jvarkit

MultiqcPostProcessor

Enhances multiqc output by reading the data folder and producing new plots (eg. boxplot per population.

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar multiqcpostproc  [options] Files

Usage: multiqcpostproc [options] Files
  Options:
    --beeswarm
      use plot_type=beeswarm instead of boxplot.
      Default: false
    --custom
      custom mapping file (undocumented
    --description
      main section description
      Default: <empty string>
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -o, --output
      output directory
    --sample2collection
      tab delimited file containing (sample-name)(TAB)(collection-name). Empty 
      lines or starting with '#' are skipped
    --title
      main section title
      Default: <empty string>
    --version
      print version and exit

Keywords

• multiqc

Creation Date

20240708

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/multiqc/MultiqcPostProcessor.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite multiqcpostproc ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Motivation

Enhances multiqc output by reading the data folder and producing new plots (eg. boxplot per population

If no group is defined and the tool can find the file dragen_ploidy.txt, this file is used to create a group with male and females

Doesn’t work for now ? https://github.com/MultiQC/MultiQC/issues/2689

Example

# run first time
multiqc --force --file-list input.list
java -jar jvarkit.jar multiqcpostproc --sample2collection sample2collection.tsv multiqc_data -o OUTDIR2
find OUTDIR2 --type f -name "*.json" >> input.list
# run second time
multiqc --force --file-list input.list

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