Brad Chapman

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  • Registered on: 06/29/2014
  • Last connection: 04/27/2017

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Reported issues: 13

04/14/2017

12:27 am Arvados Bug #11495: bcbio NA12878 validation runs: job re-use failure with non-existant collection
Thanks Bryan for the digging on this. I didn't intentionally delete any log files but am not sure if the failed retri...

04/13/2017

01:46 pm Arvados Bug #11495 (New): bcbio NA12878 validation runs: job re-use failure with non-existant collection
Due to failures reported in #11494 I tried to re-run the bcbio CWL validation pipeline with re-use enabled and I get ...
01:43 pm Arvados Bug #11494 (New): bcbio NA12878 validation runs: failed steps due to being unable to setup container
I'm running bcbio CWL validation workflows on NA12878 chr20 in preparation for the GA4GH workflow challenge:
https...

10/18/2016

05:16 pm Arvados Bug #10292 (Resolved): [CWL] Sometimes deadlocks on completion of subworkflow

Peter;
This is a ticket to follow up on our discussion about deadlocks during bcbio CWL runs. These are intermitte...

06/23/2016

03:21 pm Arvados Bug #9485: [bcbio] Changing truth vcf/bed prevents variant calling jobs being reused in bcbio cwl...
You're right sorry for giving you the wrong answer on this before. The reason for this is that we pack the inputs int...

06/09/2016

10:38 am Arvados Bug #9361 (Resolved): [CWL] arvados-cwl-runner unknown issue of job reuse
Jiayong;
Thanks for the report. This was a bug from me when we moved to CWL definitions that enable re-use and requi...

03/15/2016

01:54 pm Arvados Task #8636 (Resolved): bcbio CWL variant call run problem: workflow cannot make any more progress
bcbio/CWL/Arvados process moved to use uploading of inputs and reference data:
https://github.com/chapmanb/bcbio-n...
01:46 pm Arvados Task #8521 (Resolved): Review 8488-cwl-crunchrunner-collection
Arvados/bcbio/CWL working well on comprehensive test runs, including full re-use of steps. Looks great:
https://cl...

03/10/2016

06:29 pm Arvados Task #8636: bcbio CWL variant call run problem: workflow cannot make any more progress
Peter;
For help with debugging here are two pipelines run with the same CWL, bcbio image and cwl-runner. The first f...
02:36 pm Arvados Task #8636: bcbio CWL variant call run problem: workflow cannot make any more progress
Peter;
We have a successful run. Awesome work:
https://cloud.curoverse.com/pipeline_instances/qr1hi-d1hrv-3q50swa...

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