Luca Beltrame
Luca Beltrame
From the implementation side, at least conceptually, everything should be in place. I can't test this here at the hackathon, so this will have to wait until I'm back to...
If I can, I'll update the nf-core modules to use a newer PureCN.
A potential issue that I've stumbled upon is that for annotation PureCN needs to process the intervals (BED), and requires that the normal data *and* the GATK data to be...
More snags: using a PoN from the GATK will remove regions, which then cause issues when comparing the normals (unfiltered) with the tumors (filtered). See https://github.com/lima1/PureCN/issues/386
Given that I can't seem to fix this issue, I have a better plan: - Use coverages from GATK4 (so we still use CRAMs) as the format is supported by...
I deeply regret trying to work on this. ;) There's yet another problem! I need PureCN 2.14.1 for the essential fixes (it's broken, if not) required, but all builds rely...
> > I need PureCN 2.14.1 for the essential fixes (it's broken, if not) required, but all builds rely on bioconda, which is one Bioconductor version behind > > Is...
Blocking issue: https://github.com/bioconda/bioconda-recipes/issues/55833
As of today, the bioconda migration to the newer bioconductor has not yet happened, so this stays blocked until further notice. If the migration happens, I can start working on...
I haven't been really using the UI anymore, relying only on the API nowadays, so I can't tell at this point. I'll close for now, and reopen if I find...