diff --git a/src/multiqc/config.vsh.yaml b/src/multiqc/config.vsh.yaml new file mode 100644 index 00000000..8c8a687e --- /dev/null +++ b/src/multiqc/config.vsh.yaml @@ -0,0 +1,194 @@ +functionality: + name: "multiqc" + description: | + MultiQC aggregates results from bioinformatics analyses across many samples into a single report. + It 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. + info: + keywords: [QC, html report, aggregate analysis] + links: + homepage: https://multiqc.info/ + documentation: https://multiqc.info/docs/ + repository: https://github.com/MultiQC/MultiQC + references: + doi: 10.1093/bioinformatics/btw354 + licence: GPL v3 or later + + argument_groups: + - name: "Input" + arguments: + - name: "--input" + type: file + multiple: true + example: data/,data/*_sample.zip,/tmp/results + description: | + File paths to be searched for analysis results to be included in the report. + - name: "--input_file" + type: file + example: path/to/input_file.txt + description: | + Supply a file containing a list of file paths to be searched, one per row + - name: "--multiqc_custom_config" + type: file + example: path/to/multiqc_config.yml + description: | + Specific config file to load, after those in MultiQC dir / home dir / working dir + + - name: "Modules and analyses to run" + arguments: + - name: "--include_modules" + type: string + multiple: true + example: fastqc,cutadapt + description: Use only these module + - name: "--exclude_modules" + type: string + multiple: true + example: fastqc,cutadapt + description: Do not use only these modules + - name: "--ignore_analysis" + type: string + multiple: true + example: run_one/*,run_two/* + - name: "--ignore_samples" + type: string + multiple: true + example: sample_1*,sample_3* + - name: "--ignore_symlinks" + type: boolean_true + description: Ignore symlinked directories and files + + - name: "Sample name handling" + arguments: + - name: "--dirs" + type: boolean_true + description: Prepend directory to sample names to avoid clashing filenames + - name: "--dirs_depth" + type: integer + description: Prepend n directories to sample names. Negative number to take from start of path. + - name: "--full_names" + type: boolean_true + description: Do not clean the sample names (leave as full file name) + - name: "--fn_as_s_name" + type: boolean_true + description: Use the log filename as the sample name + - name: "--replace_names" + type: file + example: replace_names.tsv + description: TSV file to rename sample names during report generation + + - name: "Report Customisation" + arguments: + - name: "--title" + type: string + description: Report title. Printed as page header, used for filename if not otherwise specified. + - name: "--comment" + type: string + description: Custom comment, will be printed at the top of the report. + - name: "--template" + type: string + choices: [default, gathered, geo, highcharts, sections, simple] + description: Report template to use. + - name: "--sample_names" + type: file + description: TSV file containing alternative sample names for renaming buttons in the report. + example: sample_names.tsv + - name: "--sample_filters" + type: file + description: TSV file containing show/hide patterns for the report + example: sample_filters.tsv + - name: "--custom_css_file" + type: file + description: Custom CSS file to add to the final report + example: custom_style_sheet.css + + - name: "MultiQC behaviour" + arguments: + - name: "--verbose" + type: boolean_true + description: Increase output verbosity. + - name: "--force" + type: boolean_true + description: Overwrite any existing reports + - name: "--quiet" + type: boolean_true + description: Only show log warnings + - name: "--strict" + type: boolean_true + description: Don't catch exceptions, run additional code checks to help development. + - name: "--development" + type: boolean_true + description: Development mode. Do not compress and minimise JS, export uncompressed plot data. + - name: "--require_logs" + type: boolean_true + description: Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error. + - name: "--no_megaqc_upload" + type: boolean_true + description: Don't upload generated report to MegaQC, even if MegaQC options are found. + - name: "--no_ansi" + type: boolean_true + description: Disable coloured log output. + + - name: "Ouput" + arguments: + - name: "--output" + type: file + direction: output + default: path/to/multiqc_report.html + - name: "--data" + type: file + direction: output + default: multiqc_data + - name: "--plots" + type: file + direction: output + default: multiqc_plots + + - name: "Output format" + arguments: + - name: "--flat" + type: boolean_true + description: Use only flat plots (static images). + - name: "--interactive" + type: boolean_true + description: Use only interactive plots (in-browser Javascript). + - name: "--export" + type: boolean_true + description: Export plots as static images in addition to the report. + - name: "--data_dir" + type: boolean_true + description: Force the parsed data directory to be created. + - name: "--no_data_dir" + type: boolean_true + description: Prevent the parsed data directory from being created. + - name: "--zip_data_dir" + type: boolean_true + description: Compress the data directory. + - name: "--data_format" + type: string + choices: [tsv, csv, json, yaml] + description: Output parsed data in a different format. + - name: "--no_report" + type: boolean_true + description: Do not generate a report, only export data and plots. + - name: "--pdf" + type: boolean_true + description: Creates PDF report with the 'simple' template. Requires Pandoc to be installed. + + resources: + - type: bash_script + path: script.sh + + test_resources: + - type: bash_script + path: test.sh + - type: file + path: test_data + +platforms: + - type: docker + image: quay.io/biocontainers/multiqc:1.20--pyhdfd78af_0 + setup: + - type: docker + run: | + multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/software_versions.txt + - type: nextflow \ No newline at end of file