[DOCKTESTERS] PCAWG Testing Group

[Miguel Vazquez]

Dear Brian,

I just got back from holidays and missed the latest action. I'm quite busy,
as I'm sure we all are, but I'm going to try to perform the tests as you
suggested. I'll keep you posted if I finally find the time.

Best regards

Miguel

On Thu, Aug 11, 2016 at 7:41 PM, Brian O'Connor <Brian.OConnor at oicr.on.ca>
wrote:

> Hi Everyone
>
> Just as a heads up we had the call today with Oliver, Denis, and Adam.  We
> came up with a very basic testing plan to get us started.  See the wiki
> pages below if you'd like to participate:
>
> * https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+Data
> * https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+SOP
>
> We'll regroup with a call in early Sept to see how each are doing on the
> testing (and communicate via this mailing list along the way).
>
> Thanks for everyone's help testing these workflows!
>
> Brian
>
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> ________________________________________
> From: docktesters-bounces+brian.oconnor=oicr.on.ca at lists.icgc.org
> [docktesters-bounces+brian.oconnor=oicr.on.ca at lists.icgc.org] on behalf
> of Brian O'Connor [Brian.OConnor at oicr.on.ca]
> Sent: Thursday, August 11, 2016 3:46 AM
> To: docktesters at lists.icgc.org
> Subject: Re: [DOCKTESTERS] PCAWG Testing Group
>
> Hi,
>
> I only heard from Denis, Junjun, and Oliver for the testing group doodle
> poll.  The best time is tomorrow (Thursday) at 10am pacific time.  I
> suggest we have a brief call for those that are available since the summer
> is slipping away quickly.
>
> Here’s a google hangouts link:
>
> https://plus.google.com/hangouts/_/ucsc.edu/broconno?
> hceid=YnJvY29ubm9AdWNzYy5lZHU._6cq30e9n6os34ba688pj2b9k60sj8b
> 9p88r3gba16ks34e9k68s30gpp70&authuser=1
>
> Brian
>
> > On Aug 8, 2016, at 7:06 AM, Brian O'Connor <briandoconnor at gmail.com>
> wrote:
> >
> > RESENDING: apologies if you get this again...
> >
> > Hi All,
> >
> > This group has been fairly inactive over the last few months.  Since the
> PCAWG tech group is rapidly wrapping up, I think it would be great to
> validate the workflows we leave the community before we all move on to
> other things.  It will also be helpful for the PCAWG tech infrastructure
> paper which any contributors to this group will be included on.  Can we
> have a call this week to go over the testing plan and who will do what?
> >
> > I think the plan will be something like the following:
> >
> > * identify the workflows we’re going to test, write an SOP:
> https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+SOP
> > * identify the test data we’re going to use, write this up:
> https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+Data
> > * divide the task of testing each available workflow, upload the results
> to GNOS or Jamboree
> > * writing a script/process to cross-check results these calls with the
> final from PCAWG
> >
> > After talking with Jonathan this morning, his ETA for the consensus
> calling/filtering workflow is 3-4 weeks. Same ETA from Gordon for the final
> Broad workflow.  That fits in with a general timeline of the end of
> September for this group to finish it’s testing activities.  So we can have
> this testing completed before the Nov/Dec timeframe for submitting our
> papers. We can test in parallel with Gordon and Jonathan’s work given that
> BWA, Sanger, EMBL, and DKFZ are available now.
> >
> > I propose we have a call this week to go over the testing process plan
> and see who has bandwidth to help (I’m out for vacation/conference
> 8/19-9/2).  Please select a time:
> >
> > http://doodle.com/poll/mmwxcv69szve4ipb
> >
> > Thanks for your help testing the PCAWG workflows!
> >
> > Brian
>
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