MultiQC_CMGG is a plugin for MultiQC containing customized modules and templates
For more information about MultiQC, see http://multiqc.info
The MultiQC_CMGG plugin add a custom template, used for internal QC reports and module customizations that can't be merged in core MultiQC.
This plugin can be installed using the following methods
- using
pip:
pip install multiqc_cmggor to get the latest version from github:
pip install --upgrade --force-reinstall git+https://github.com/CenterForMedicalGeneticsGhent/MultiQC_CMGG.git- using
docker:
docker pull quay.io/cmgg/multiqc_cmgg:latestor to build the image yourself:
docker build https://github.com/CenterForMedicalGeneticsGhent/MultiQC_CMGG.git -t multiqc_cmgg| 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> |
| targeted_MSH2 | 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 targeted_MSH2 and -c/--config <path_to_multiqc_config_targeted_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.
| 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. |
This project uses pixi for dependency management and development.
To install the project dependencies and set up the development environment:
pixi installTo run the plugin against the provided test data:
pixi run multiqc test_dataThis command will execute MultiQC using the plugin on the files in the test_data directory.