Closed gregdenay closed 1 month ago
@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 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.
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.
Fixed in 99fd51491c92a08b7f6485fc94191130296c2bd2
so i did break things, I knew it couldn't be that easy. Thanks for the fix
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.