Hi,
I’m trying to incorperate the Picard QualityYieldMetrics into my QC report, which should be included in the MultiQC configurations and the file itself seems to be parsed. However, only one column appears in the QC report (TOTAL_READS), even though when I checked the multiqc_data.json file, all data seems to be there.
Is there a way to fix that? Maybe some lines I can add to the config file?
Thanks
Hi @AldisiRana,
It’s by design that MultiQC doesn’t show all data in the General Stats table, we try to keep it as narrow as possible for quick reference and so part of writing a module is picking “only the essential” columns to go there.
That said, because Picard has so many fields available and can be used in so many different contexts, several Picard modules have options to customise which columns are shown - see the docs:
I’m not entirely sure if this option is available for QualityYieldMetrics though. If not then please create an issue on the GitHub repo for MultiQC and we can look into adding that for you.
Phil
Hi @ewels,
Yes, indeed, the documentation doesn’t say anything about the QualityYieldMetrics. And when I scanned the code of the picard module, I couldn’t find anything other than the TOTAL_READS metric implemented. For now, I did a work around where I create a table myself so that multiqc pipeline can recognize it. But I will create an issue on the GitHub as well.
Thanks for the help!
Rana
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