# Single cell multiqc report

**URL:** <https://community.seqera.io/t/single-cell-multiqc-report/1226>\
**Category:** Ask for help\
**Tags:** multiqc\
**Created:** [September 26, 2024, 6:31pm UTC](https://community.seqera.io/t/single-cell-multiqc-report/1226 "2024-09-26T18:31:25Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![yinshiyi](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/yinshiyi/32/1091_2.png) [@yinshiyi](https://community.seqera.io/u/yinshiyi)\
**Post date:** [September 26, 2024, 6:31pm UTC](https://community.seqera.io/t/single-cell-multiqc-report/1226/1 "2024-09-26T18:31:25Z")

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I have 5000-50,000 cells DNA, using nextflow I aligned them to genome then I use picard to get some stats. I have the metadata file go with it.  
I have been plotting the summary stat distribution in R (violin) or python. It would be great if I can use multiQC to do it and generate a report.  
if I just use multiqc directly, it will have 5,000 rows and not grouped by samples, so it is not very helpful.  
Is there metadata groupby integration from multiqc?  
Thanks!

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**Author:** ![ewels](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/ewels/32/1_2.png) [@ewels](https://community.seqera.io/u/ewels)\
**Post date:** [October 1, 2024, 2:17pm UTC](https://community.seqera.io/t/single-cell-multiqc-report/1226/2 "2024-10-01T14:17:42Z")

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There’s no obvious way to do this currently, though one way could be to run the Picard multiple times using path filters. Then at least you’d get separate plots for each group of samples:

> **[Customising reports | Seqera Docs](https://docs.seqera.io/multiqc/reports/customisation#running-modules-multiple-times)**
>
> Making MultiQC reports bespoke for your use case

Note that you can also use MultiQC within scripts, which may be a better approach:

> **[Using MultiQC in scripts | Seqera Docs](https://docs.seqera.io/multiqc/usage/scripts)**
>
> Importing MultiQC as a library in scripts and notebooks

Phil

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**Author:** ![system](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/system/32/2402_2.png) [@system](https://community.seqera.io/u/system)\
**Post date:** [November 11, 2024, 12:25pm UTC](https://community.seqera.io/t/single-cell-multiqc-report/1226/3 "2024-11-11T12:25:03Z")

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