fastp after_filtering_q30_rate shows zero in the General Statistics table

[pixuenan]

Description of bug:
When show fastp data in the General Statistics table, the column of fastp M Q30 reads (after_filtering_q30_rate) showed zero. Besides, if you open the Config Columns table, you willl find the column M Q30 reads with description Reads > Q30 after filtering (millions) has an ID after_filtering_q30_rate, which seems incorrect.

File that triggers the error:
fastp_failure.zip

MultiQC run details (please complete the following):

• Command used to run MultiQC: multiqc . -c multiqc_config.yaml -o multiqc
• MultiQC Version: v1.7dev0, v1.7
• Operating System: CentOS 7, Ubuntu 16.04.5
• Python Version: 3.6.7
• Method of MultiQC installation: conda

[ewels]

Hi @pixuenan,

Thanks for reporting this. You're completely right - looks like a mistake when writing the module.

Header config:
https://github.com/ewels/MultiQC/blob/d4a622d837a76c8a17d7d0213f3f83dad5a61e0f/multiqc/modules/fastp/fastp.py#L288-L296

Example input data:

"after_filtering": {
    "total_reads":16034314,
    "total_bases":1722358455,
    "q20_bases":1659758686,
    "q30_bases":1622286535,
    "q20_rate":0.963655,
    "q30_rate":0.941898,
    "gc_content":0.467941
}

So yeah - the _rate field is incorrectly being labelled and treated as a read count. Should be an easy fix.

Phil

[ewels]

Hi @pixuenan,

I've updated the code, it should make more sense now. If you could give it a spin and let me know how you get on, that would be great.

Thanks!

Phil

[pixuenan]

Hi @ewels,

The statistics of fastp Q30 is correct now, thanks for the quick reply and fix.

Regards,

Xuenan

[ewels]

Great! Thanks for getting back to me 👍