CI
18d6cad4c4
Build pipeline: viash-hub.biobox.main-bjgnf
Source commit: 2b29a47575
Source message: Bedtools GroupBY (#123)
* Initial Commit
* Update config.vsh.yaml
* config file
* script.sh
* adding some tests
* more test
* Update CHANGELOG.md
* deleted test_data
* bug fix
* Update config.vsh.yaml
* adding more links
* exit on error
* $TMPDIR
* Update script.sh
* Update config.vsh.yaml
* Suggested change on column option
---------
Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com>
530 lines
19 KiB
JSON
530 lines
19 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/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\u0027s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n",
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"type": "object",
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"definitions": {
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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":
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"string",
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"description": "Type: List of `file`, required, example: `data/results`, multiple_sep: `\";\"`. File paths to be searched for analysis results to be included in the report",
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"help_text": "Type: List of `file`, required, example: `data/results`, multiple_sep: `\";\"`. File paths to be searched for analysis results to be included in the report.\n"
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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":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_report.html`, example: `multiqc_report.html`. Filepath of the generated report",
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"help_text": "Type: `file`, default: `$id.$key.output_report.html`, example: `multiqc_report.html`. Filepath of the generated report.\n"
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,
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"default": "$id.$key.output_report.html"
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}
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,
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"output_data": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files",
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"help_text": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files. If not provided, parsed data will not be published.\n"
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,
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"default": "$id.$key.output_data.output_data"
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}
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,
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"output_plots": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots",
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"help_text": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots. If not provided, plots will not be published.\n"
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,
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"default": "$id.$key.output_plots.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":
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"string",
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"description": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Use only these module",
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"help_text": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Use only these module"
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}
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,
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"exclude_modules": {
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"type":
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"string",
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"description": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Do not use only these modules",
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"help_text": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Do not use only these modules"
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}
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,
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"ignore_analysis": {
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"type":
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"string",
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"description": "Type: List of `string`, example: `run_one/*;run_two/*`, multiple_sep: `\";\"`. ",
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"help_text": "Type: List of `string`, example: `run_one/*;run_two/*`, multiple_sep: `\";\"`. "
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}
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,
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"ignore_samples": {
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"type":
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"string",
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"description": "Type: List of `string`, example: `sample_1*;sample_3*`, multiple_sep: `\";\"`. ",
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"help_text": "Type: List of `string`, example: `sample_1*;sample_3*`, multiple_sep: `\";\"`. "
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}
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,
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"ignore_symlinks": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Ignore symlinked directories and files",
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"help_text": "Type: `boolean_true`, default: `false`. Ignore symlinked directories and files"
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,
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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":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Prepend directory to sample names to avoid clashing filenames",
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"help_text": "Type: `boolean_true`, default: `false`. Prepend directory to sample names to avoid clashing filenames"
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,
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"default": "False"
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}
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,
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"dirs_depth": {
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"type":
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"integer",
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"description": "Type: `integer`. Prepend n directories to sample names",
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"help_text": "Type: `integer`. Prepend n directories to sample names. Negative number to take from start of path."
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}
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,
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"full_names": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Do not clean the sample names (leave as full file name)",
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"help_text": "Type: `boolean_true`, default: `false`. Do not clean the sample names (leave as full file name)"
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,
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"default": "False"
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}
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,
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"fn_as_s_name": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Use the log filename as the sample name",
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"help_text": "Type: `boolean_true`, default: `false`. Use the log filename as the sample name"
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,
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"default": "False"
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}
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,
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"replace_names": {
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"type":
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"string",
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"description": "Type: `file`, example: `replace_names.tsv`. TSV file to rename sample names during report generation",
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"help_text": "Type: `file`, example: `replace_names.tsv`. TSV file to rename sample names during report generation"
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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":
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"string",
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"description": "Type: `string`. Report title",
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"help_text": "Type: `string`. Report title. Printed as page header, used for filename if not otherwise specified.\n"
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}
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,
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"comment": {
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"type":
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"string",
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"description": "Type: `string`. Custom comment, will be printed at the top of the report",
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"help_text": "Type: `string`. Custom comment, will be printed at the top of the report.\n"
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}
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,
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"template": {
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"type":
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"string",
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"description": "Type: `string`, choices: ``default`, `gathered`, `geo`, `highcharts`, `sections`, `simple``. Report template to use",
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"help_text": "Type: `string`, choices: ``default`, `gathered`, `geo`, `highcharts`, `sections`, `simple``. Report template to use.\n",
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"enum": ["default", "gathered", "geo", "highcharts", "sections", "simple"]
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}
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,
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"sample_names": {
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"type":
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"string",
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"description": "Type: `file`, example: `sample_names.tsv`. TSV file containing alternative sample names for renaming buttons in the report",
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"help_text": "Type: `file`, example: `sample_names.tsv`. TSV file containing alternative sample names for renaming buttons in the report.\n"
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}
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,
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"sample_filters": {
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"type":
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"string",
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"description": "Type: `file`, example: `sample_filters.tsv`. TSV file containing show/hide patterns for the report\n",
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"help_text": "Type: `file`, example: `sample_filters.tsv`. TSV file containing show/hide patterns for the report\n"
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}
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,
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"custom_css_file": {
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"type":
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"string",
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"description": "Type: `file`, example: `custom_style_sheet.css`. Custom CSS file to add to the final report\n",
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"help_text": "Type: `file`, example: `custom_style_sheet.css`. Custom CSS file to add to the final report\n"
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}
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,
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"profile_runtime": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Add analysis of how long MultiQC takes to run to the report\n",
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"help_text": "Type: `boolean_true`, default: `false`. Add analysis of how long MultiQC takes to run to the report\n"
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,
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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":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Increase output verbosity",
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"help_text": "Type: `boolean_true`, default: `false`. Increase output verbosity.\n"
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"default": "False"
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}
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,
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"quiet": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Only show log warnings\n",
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"help_text": "Type: `boolean_true`, default: `false`. Only show log warnings\n"
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,
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"default": "False"
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}
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,
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"strict": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Don\u0027t catch exceptions, run additional code checks to help development",
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"help_text": "Type: `boolean_true`, default: `false`. Don\u0027t catch exceptions, run additional code checks to help development.\n"
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,
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"default": "False"
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}
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,
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"development": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Development mode",
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"help_text": "Type: `boolean_true`, default: `false`. Development mode. Do not compress and minimise JS, export uncompressed plot data.\n"
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,
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"default": "False"
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}
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,
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"require_logs": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Require all explicitly requested modules to have log files",
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"help_text": "Type: `boolean_true`, default: `false`. Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error.\n"
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,
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"default": "False"
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}
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,
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"no_megaqc_upload": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Don\u0027t upload generated report to MegaQC, even if MegaQC options are found",
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"help_text": "Type: `boolean_true`, default: `false`. Don\u0027t upload generated report to MegaQC, even if MegaQC options are found.\n"
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,
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"default": "False"
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}
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,
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"no_ansi": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Disable coloured log output",
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"help_text": "Type: `boolean_true`, default: `false`. Disable coloured log output.\n"
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,
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"default": "False"
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}
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,
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"cl_config": {
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"type":
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"string",
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"description": "Type: `string`, example: `qualimap_config: { general_stats_coverage: [20,40,200] }`. YAML formatted string that allows to customize MultiQC behaviour like input file detection",
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"help_text": "Type: `string`, example: `qualimap_config: { general_stats_coverage: [20,40,200] }`. YAML formatted string that allows to customize MultiQC behaviour like input file detection.\n"
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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":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Use only flat plots (static images)",
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"help_text": "Type: `boolean_true`, default: `false`. Use only flat plots (static images).\n"
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,
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"default": "False"
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}
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,
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"interactive": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Use only interactive plots (in-browser Javascript)",
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"help_text": "Type: `boolean_true`, default: `false`. Use only interactive plots (in-browser Javascript).\n"
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,
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"default": "False"
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}
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,
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"data_dir": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Force the parsed data directory to be created",
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"help_text": "Type: `boolean_true`, default: `false`. Force the parsed data directory to be created.\n"
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,
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"default": "False"
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}
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,
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"no_data_dir": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Prevent the parsed data directory from being created",
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"help_text": "Type: `boolean_true`, default: `false`. Prevent the parsed data directory from being created.\n"
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,
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"default": "False"
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}
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,
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"zip_data_dir": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Compress the data directory",
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"help_text": "Type: `boolean_true`, default: `false`. Compress the data directory.\n"
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,
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"default": "False"
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}
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,
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"data_format": {
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"type":
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"string",
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"description": "Type: `string`, choices: ``tsv`, `csv`, `json`, `yaml``. Output parsed data in a different format than the default \u0027txt\u0027",
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"help_text": "Type: `string`, choices: ``tsv`, `csv`, `json`, `yaml``. Output parsed data in a different format than the default \u0027txt\u0027.\n",
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"enum": ["tsv", "csv", "json", "yaml"]
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}
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,
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"pdf": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Creates PDF report with the \u0027simple\u0027 template",
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"help_text": "Type: `boolean_true`, default: `false`. Creates PDF report with the \u0027simple\u0027 template. Requires Pandoc to be installed.\n"
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,
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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":
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"string",
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"description": "Type: `string`, required, example: `output/`. Path to an output directory",
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"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
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}
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,
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"param_list": {
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"type":
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"string",
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"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
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"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
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"hidden": true
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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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"$ref": "#/definitions/input"
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},
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{
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"$ref": "#/definitions/ouput"
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},
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{
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"$ref": "#/definitions/modules and analyses to run"
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},
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{
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"$ref": "#/definitions/sample name handling"
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},
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{
|
|
"$ref": "#/definitions/report customisation"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/multiqc behaviour"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/output format"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/nextflow input-output arguments"
|
|
}
|
|
]
|
|
}
|