JSON Output

[oschwengers]

Hi and thanks for this wonderful FastQC alternative!

Would it be possible to export all results in a standardized machine readable JSON file like for example fastp?
That would be awesome.

[guilhermesena1]

Thank you for the suggestion and apologies for the delayed response! We are working on creating a -J flag that may replace the fastqc_data.txt format as JSON.

While I fully agree that a direct JSON output is desirable, if you immediately need your fastqc_data.txt file as JSON, I can recommend using python or R libraries that can parse fastqc_data.txt as internal objects (e.g. lists in R), then using a second library to output the list in JSON format. For instance, fastqcr reads the fastqc data input and then rjson can be used to save in JSON.

In any case we appreciate the suggestion and will work on implementing this in the future versions!