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smithlabcode / falco

A C++ drop-in replacement of FastQC to assess the quality of sequence read data
https://falco.readthedocs.io
GNU General Public License v3.0
96 stars 10 forks source link

JSON Output #21

Open oschwengers opened 2 years ago

oschwengers commented 2 years ago

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 commented 2 years ago

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!