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| ```bash | ||
| multiqc --help | ||
| ``` | ||
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| /// MultiQC 🔍 | v1.20 | ||
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| Usage: multiqc [OPTIONS] [ANALYSIS DIRECTORY] | ||
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| 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 .' | ||
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| ╭─ 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. │ | ||
| ╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ | ||
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| See http://multiqc.info for more details. |