[DOCKTESTERS] Fwd: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference

Fri Sep 30 10:46:11 EDT 2016

Dear Francis,

I haven't had a chance to go at it again since the meeting, I got a new
position in Norway, but next week I will try to find some time. I think I
might just try another pipeline, since it seems like the Sanger pipeline
needs fixing. Although perhaps I will first try Denis test data again and
see if I can reproduce the error, after which we probably should contact
the person in charge.

Best

M

On Fri, Sep 30, 2016 at 3:52 PM, Francis Ouellette <francis at oicr.on.ca>
wrote:

> Dear Miguel and Junjun,
>
> Any more attempts on testing the PCAWG sanger docker container?
>
> If you reproduce the same error, we will need to involve Bryan and
> Keiran Raine <kr2 at sanger.ac.uk> (author of the container).
>
> Let’s get this one figured out.
>
> I am going to assume that the making of the docker container is what
> needs resolving.
>
> Brian: We may need your input here.
>
> Details of our current experiment should continue to be posted here:
>
> https://goo.gl/XX5BG9
>
> Thank you all,
>
> francis
>
> PS would be good for others on list to follow directions on above google
> doc and also see if they can succeed on this workflow.
>
> Junjun and Miguel have tried different clouds, but used the sanger
> workflow, on the same data set.
>
> Thank you for trying to do this.
>
> Would be good if I heard back from anybody before Monday AM (tech call).
>
> @bffo
>
> PS I CCed Keiran, but waiting to hear back from Brian before we need to
> involve him some more.
> PPS Junjun/Miguel: maybe you can try the DKFZ docker as well? (on the same
> data set).
>
>
> --
> B.F. Francis Ouellette          http://oicr.on.ca/person/francis-ouellette
>
>
>
>
> Begin forwarded message:
>
> *From: *Christina Yung <Christina.Yung at oicr.on.ca>
> *Subject: **[PAWG-TECH] Draft agenda for PCAWG-TECH teleconference*
> *Date: *September 30, 2016 at 9:19:39 AM EDT
> *To: *"pawg-tech (pawg-tech at lists.icgc.org)" <pawg-tech at lists.icgc.org>
>
> Hi Everyone,
>
>
>
> Below is a draft agenda for Monday’s tech call.  Please let me know if you
> have any agenda items for discussion.
>
> https://wiki.oicr.on.ca/display/PANCANCER/2016-10-03+
> PCAWG-TECH+Teleconference
>
>
>
> Have a great weekend!
>
> Christina
>
>
> Call Info
>
> *Usual Time            9 AM Eastern Time, Mondays*
>
> *UK                          0208 322 2500*
>
> *Canada                  1-866-220-6419*
>
> *United States        **1-877-420-0272*
>
> *All Others              Please see attached PDF file
> <https://wiki.oicr.on.ca/download/attachments/57776990/PAWG-TECH-Telecon-International-Numbers.pdf?version=1&modificationDate=1401456003000&api=v2> with
> a list of numbers for other countries.*
>
> *Participant Code  5910819#*
> Agenda
>
>
>
> *Time*
>
> *Item*
>
> *Who*
>
> *Attachments/Links*
>
> 5min
>
> Welcome. Wait for group members to log on
>
> Christina Yung <https://wiki.oicr.on.ca/display/~cyung>, OICR
>
> 10min
>
> Overall status
> Christina Yung <https://wiki.oicr.on.ca/display/~cyung>, OICR
>
> ·         Linkouts to Most Current PCAWG Data
> <https://wiki.oicr.on.ca/display/PANCANCER/Linkouts+to+Most+Current+PCAWG+Data>
>
> ·         Report data issues to pcawg-data at icgc.org, GNOS issue to:
> Help at annaisystems.com
>
> ·         From Boston F2F: PCAWG datasets & dependencies
> <https://docs.google.com/spreadsheets/d/1VltMMLL5XDIFipM3zzLqZOGj5z-UxIMKLDbsuDiD2Q8/edit?usp=sharing>
>
> *Action Items*
>
> 1.       [Joachim] Consensus SV - final?
>
> 2.       [Jakob] Consensus SNVs - changes to "SNV near indels" annotation?
>
> 3.       [Junjun] Specimen ID mapping for miRNA and methylation
>
> 4.       [Jonathan & Joachim] Consensus calls for cell lines, followed by
> filtering
>
> 5.       [Matthias & Gordon] Docker containers for filtering methods
>
> 6.       [Christina] Run alignment & variant workflows on medulloblastoma
> sample (tumor 40x, normal 30x) from ICGC benchmark to estimate false
> negative rate
>
> 7.       [Christina] Follow up with institutes interested in hosting
> PCAWG data long-term
>
> 8.       [All] As per Jennifer's email on Sept 16, please provide
> authorship information again or for the first time using PCAWG Author Form (
> http://goo.gl/forms/5Wq5x5X1DK). Save the link "Edit your response" so
> you can go back later to provide updates, for example about your evolving
> role in writing specific papers.
>
> 9.       [All] Contribute to the manuscripts on
>
> a.       infrastructure: https://docs.google.com/
> document/d/10alAxrWLdLSyhci-rfNuVH13rFXCJkaY_rzf1KJn7nc/edit
>
> b.       variants: Paper ( https://goo.gl/g9CLsu ), Supplement (
> https://goo.gl/EWYh7e )
>
> c.       Rogue's Gallery of Cancer Genome Sequencing Artifacts ( outline
> <https://wiki.oicr.on.ca/download/attachments/66958609/Rogues%E2%80%99%20Gallery%20of%20Cancer%20Genome%20Sequencing%20Artefacts.pdf?version=1&modificationDate=1469802643000&api=v2>
> )
>
> 10.   [Junjun] Discuss PCAWG vs DCC glossary terms at next PCAWG-10/13
> conference
>
> 10min
>
> Status of dockerizing workflows
> Brian O'Connor <https://wiki.oicr.on.ca/display/~boconnor>, UCSC
>
> Gordon Saksena
> <https://wiki.oicr.on.ca/display/~gsaksena@broadinstitute.org>, Broad
>
> Francis Ouellette <https://wiki.oicr.on.ca/display/~francis>, OICR
> *Status of PCAWG Workflow ports to Dockstore*:
>
> Denis has been porting the Dockstore entries to CWL version 1.0 which is
> part of our effort to publish Dockstore (this doesn't affect the content of
> the pipelines, simply their "descriptors" which allow them to be runnable
> via Dockstore). Denis has also worked on testing BWA-Mem, Sanger, EMBL
> (which all work with CWL 1.0 and Kerian's test dataset) and has fixed
> issues with DKFZ and is testing the latter with a real sample shortly.
>
> 1.       BWA-Mem - Ready for testing by Francis' team
>
> 2.       Sanger - Ready for testing by Francis' team.
>
> 3.       EMBL - Ready for testing by Francis' team.
>
> 4.       DKFZ - Ready for testing by Francis' team. I've exchanged emails
> with Manuel Ballesteros who has been testing this pipeline.
>
> 5.       Broad - Variant calling (MuTect, dRanger, snowman), need some
> work, Gordan sent details previously
>
> 6.       OxoG - Waiting for Dimitri to provide OxoG docker
>
> 7.       Variantbam
>
> 8.       Consensus algorithm
>
> PCAWG Docker (Dockstore) Testing Working Group
> <https://wiki.oicr.on.ca/display/PANCANCER/PCAWG+Docker+%28Dockstore%29+Testing+Working+Group>
>
> 5min
>
> Other business?
>
> Group
>
>
>
>
>
>
>
> *Christina K. Yung, PhD*
> Project Manager, Cancer Genome Collaboratory
>
> *Ontario Institute for Cancer Research*
> MaRS Centre
>
> 661 University Avenue, Suite 510
> Toronto, Ontario, Canada M5G 0A3
> Tel: 416-673-8578
>
> www.oicr.on.ca
>
>
>
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