multiqc1

Output integration for rna sequencing across tools and samples

Usage

multiqc [OPTIONS] <analysis directory>

Overview

: 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. To run here, use 'multiqc .'

: See http://multiqc.info for more details.

: Author: Phil Ewels (http://phil.ewels.co.uk)

Options

-f, --force: Overwrite any existing reports

-d, --dirs: Prepend directory to sample names

-dd, --dirs-depth INTEGER: Prepend [INT] directories to sample names. Negative number to take from start of path.

-s, --fullnames: Do not clean the sample names (leave as full file name)

-i, --title TEXT: Report title. Printed as page header, used for filename if not otherwise specified.

-b, --comment TEXT: Custom comment, will be printed at the top of the report.

-n, --filename TEXT: Report filename. Use 'stdout' to print to standard out.

-o, --outdir TEXT: Create report in the specified output directory.

-t, --template [default|default_dev|gathered|geo|sections|simple]: Report template to use.

--tag TEXT: Use only modules which tagged with this keyword, eg. RNA

--view-tags, --view_tags: View the available tags and which modules they load

-x, --ignore TEXT: Ignore analysis files (glob expression)

--ignore-samples TEXT: Ignore sample names (glob expression)

--ignore-symlinks: Ignore symlinked directories and files

--fn_as_s_name: Use the log filename as the sample name

--replace-names PATH: Path to TSV file to rename sample names during report generation

--sample-names PATH: Path to TSV file containing alternative sample names for renaming buttons in the report

--sample-filters PATH: Path to TSV file containing show/hide patterns for the report

-l, --file-list: Supply a file containing a list of file paths to be searched, one per row

`-e, --exclude [module name]`	Do not use this module. Can specify multiple times.
`-m, --module [module name]`	Use only this module. Can specify multiple times.

--data-dir: Force the parsed data directory to be created.

--no-data-dir: Prevent the parsed data directory from being created.

-k, --data-format [tsv|json|yaml]: Output parsed data in a different format. Default: tsv

-z, --zip-data-dir: Compress the data directory.

-p, --export: Export plots as static images in addition to the report

-fp, --flat: Use only flat plots (static images)

-ip, --interactive: Use only interactive plots (HighCharts Javascript)

--lint: Use strict linting (validation) to help code development

--pdf: Creates PDF report with 'simple' template. Requires Pandoc to be installed.

--no-megaqc-upload: Don't upload generated report to MegaQC, even if MegaQC options are found

-c, --config PATH: Specific config file to load, after those in MultiQC dir / home dir / working dir.

--cl-config, --cl_config TEXT: Specify MultiQC config YAML on the command line

-v, --verbose: Increase output verbosity.

-q, --quiet: Only show log warnings

--profile-runtime: Add analysis of how long MultiQC takes to run to the report

--no-ansi: Disable coloured log output

--version: Show the version and exit.

-h, --help: Show this message and exit.

Releases

3 releases since Debian 11 (Bullseye); the text changed 1 time.

11
12–13

--fn_as_s_name since Debian 12 (Bookworm); --no-ansi since Debian 12 (Bookworm); --profile-runtime since Debian 12 (Bookworm); --replace-names since Debian 12 (Bookworm); --sample-filters since Debian 12 (Bookworm).