Nextflow Registry | nf-core/multiqcsav@0.0.0-be790aa

nf-core/multiqcsav @ 0.0.0-be790aa

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

Latest version: 0.0.0-be790aa

Total downloads: 10

Source: nf-core/modules

Authors: @matthdsm @delfiterradas

Maintainers: @matthdsm

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

Add the following snippet to your workflow script to include this module.

include { MULTIQCSAV } from 'nf-core/multiqcsav'

MIT License

Process

`Name`	`MULTIQCSAV`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
`xml` file	xml files from an Illumina sequencing run `*.xml`
`interop_bin` file	Illumina InterOp binary files `InterOp/*.bin`
`extra_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}`
`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 6 channels

#1 data tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
`*_data` directory	MultiQC data dir `multiqc_data`

#2 plots tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
`*_plots` file	Plots created by MultiQC `*_data`

#3 report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
`*.html` file	MultiQC report file `.html`

#4 versions tuple

`${task.process}` string	The process the versions were collected from
`multiqc` string	The tool name
`multiqc --version \| sed "s/.* //g"` eval	The expression to obtain the version of the tool

#5 versions_interop tuple

`${task.process}` string	The process the versions were collected from
`interop` string	The tool name
`python -c "import interop; print(interop.__version__)"` eval	The expression to obtain the version of the tool

#6 versions_multiqcsav tuple

`${task.process}` string	The process the versions were collected from
`multiqcsav` string	The name of the tool
`python -c "import multiqc_sav; print(multiqc_sav.__version__)"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
multiqc	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.	https://multiqc.info/

Version	0.0.0-be790aa
Commit ID	be790aafaa178554b403f862164eb27042f0b35a