Open dpark01 opened 8 years ago
As we've factored it, scaffold does call assembly.py impute_from_reference
which does use novoalign. GATK could be moved
I'm pretty sure the only Novoalign that is happening in impute_from_reference
is novoindex. I don't think novoindex benefits from having a license (or being multithreaded) and I don't know that you're even using the index anyway (don't you regenerate it in the refine steps?). I think you can just use the conda installed novoindex (the unlicensed/free/single-threaded version) for scaffolding.
@tomkinsc I'm slightly inclined to not even expose the --novoalign_license_path
for impute_from_reference
in our own codebase? What do you think?
Currently, the assembly workflows ask for the
gatk_tarball
parameter (required) andnovocraft_license
parameter (optional) in the scaffolding stage. However, these tools aren't even used in the scaffolding stage. Let's move these inputs to the refine1 stage (and carry them forward to the downstream stages as currently), as that is the first place that they are needed.