roger that on the partial, I noticed that for last night's alignments they
were still in the .partial,  but I understand if thats not going to be the
plan going forward.


On Mon, Apr 28, 2014 at 2:27 PM, Kyle Ellrott <notifications@github.com>wrote:

> In job_upload.sh:
>
> > @@ -9,7 +12,7 @@ UUID=$2
> >  . $BASEDIR/align.conf
> >
> >
> > -BAM_DIR=$VOLUME/output/$UUID
> > +BAM_DIR=$VOLUME/output/$UUID.partial
>
> I think the output directory should be $VOLUME/output/$UUID, the .partial
> directory is for (or should) half formed results
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/kellrott/tcga_realign/pull/2/files#r12068797>
> .
>