[DOCKTESTERS] PCAWG Testing Group

[Brian O'Connor]

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._6cq30e9n6os34ba688pj2b9k60sj8b9p88r3gba16ks34e9k68s30gpp70&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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