Open lbeltrame opened 3 years ago
In fact the whole part without a normal DB cannot run because it was not ported to the new way of using Rscript and relies on GATK and CNVkit. It needs a rewrite to handle a paired normal: given the fact that I actually need this, I might get to it if anyone doesn't beat me to it.
Hi @lbeltrame !
Yes, those are remains of the old cnvkit + purecn workflow. Given that running without PON is discouraged, we are usually running PureCN T/N analyses w PON as well or just T only + PON, according to the docs: https://bcbio-nextgen.readthedocs.io/en/latest/contents/purecn.html
Please fill free to PR!
SN
Version info
bcbio_nextgen.py --version
): 1.2.7lsb_release -ds
): Debian GNU/Linux 10 (buster)To Reproduce Exact bcbio command you have used:
Your sample configuration file:
Observed behavior Error message or bcbio output:
Expected behavior bcbio should use PureCN's own method for paired normal in absence of a normalDB (documented in the PureCN docs).
Additional context This happens because the code assumes CNVkit will run even if it won't. And it's not even necessary to run CNVkit to have PureCN use a normal file (although it is not recommended by PureCN upstream).