You can how we use multiQC in our protocol for quality checking raw reads here
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You can how we use multiQC in our protocol for quality checking raw reads here
Usage: multiqc [OPTIONS] <analysis directory>
Main MultiQC run command for use with the click command line, complete
with all click function decorators. To make it easy to use MultiQC within
notebooks and other locations that don't need click, we simply pass the
parsed variables on to a vanilla python function.
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
--sample-names PATH File containing alternative sample names
--sample-filters PATH 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.