 ```bash
multiqc --help
```

/// MultiQC 🔍 | v1.20                                                                                                                                                                          
                                                                                                                                                                                                 
 Usage: multiqc [OPTIONS] [ANALYSIS DIRECTORY]                                                                                                                                                   
                                                                                                                                                                                                 
 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.                     
 To run, supply with one or more directory to scan for analysis results. For example, to run in the current working directory, use 'multiqc .'                                                   
                                                                                                                                                                                                 
╭─ Main options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --force            -f  Overwrite any existing reports                                                                                                                                         │
│ --config           -c  Specific config file to load, after those in MultiQC dir / home dir / working dir. (PATH)                                                                              │
│ --cl-config            Specify MultiQC config YAML on the command line (TEXT)                                                                                                                 │
│ --filename         -n  Report filename. Use 'stdout' to print to standard out. (TEXT)                                                                                                         │
│ --outdir           -o  Create report in the specified output directory. (TEXT)                                                                                                                │
│ --ignore           -x  Ignore analysis files (GLOB EXPRESSION)                                                                                                                                │
│ --ignore-samples       Ignore sample names (GLOB EXPRESSION)                                                                                                                                  │
│ --ignore-symlinks      Ignore symlinked directories and files                                                                                                                                 │
│ --file-list        -l  Supply a file containing a list of file paths to be searched, one per row                                                                                              │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Choosing modules to run ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --module   -m  Use only this module. Can specify multiple times. (MODULE NAME)                                                                                                                │
│ --exclude  -e  Do not use this module. Can specify multiple times. (MODULE NAME)                                                                                                              │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Sample handling ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --dirs           -d   Prepend directory to sample names                                                                                                                                       │
│ --dirs-depth     -dd  Prepend n directories to sample names. Negative number to take from start of path. (INTEGER)                                                                            │
│ --fullnames      -s   Do not clean the sample names (leave as full file name)                                                                                                                 │
│ --fn_as_s_name        Use the log filename as the sample name                                                                                                                                 │
│ --replace-names       TSV file to rename sample names during report generation (PATH)                                                                                                         │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Report customisation ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --title            -i  Report title. Printed as page header, used for filename if not otherwise specified. (TEXT)                                                                             │
│ --comment          -b  Custom comment, will be printed at the top of the report. (TEXT)                                                                                                       │
│ --template         -t  Report template to use. (default|gathered|geo|highcharts|sections|simple)                                                                                              │
│ --sample-names         TSV file containing alternative sample names for renaming buttons in the report (PATH)                                                                                 │
│ --sample-filters       TSV file containing show/hide patterns for the report (PATH)                                                                                                           │
│ --custom-css-file      Custom CSS file to add to the final report (PATH)                                                                                                                      │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Output files ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --flat          -fp  Use only flat plots (static images)                                                                                                                                      │
│ --interactive   -ip  Use only interactive plots (in-browser Javascript)                                                                                                                       │
│ --export        -p   Export plots as static images in addition to the report                                                                                                                  │
│ --data-dir           Force the parsed data directory to be created.                                                                                                                           │
│ --no-data-dir        Prevent the parsed data directory from being created.                                                                                                                    │
│ --data-format   -k   Output parsed data in a different format. (tsv|csv|json|yaml)                                                                                                            │
│ --zip-data-dir  -z   Compress the data directory.                                                                                                                                             │
│ --no-report          Do not generate a report, only export data and plots                                                                                                                     │
│ --pdf                Creates PDF report with the 'simple' template. Requires Pandoc to be installed.                                                                                          │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ MultiQC behaviour ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --verbose            -v  Increase output verbosity. (INTEGER RANGE)                                                                                                                           │
│ --quiet              -q  Only show log warnings                                                                                                                                               │
│ --strict                 Don't catch exceptions, run additional code checks to help development.                                                                                              │
│ --development,--dev      Development mode. Do not compress and minimise JS, export uncompressed plot data                                                                                     │
│ --require-logs           Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error.                                                                 │
│ --profile-runtime        Add analysis of how long MultiQC takes to run to the report                                                                                                          │
│ --no-megaqc-upload       Don't upload generated report to MegaQC, even if MegaQC options are found                                                                                            │
│ --no-ansi                Disable coloured log output                                                                                                                                          │
│ --version                Show the version and exit.                                                                                                                                           │
│ --help               -h  Show this message and exit.                                                                                                                                          │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
                                                                                                                                                                                                 
 See http://multiqc.info for more details.      