[Feature] Add per-sample JSON report

[gregdenay]

We currently only have non-computer-friendly output types (Krona, XLSX, MultiQC). I think it would be nice to also have a JSON for each sample. I am thinking of wiring this into an automatic pipeline to send results into our LIMS, for example.

• QC Werte
• read count before after trimming
• taxa table
• pipeline version
• databases version

[gregdenay]

@marchoeppner could you check the latest commit ? I implemented the sample-wise JSON report. It is tested for Illumina data with conda so Ithink I didn't break anything but it would be great if you could check it with your ONT data and singularity/docker just to be sure everything works fine.

[marchoeppner]

@marchoeppner could you check the latest commit ? I implemented the sample-wise JSON report. It is tested for Illumina data with conda so Ithink I didn't break anything but it would be great if you could check it with your ONT data and singularity/docker just to be sure everything works fine.

Runs through just fine on my end, good job! The JSON is pretty "dense" (i.e. all the blast hits) - which is maybe a little confusing for some users, but ultimately fine with me. Definitely useful to have the option to keep that information somewhere.

[marchoeppner]

Ah, it seems the various files are not correctly joint along the way so you end up with mis-matching reports:

dada_mqc.json
ERR10436092.filtered.json
ERR10436094.composition.json
ERR10436102.consensus.json
ERR10436102.cutadapt_mqc.json
software_versions.yml

I'll see if I can fix that real quick.

[marchoeppner]

Fixed in 99fd51491c92a08b7f6485fc94191130296c2bd2

See: https://github.com/bio-raum/FooDMe2/blob/99fd51491c92a08b7f6485fc94191130296c2bd2/subworkflows/reporting/main.nf#L42

[gregdenay]

so i did break things, I knew it couldn't be that easy. Thanks for the fix