Description

Aggregate results from bioinformatics analyses across many samples into a single report, with support for multiqc_sav plugin

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘sample1’, single_end:false ]

xml{:bash}

:file

xml files from an Illumina sequencing run

*.xml

interop_bin{:bash}

:file

Illumina InterOp binary files

InterOp/*.bin

extra_multiqc_files{:bash}

:file

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

multiqc_config{:bash}

:file

Optional config yml for MultiQC

*.{yml,yaml}

multiqc_logo{:bash}

:file

Optional logo file for MultiQC

*.{png}

replace_names{:bash}

: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{:bash}

:file

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

*.{tsv}

Output

name:type
description
pattern

report{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘sample1’, single_end:false ]

*.html{:bash}

:file

MultiQC report file

.html

data{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘sample1’, single_end:false ]

*_data{:bash}

:directory

MultiQC data dir

multiqc_data

plots{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘sample1’, single_end:false ]

*_plots{:bash}

:file

Plots created by MultiQC

*_data

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

multiqc{:bash}

:string

The tool name

multiqc --version | sed "s/.* //g"{:bash}

:eval

The expression to obtain the version of the tool

versions_interop{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

interop{:bash}

:string

The tool name

python -c "import interop; print(interop.__version__)"{:bash}

:eval

The expression to obtain the version of the tool

versions_multiqcsav{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

multiqcsav{:bash}

:string

The name of the tool

python -c "import multiqc_sav; print(multiqc_sav.__version__)"{:bash}

:eval

The expression to obtain 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
maintainer
Github user matthdsm
get in touch
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