Improve QC reports

[grst]

Is your feature request related to a problem? Please describe

I find quality control reports per sample (number of detected cells, number of genes per cell etc.) very useful to
get a first idea if the sequencing experiment was successful. As far as I can tell this is currently only implemented for Salmon/Alevin using the AlevinQC module.

Even better would be, if in addition to one report per sample, a summary of the results would show in the multiqc report. This would be particularly useful for experiments with many samples (no tedious checking of the individual reports).

Describe the solution you'd like

• Produce one HTML report with summary statistics (like AlevinQC or cellranger reports) for each sample
• Show summary statistics for all samples in the multiqc report.

[grst]

This looks like exactly what we need 😍 :
https://github.com/becavin-lab/checkatlas

Example QC report:
https://checkatlas.readthedocs.io/en/stable/CheckAtlas_example_2/CheckAtlas_example_2.html

[apeltzer]

Looks really beautiful - also nice that we could integrate it into MultiQC directly so it is all in one nice report 👍🏻

[apeltzer]

MultiQC PR is still open 👍🏻 MultiQC/MultiQC#1713

[grst]

There's also a multiqc module for cellranger:
MultiQC/MultiQC#1689

[grst]

The cellranger multiqc module has been merged, example:
https://github.com/ewels/MultiQC/files/10086650/multiqc_report_cellranger.html.zip

The checkatlas example multiqc reports start looking more mature now as well:
https://checkatlas.readthedocs.io/en/stable/CheckAtlas_example_2/CheckAtlas_example_2.html

We should probably add both!