. ",
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"default": "$id.$key.output_report.html"
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},
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"output_data": {
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"type": "string",
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"format": "path",
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"description": "Output directory for parsed data files",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_data\"`, direction: `output`, example: `\"multiqc_data\"`. ",
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"default": "$id.$key.output_data"
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},
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"output_plots": {
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"type": "string",
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"format": "path",
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"description": "Output directory for generated plots",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_plots\"`, direction: `output`, example: `\"multiqc_plots\"`. ",
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"default": "$id.$key.output_plots"
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}
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}
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},
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"modules and analyses to run": {
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"title": "Modules and analyses to run",
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"type": "object",
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"description": "No description",
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"properties": {
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"include_modules": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"description": "Use only these module",
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"help_text": "Type: `string`, multiple: `True`, example: `[\"fastqc\";\"cutadapt\"]`. "
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},
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"exclude_modules": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"description": "Do not use only these modules",
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"help_text": "Type: `string`, multiple: `True`, example: `[\"fastqc\";\"cutadapt\"]`. "
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},
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"ignore_analysis": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"description": "",
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"help_text": "Type: `string`, multiple: `True`, example: `[\"run_one/*\";\"run_two/*\"]`. "
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},
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"ignore_samples": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"description": "",
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"help_text": "Type: `string`, multiple: `True`, example: `[\"sample_1*\";\"sample_3*\"]`. "
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},
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"ignore_symlinks": {
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"type": "boolean",
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"description": "Ignore symlinked directories and files",
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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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"sample name handling": {
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"title": "Sample name handling",
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"type": "object",
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"description": "No description",
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"properties": {
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"dirs": {
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"type": "boolean",
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"description": "Prepend directory to sample names to avoid clashing filenames",
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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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"dirs_depth": {
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"type": "integer",
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"description": "Prepend n directories to sample names",
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"help_text": "Type: `integer`, multiple: `False`. "
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},
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"full_names": {
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"type": "boolean",
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"description": "Do not clean the sample names (leave as full file name)",
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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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"fn_as_s_name": {
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"type": "boolean",
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"description": "Use the log filename as the sample name",
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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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"replace_names": {
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"type": "string",
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"format": "path",
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"description": "TSV file to rename sample names during report generation",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"replace_names.tsv\"`. "
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}
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}
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},
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"report customisation": {
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"title": "Report Customisation",
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"type": "object",
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"description": "No description",
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"properties": {
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"title": {
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"type": "string",
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"description": "Report title",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"comment": {
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"type": "string",
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"description": "Custom comment, will be printed at the top of the report.\n",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"template": {
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"type": "string",
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"description": "Report template to use.\n",
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"help_text": "Type: `string`, multiple: `False`, choices: ``default`, `gathered`, `geo`, `highcharts`, `sections`, `simple``. ",
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"enum": [
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"default",
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"gathered",
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"geo",
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"highcharts",
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"sections",
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"simple"
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]
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},
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"sample_names": {
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"type": "string",
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"format": "path",
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"description": "TSV file containing alternative sample names for renaming buttons in the report.\n",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"sample_names.tsv\"`. "
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},
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"sample_filters": {
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"type": "string",
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"format": "path",
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"description": "TSV file containing show/hide patterns for the report\n",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"sample_filters.tsv\"`. "
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},
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"custom_css_file": {
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"type": "string",
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"format": "path",
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"description": "Custom CSS file to add to the final report\n",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_style_sheet.css\"`. "
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},
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"profile_runtime": {
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"type": "boolean",
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"description": "Add analysis of how long MultiQC takes to run to the report\n",
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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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"multiqc behaviour": {
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"title": "MultiQC behaviour",
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"type": "object",
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"description": "No description",
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"properties": {
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"verbose": {
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"type": "boolean",
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"description": "Increase output verbosity.\n",
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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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"quiet": {
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"type": "boolean",
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"description": "Only show log warnings\n",
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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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"strict": {
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"type": "boolean",
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"description": "Don't catch exceptions, run additional code checks to help development.\n",
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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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"development": {
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"type": "boolean",
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"description": "Development mode",
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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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"require_logs": {
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"type": "boolean",
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"description": "Require all explicitly requested modules to have log files",
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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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"no_megaqc_upload": {
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"type": "boolean",
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"description": "Don't upload generated report to MegaQC, even if MegaQC options are found.\n",
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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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"no_ansi": {
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"type": "boolean",
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"description": "Disable coloured log output.\n",
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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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"cl_config": {
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"type": "string",
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"description": "YAML formatted string that allows to customize MultiQC behaviour like input file detection.\n",
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"help_text": "Type: `string`, multiple: `False`, example: `\"qualimap_config: { general_stats_coverage: [20,40,200] }\"`. "
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}
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}
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},
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"output format": {
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"title": "Output format",
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"type": "object",
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"description": "No description",
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"properties": {
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"flat": {
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"type": "boolean",
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"description": "Use only flat plots (static images).\n",
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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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"interactive": {
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"type": "boolean",
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"description": "Use only interactive plots (in-browser Javascript).\n",
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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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"data_dir": {
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"type": "boolean",
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"description": "Force the parsed data directory to be created.\n",
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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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"no_data_dir": {
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"type": "boolean",
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"description": "Prevent the parsed data directory from being created.\n",
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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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"zip_data_dir": {
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"type": "boolean",
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"description": "Compress the data directory.\n",
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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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"data_format": {
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"type": "string",
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"description": "Output parsed data in a different format than the default 'txt'.\n",
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"help_text": "Type: `string`, multiple: `False`, choices: ``tsv`, `csv`, `json`, `yaml``. ",
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"enum": [
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"tsv",
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"csv",
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"json",
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"yaml"
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]
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},
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"pdf": {
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"type": "boolean",
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"description": "Creates PDF report with the 'simple' template",
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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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"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/input"
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},
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{
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"$ref": "#/$defs/ouput"
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},
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{
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"$ref": "#/$defs/modules and analyses to run"
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},
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{
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"$ref": "#/$defs/sample name handling"
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},
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{
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"$ref": "#/$defs/report customisation"
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},
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{
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"$ref": "#/$defs/multiqc behaviour"
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},
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{
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"$ref": "#/$defs/output format"
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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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