MultiQC plugin

[pontushojer]

I have started working on a MultiQC plugin for the pipeline. It is currently situated under my github page.

The plugin includes two modules so far.

• stats: For general BLR statistics. This reads the log files outputted by the various blr.cli tools to gather stats from the section starting with "STATS SUMMARY - blr.cli. " .
• hapcut2: For hapcut2 output files. Currently takes the mapped.phasing_stats.txt for phasing statistics and the mapped.calling.phase file to plot phaseblock lengths.

As the plugin can handle the mapped.phasing_stats.txt directly there is no need to keep the mapped.phasing_stats.tsv. Thus I have done some edits to remove this from the pipeline and also modified the multiqc_configs.yaml.

Currently the plugin can be installed in an active conda environment by running:

- pip install git+https://github.com/pontushojer/MultiQC_BLR

I started working on including it in the environment.yaml file but this run into some issues with the misc/condalock.sh script to generate the "locked" environments. I started working on a fix but it go quite dirty so I desided to leave it out for now (you can look at the multiqc-plugin branch if you want).

Edit: Added plugin as a part of the BLR package. It is now installed directly.

[marcelm]

I think you could actually make the plugin part of BLR itself to simplify the packaging problem. That is, installing BLR would also install the plugin. For the plugin to be recognized as such, you only need to have the proper entry_points defined in setup.py, and you can do that in the setup.py that comes with BLR just as well.

[pontushojer]

Thanks for the suggestion @marcelm! I followed this an now it is included as a part of the BLR package.

[pontushojer]

I will merge this as the new version has gotten approval from @FrickTobias.