multiqc
- Version:
1.28
- Category:
bio
- Cluster:
Vali
Description
MultiQC aggregates results from bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles an 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.
Documentation
Usage: multiqc [OPTIONS] [ANALYSIS DIRECTORY]
╭─ 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) │
│ --require-logs Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error. │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ 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|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/--no-data-dir Force the parsed data directory to be 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 │
│ --clean-up/--no-clean-up Remove the temporary directory and log file after finishing │
│ --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 │
│ --no-version-check Disable checking the latest MultiQC version on the server │
│ --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 │
│ --profile-runtime Add analysis of how long MultiQC takes to run to the report │
│ --profile-memory Add analysis of how much memory each module uses. Note that tracking memory will increase the runtime, so the runtime metrics could scale up a few times │
│ --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. │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ AI Features ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --ai,--ai-summary Generate an AI summary of the report │
│ --ai-summary-full Generate a detailed AI summary of the report │
│ --ai-provider Select AI provider for report summarization. (Default: seqera) (seqera|openai|anthropic|custom) │
│ --no-ai Disable AI toolbox and buttons in the report │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --ai-model Select AI model to use for report summarization (TEXT) │
│ --ai-custom-endpoint Custom AI endpoint to use with OpenAI API (TEXT) │
│ --ai-custom-context-window Custom context window to use with OpenAI API (default: 128000) (INTEGER) │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
See http://multiqc.info for more details.
Examples/Usage
List available modules:
$ module avail multiqc
Load the Anaconda module:
$ module load MultiQC/1.28-foss-2024a
Check the loaded modules:
$ module list
Unload the Anaconda module:
$ module unload MultiQC/1.28-foss-2024a
To run in the current working directory:
$ multiqc .
Installation
Source code is obtained from multiqc