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

Wed Oct 5 11:43:13 EDT 2016

Hi,
Heads-up, is that token in https://github.com/mikisvaz/PCAWG-Docker-Test/blob/master/icgc-storage-client-1.0.19/conf/application.properties a real token?

As for workflows, I would probably go in the order bwa-mem, delly, sanger (which you have already done), dkfz

________________________________
From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Miguel Vazquez [miguel.vazquez at cnio.es]
Sent: October 5, 2016 4:44 AM
To: Francis Ouellette
Cc: kr2 at sanger.ac.uk; docktesters at lists.icgc.org
Subject: Re: [DOCKTESTERS] Fwd: [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference

Hello all,

I've created a repository in

https://github.com/mikisvaz/PCAWG-Docker-Test<redir.aspx?REF=DwEE_BTpbbRUOs-4jzs6R99e7GSHbNv6G7CM-jqjXKJiRGkANu3TCAFodHRwczovL2dpdGh1Yi5jb20vbWlraXN2YXovUENBV0ctRG9ja2VyLVRlc3Q.>

With scripts that can help you run the tests. They can help download samples, prepare the Dockerstore.json files and run them. I've added an entry in the google doc.

I've ran the Sanger on the HCC1143 (Test) data and it seemed to have completed correctly (I updated the table). I'm in the process now of running the same test data in the DKFZ and sample DO50311 on the Delly workflow.

I have two standing questions:

- What are the other workflows I need to test?
- What is the bedpe file used by DKFZ and how to produce it. Denis has pointed me to some forum threads that I have to study a bit, but it seems that we need to run something to produce it before we can run the workflow, and I wonder how this fits into our testing scheme. I'll read more about it when I have a chance.

Best regards

On Fri, Sep 30, 2016 at 3:52 PM, Francis Ouellette <francis at oicr.on.ca<redir.aspx?REF=Ykp1pk_j-939v485SO7ZvRgKCHD_y7ih6qgh9sxdprliRGkANu3TCAFtYWlsdG86ZnJhbmNpc0BvaWNyLm9uLmNh>> 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<redir.aspx?REF=sdarGB5LqxD0pGW1mFGxJOAjRDllrymFGrUVS0I_yhNiRGkANu3TCAFtYWlsdG86a3IyQHNhbmdlci5hYy51aw..>> (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<redir.aspx?REF=IcHK7793Lku63ffvEQkvDZDmSMBXLpeE4veIMVsE1R5iRGkANu3TCAFodHRwczovL2dvby5nbC9YWDVCRzk.>

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<redir.aspx?REF=g0st_SL-xOm-ogkHB8RZA0pckR8AcKnZjj0SGI8I5_BiRGkANu3TCAFodHRwOi8vb2ljci5vbi5jYS9wZXJzb24vZnJhbmNpcy1vdWVsbGV0dGU.>

Begin forwarded message:

From: Christina Yung <Christina.Yung at oicr.on.ca<redir.aspx?REF=-VJycnKoIlh8qL33D7winoK5Y0DvobanYBooM72JIjZiRGkANu3TCAFtYWlsdG86Q2hyaXN0aW5hLll1bmdAb2ljci5vbi5jYQ..>>
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<redir.aspx?REF=3L1LSVSs_RMmtvSp5XjHahAZ8jegqomkNo0C8KcXuH1iRGkANu3TCAFtYWlsdG86cGF3Zy10ZWNoQGxpc3RzLmljZ2Mub3Jn>)" <pawg-tech at lists.icgc.org<redir.aspx?REF=3L1LSVSs_RMmtvSp5XjHahAZ8jegqomkNo0C8KcXuH1iRGkANu3TCAFtYWlsdG86cGF3Zy10ZWNoQGxpc3RzLmljZ2Mub3Jn>>

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<redir.aspx?REF=135ld0s1aqPNiHPlSSNB6yH5piTbSz5_-YDgDdjfgZe8pmsANu3TCAFodHRwczovL3dpa2kub2ljci5vbi5jYS9kaXNwbGF5L1BBTkNBTkNFUi8yMDE2LTEwLTAzK1BDQVdHLVRFQ0grVGVsZWNvbmZlcmVuY2U.>

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<redir.aspx?REF=GY0dU51pAzZ6cAGe6PBPKEcU5CCbKYEHgcnPNrMfvwO8pmsANu3TCAFodHRwczovL3dpa2kub2ljci5vbi5jYS9kb3dubG9hZC9hdHRhY2htZW50cy81Nzc3Njk5MC9QQVdHLVRFQ0gtVGVsZWNvbi1JbnRlcm5hdGlvbmFsLU51bWJlcnMucGRmP3ZlcnNpb249MSZtb2RpZmljYXRpb25EYXRlPTE0MDE0NTYwMDMwMDAmYXBpPXYy> 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<redir.aspx?REF=McninUu1GX3tIKsAgeDugDzOpKDyh4sBWAMXKlg_Hy28pmsANu3TCAFodHRwczovL3dpa2kub2ljci5vbi5jYS9kaXNwbGF5L35jeXVuZw..>, OICR

10min

Overall status

Christina Yung<redir.aspx?REF=McninUu1GX3tIKsAgeDugDzOpKDyh4sBWAMXKlg_Hy28pmsANu3TCAFodHRwczovL3dpa2kub2ljci5vbi5jYS9kaXNwbGF5L35jeXVuZw..>, OICR

•         Linkouts to Most Current PCAWG Data<redir.aspx?REF=CVvTfKnivSfrHwgGwbOyVQHR07pxC8B4-tzxF2n66oG8pmsANu3TCAFodHRwczovL3dpa2kub2ljci5vbi5jYS9kaXNwbGF5L1BBTkNBTkNFUi9MaW5rb3V0cyt0bytNb3N0K0N1cnJlbnQrUENBV0crRGF0YQ..>
•         Report data issues to pcawg-data at icgc.org<redir.aspx?REF=BOXVT2iG2w3DXKEyiNY91Lhj3lqutDEuO-VMLGzpt_S8pmsANu3TCAFtYWlsdG86cGNhd2ctZGF0YUBpY2djLm9yZw..>, GNOS issue to: Help at annaisystems.com<redir.aspx?REF=sYH6haoWJtI7JEv3KFvvkA4YXqpSrKGPYzC-WRpWH3u8pmsANu3TCAFtYWlsdG86SGVscEBhbm5haXN5c3RlbXMuY29t>
•         From Boston F2F: PCAWG datasets & dependencies<redir.aspx?REF=v18JhTsOv_nvCIfcIu0M9K87eRwLhUojLmlKb5O27Ve8pmsANu3TCAFodHRwczovL2RvY3MuZ29vZ2xlLmNvbS9zcHJlYWRzaGVldHMvZC8xVmx0TU1MTDVYRElGaXBNM3p6THFaT0dqNXotVXhJTUtMRGJzdURpRDJROC9lZGl0P3VzcD1zaGFyaW5n>

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<redir.aspx?REF=UCwKCEJ68smUM-5oT0mgNQB7nTHayCeDHTzoO91UfVm8pmsANu3TCAFodHRwOi8vZ29vLmdsL2Zvcm1zLzVXcTV4NVgxREs.>). 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<redir.aspx?REF=rUgnOBRme3KDHasDyhPqnHdNNdpi6ZtCk3KP1r5XsTG8pmsANu3TCAFodHRwczovL2RvY3MuZ29vZ2xlLmNvbS9kb2N1bWVudC9kLzEwYWxBeHJXTGRMU3loY2ktcmZOdVZIMTNyRlhDSmthWV9yemYxS0puN25jL2VkaXQ.>
b.       variants: Paper ( https://goo.gl/g9CLsu<redir.aspx?REF=KyTZL96L4GqoOVYtxIsxC7ZwJJlfdno7pkQ3x1tZuoe8pmsANu3TCAFodHRwczovL2dvby5nbC9nOUNMc3U.> ), Supplement ( https://goo.gl/EWYh7e<redir.aspx?REF=JDnRs5YrCC5z1b8K2PvKQe1pCFOsQrEVBSgupE_F_6q8pmsANu3TCAFodHRwczovL2dvby5nbC9FV1loN2U.> )
c.       Rogue's Gallery of Cancer Genome Sequencing Artifacts ( outline<redir.aspx?REF=3kwSJiKn8BNoqYiNxrog1lMumN5AZlJwG2yDwiCuXaa8pmsANu3TCAFodHRwczovL3dpa2kub2ljci5vbi5jYS9kb3dubG9hZC9hdHRhY2htZW50cy82Njk1ODYwOS9Sb2d1ZXMlRTIlODAlOTklMjBHYWxsZXJ5JTIwb2YlMjBDYW5jZXIlMjBHZW5vbWUlMjBTZXF1ZW5jaW5nJTIwQXJ0ZWZhY3RzLnBkZj92ZXJzaW9uPTEmbW9kaWZpY2F0aW9uRGF0ZT0xNDY5ODAyNjQzMDAwJmFwaT12Mg..> )
10.   [Junjun] Discuss PCAWG vs DCC glossary terms at next PCAWG-10/13 conference

10min

Status of dockerizing workflows

Brian O'Connor<redir.aspx?REF=Nww5R0wY9kXmjpz7u6WJIRQ0W21w3_LLFPMHZn9rePe8pmsANu3TCAFodHRwczovL3dpa2kub2ljci5vbi5jYS9kaXNwbGF5L35ib2Nvbm5vcg..>, UCSC

Gordon Saksena<redir.aspx?REF=88sYlObg1XXC9u-ILLRVxL4iYQHqEhz6NvQreunO9Ya8pmsANu3TCAFodHRwczovL3dpa2kub2ljci5vbi5jYS9kaXNwbGF5L35nc2Frc2VuYUBicm9hZGluc3RpdHV0ZS5vcmc.>, Broad

Francis Ouellette<redir.aspx?REF=xCnleBg49HMljOwCtFUjdKXBI8zmZAGO4xDDgmdhqPm8pmsANu3TCAFodHRwczovL3dpa2kub2ljci5vbi5jYS9kaXNwbGF5L35mcmFuY2lz>, 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<redir.aspx?REF=Yxv70U1kFNEYx3goPd27mlBrRTPaCsT8dO6N2B8emUK8pmsANu3TCAFodHRwczovL3dpa2kub2ljci5vbi5jYS9kaXNwbGF5L1BBTkNBTkNFUi9QQ0FXRytEb2NrZXIrJTI4RG9ja3N0b3JlJTI5K1Rlc3RpbmcrV29ya2luZytHcm91cA..>

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<redir.aspx?REF=txLSQ43Fu-ln35lqe9_7Cn6g9uEEj27drOGh36QhGla8pmsANu3TCAFodHRwOi8vd3d3Lm9pY3Iub24uY2Ev>

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