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OpenGene / fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
MIT License
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Why does the report "after filtering" results when no filtering is performed? #223

Open dominikburri opened 4 years ago

dominikburri commented 4 years ago

I want to run fastp for quality control only. I ran 

fastp -i  MYFILE.fq.gz \
    --disable_adapter_trimming \
    --disable_quality_filtering \
    --disable_length_filtering \
    --disable_trim_poly_g \
    -h fastp_res.html

and get fastp_res.html which does contain the sections for "after filtering" including the figures. Why are these sections there if no filtering was performed?

Also, the runtime compared to 

fastp -i  MYFILE.fq.gz \
    --disable_adapter_trimming \
    -h fastp_res.html

is the same. Does it need to take the same time?

sfchen commented 4 years ago

Don't mind the the "after filtering" section if you don't do any real filtering.

dominikburri commented 4 years ago

It is kind of confusing having the results for filtering when none is done. Especially when one sends the report to a no-user. Also, the runtime could be cut into half if the graphs are not computed again "after filtering".

sfchen commented 4 years ago

I think I should add a qc_only option to just do quality control, without any filtering.

dominikburri commented 4 years ago

Yes, that would be great :)