multiqc

Description

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.

Input

Name	Type & Properties	Description
--input	file required multiple	File paths to be searched for analysis results to be included in the report.

Name

Type & Properties

--input

file

required

multiple

Ouput

Name	Type & Properties	Description
--output_report	file output	Filepath of the generated report.
--output_data	file output	Output directory for parsed data files. If not provided, parsed data will not be published.
--output_plots	file output	Output directory for generated plots. If not provided, plots will not be published.

Name

Type & Properties

--output_report

file

output

--output_data

file

output

--output_plots

file

output

Modules and analyses to run

Name	Type & Properties	Description
--include_modules	string multiple	Use only these module
--exclude_modules	string multiple	Do not use only these modules
--ignore_analysis	string multiple
--ignore_samples	string multiple
--ignore_symlinks	boolean_true	Ignore symlinked directories and files

Name

Type & Properties

--include_modules

string

multiple

--exclude_modules

string

multiple

--ignore_analysis

string

multiple

--ignore_samples

string

multiple

--ignore_symlinks

boolean_true

Sample name handling

Name	Type & Properties	Description
--dirs	boolean_true	Prepend directory to sample names to avoid clashing filenames
--dirs_depth	integer	Prepend n directories to sample names. Negative number to take from start of path.
--full_names	boolean_true	Do not clean the sample names (leave as full file name)
--fn_as_s_name	boolean_true	Use the log filename as the sample name
--replace_names	file	TSV file to rename sample names during report generation

Name

Type & Properties

--dirs

boolean_true

--dirs_depth

integer

--full_names

boolean_true

--fn_as_s_name

boolean_true

--replace_names

file

Report Customisation

Name	Type & Properties	Description
--title	string	Report title. Printed as page header, used for filename if not otherwise specified.
--comment	string	Custom comment, will be printed at the top of the report.
--template	string	Report template to use.
--sample_names	file	TSV file containing alternative sample names for renaming buttons in the report.
--sample_filters	file	TSV file containing show/hide patterns for the report
--custom_css_file	file	Custom CSS file to add to the final report
--profile_runtime	boolean_true	Add analysis of how long MultiQC takes to run to the report

Name

Type & Properties

--title

string

--comment

string

--template

string

--sample_names

file

--sample_filters

file

--custom_css_file

file

--profile_runtime

boolean_true

MultiQC behaviour

Name	Type & Properties	Description
--verbose	boolean_true	Increase output verbosity.
--quiet	boolean_true	Only show log warnings
--strict	boolean_true	Don't catch exceptions, run additional code checks to help development.
--development	boolean_true	Development mode. Do not compress and minimise JS, export uncompressed plot data.
--require_logs	boolean_true	Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error.
--no_megaqc_upload	boolean_true	Don't upload generated report to MegaQC, even if MegaQC options are found.
--no_ansi	boolean_true	Disable coloured log output.
--cl_config	string	YAML formatted string that allows to customize MultiQC behaviour like input file detection.

Name

Type & Properties

--verbose

boolean_true

--quiet

boolean_true

--strict

boolean_true

--development

boolean_true

--require_logs

boolean_true

--no_megaqc_upload

boolean_true

--no_ansi

boolean_true

--cl_config

string

Output format

Name	Type & Properties	Description
--flat	boolean_true	Use only flat plots (static images).
--interactive	boolean_true	Use only interactive plots (in-browser Javascript).
--data_dir	boolean_true	Force the parsed data directory to be created.
--no_data_dir	boolean_true	Prevent the parsed data directory from being created.
--zip_data_dir	boolean_true	Compress the data directory.
--data_format	string	Output parsed data in a different format than the default 'txt'.
--pdf	boolean_true	Creates PDF report with the 'simple' template. Requires Pandoc to be installed.

Name

Type & Properties

--flat

boolean_true

--interactive

boolean_true

--data_dir

boolean_true

--no_data_dir

boolean_true

--zip_data_dir

boolean_true

--data_format

string

--pdf

boolean_true

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output_report: "$id.$key.output_report.html"  
output_data: "$id.$key.output_data.multiqc_data"  
output_plots: "$id.$key.output_plots.multiqc_plots"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/multiqc/main.nf \  
  -params-file params.yaml

multiqc

Input

Ouput

Modules and analyses to run

Sample name handling

Report Customisation

MultiQC behaviour

Output format

Run this component

Relationships

Used by

Uses