MultiQC_CMGG is a plugin for MultiQC containing customized modules and templates

For more information about MultiQC, see http://multiqc.info

Description

The MultiQC_CMGG plugin add a custom template, used for internal QC reports and module customizations that can't be merged in core MultiQC.

Installation

This plugin can be installed using the following methods

• using pip:

pip install --upgrade --force-reinstall git+https://github.com/CenterForMedicalGeneticsGhent/MultiQC_CMGG.git

• using docker:

docker build https://github.com/CenterForMedicalGeneticsGhent/MultiQC_CMGG.git -t multiqc_cmgg

Usage

Modules

Name	Description
sample_gender	Parse and merges ngs-bits SampleGender output from xy, hetx, sry method into a sensible table. Based of ngs-bits MultiQC module. To use module add -m/--module sample_gender.
coverage	Parse Mosdepth region files into tables based on genome panels. Based of Mosdepth MultiQC module . To use module add -m/--module coverage and -c/--config <path_to_multiqc_config_coverage.yaml>
MSH2_hotspot_varcount	Parses count files of a MSH2 hotspot variant from nf-cmgg/report pipeline to make a report in MultiQC. To use module add -m/--module MSH2_hotspot_varcount and -c/--config <path_to_multiqc_config_msh2.yaml>
msi_sensor_pro	Parses output from msisensor-pro, generating an overview table from the summary file and a detailed table of MSI status for each locus from all results file. Also creates a bargraph visualizing the msisensor-pro scores.

More thorough explaination on setting up modules, installation and integration into nextflow pipelines can be found here.

Template

Name	Description
cmgg	CMGG specfic template with custom logo's and affiliate links. To enable this template, add the -t/--template cmgg option to the command line.