modules/multiqc

Aggregate results from bioinformatics analyses across many samples into a single report

QCbioinformatics toolsBeautiful stand-alone HTML report

https://github.com/nf-core/modules/[...]/modules/nf-core/multiqc

Description

Aggregate results from bioinformatics analyses across many samples into a single report

Input

name:type

description

pattern

`multiqc_files`
`:file`

List of reports / files recognised by MultiQC, for example the html and zip output of FastQC

`multiqc_config`
`:file`

Optional config yml for MultiQC

*.{yml,yaml}

`extra_multiqc_config`
`:file`

Second optional config yml for MultiQC. Will override common sections in multiqc_config.

*.{yml,yaml}

`multiqc_logo`
`:file`

Optional logo file for MultiQC

*.{png}

`replace_names`
`:file`

Optional two-column sample renaming file. First column a set of patterns, second column a set of corresponding replacements. Passed via MultiQC’s --replace-names option.

*.{tsv}

`sample_names`
`:file`

Optional TSV file with headers, passed to the MultiQC —sample_names argument.

*.{tsv}

Output

name:type

description

pattern

`report`

`*.html`
`:file`

MultiQC report file

.html

`data`

`*_data`
`:directory`

MultiQC data dir

multiqc_data

`plots`

`*_plots`
`:file`

Plots created by MultiQC

*_data

`versions_multiqc`

`${task.process}`
`:string`

The process the versions were collected from

`multiqc`
`:string`

The tool name

`multiqc --version | sed "s/.* //g`
`:string`

The command used to generate the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`multiqc`
`:string`

The tool name

`multiqc --version | sed "s/.* //g`
`:string`

The command used to generate the version of the tool

Tools

multiqc
GPL-3.0-or-later

MultiQC 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.

multiqc.info multiqc.info/docs

modules/multiqc

Description

Input

`multiqc_files`
`:file`

`multiqc_config`
`:file`

`extra_multiqc_config`
`:file`

`multiqc_logo`
`:file`

`replace_names`
`:file`

`sample_names`
`:file`

Output

`report`

`*.html`
`:file`

`data`

`*_data`
`:directory`

`plots`

`*_plots`
`:file`

`versions_multiqc`

`${task.process}`
`:string`

`multiqc`
`:string`

`multiqc --version | sed "s/.* //g`
`:string`

Topics

`versions`

`${task.process}`
`:string`

`multiqc`
`:string`

`multiqc --version | sed "s/.* //g`
`:string`

Tools

multiqc
GPL-3.0-or-later

included in

maintainers

get in touch

modules/multiqc

Description

Input

multiqc_files:file

multiqc_config:file

extra_multiqc_config:file

multiqc_logo:file

replace_names:file

sample_names:file

Output

report

*.html:file

data

*_data:directory

plots

*_plots:file

versions_multiqc

${task.process}:string

multiqc:string

multiqc --version | sed "s/.* //g:string

Topics

versions

${task.process}:string

multiqc:string

multiqc --version | sed "s/.* //g:string

Tools

multiqc GPL-3.0-or-later

included in

maintainers

get in touch

`multiqc_files`
`:file`

`multiqc_config`
`:file`

`extra_multiqc_config`
`:file`

`multiqc_logo`
`:file`

`replace_names`
`:file`

`sample_names`
`:file`

`report`

`*.html`
`:file`

`data`

`*_data`
`:directory`

`plots`

`*_plots`
`:file`

`versions_multiqc`

`${task.process}`
`:string`

`multiqc`
`:string`

`multiqc --version | sed "s/.* //g`
`:string`

`versions`

`${task.process}`
`:string`

`multiqc`
`:string`

`multiqc --version | sed "s/.* //g`
`:string`

multiqc
GPL-3.0-or-later