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Dev #47

Merged
merged 28 commits into from
Jan 13, 2020
Merged

Dev #47

merged 28 commits into from
Jan 13, 2020

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bshifaw
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@bshifaw bshifaw commented Dec 3, 2019

  • Updated haplotypecaller to WDL 1.0, removed comments from haplotypecaller JSON
  • Added allele-specific annotations to HC
  • Replaced joint-discovery with JointGenotyping workflow,
  • Added Terra version for JointGenotyping workflow
  • Added urls for imports for JointGenotyping workflows
  • Updated ReadMe to reflect changes to JointGenotyping workflow

bshifaw added 19 commits February 22, 2019 21:25
* added updated joint-discovery wdl, needs testing

* Added place holder for terra verion of JointGenotyping wdl

* Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow

* updated the terra version of the JointGenotyping

* added urls for imports for JointGenotyping workflows

* Updated ReadMe
* added updated joint-discovery wdl, needs testing

* Added place holder for terra verion of JointGenotyping wdl

* Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow

* updated the terra version of the JointGenotyping

* added urls for imports for JointGenotyping workflows

* Updated ReadMe

* added missing runtime variables

* added missing runtime variable
* added updated joint-discovery wdl, needs testing

* Added place holder for terra verion of JointGenotyping wdl

* Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow

* updated the terra version of the JointGenotyping

* added urls for imports for JointGenotyping workflows

* Updated ReadMe

* added missing runtime variables

* added missing runtime variable
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bshifaw added 2 commits December 3, 2019 12:05
* added updated joint-discovery wdl, needs testing

* Added place holder for terra verion of JointGenotyping wdl

* Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow

* updated the terra version of the JointGenotyping

* added urls for imports for JointGenotyping workflows

* Updated ReadMe

* added missing runtime variables

* added missing runtime variable

* added recent updates from dsde-pipelines repo to terra version
@bshifaw bshifaw requested a review from ldgauthier December 16, 2019 14:23
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@ldgauthier ldgauthier left a comment

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Some additional updates to the joint genotyping caveats and minor comments.

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Once the HC workflow updated with AS annotations you can merge this.

@bshifaw bshifaw merged commit c8d0d63 into master Jan 13, 2020
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2 participants