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Revise structure of pipelines #31

Merged
merged 1 commit into from
Jun 30, 2020
Merged

Revise structure of pipelines #31

merged 1 commit into from
Jun 30, 2020

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gbggrant
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In this PR I'm doing a couple of things:

  • broke the main pipeline wdl into separate workflow, tasks and structs (each of which are in separate directories)
  • added platform-specific versions of the workflow, tasks and structs. Unfortunately there's still a lot of redundant code between them, this does make it easier to maintain and package releases for different versions.
  • added a script that builds a 'pipeline release' by zipping up tasks/structs used by a pipeline wdl into a flattened zip file appropriate for submission to cromwell.
  • reorganized example input files.
  • added a minimal amount of documentation.

tnguyensanger
tnguyensanger reviewed Jun 22, 2020
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@alimanfoo @gbggrant

Do we want to make a private repo for the input JSON files containing paths on Sanger systems?

jessicaway
jessicaway approved these changes Jun 25, 2020
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This looks good! It would be great to get this down to one wdl that can be built for either runtime. Happy to help figure that out in the future

@samuelklee samuelklee mentioned this pull request Jun 29, 2020
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@gbggrant
Restructured repo to add directories for pipelines, tasks and structs
b8432d2 
Currently these are in platform-specific and non-specific directories
Added scripts directory for building releases
Added plumbing test files (minimal input) for farm5
Added documentation
@gbggrant gbggrant force-pushed the gg_issue1_AddStructureToRepo branch from 57c7b4c to b8432d2 Compare June 30, 2020 12:35
@gbggrant gbggrant merged commit 991b032 into master Jun 30, 2020
@gbggrant gbggrant deleted the gg_issue1_AddStructureToRepo branch June 30, 2020 12:39
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@tnguyensanger tnguyensanger tnguyensanger left review comments

@jessicaway jessicaway jessicaway approved these changes

@alimanfoo alimanfoo Awaiting requested review from alimanfoo

@JonKeatley112 JonKeatley112 Awaiting requested review from JonKeatley112

@pshapiro4broad pshapiro4broad Awaiting requested review from pshapiro4broad

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3 participants
@gbggrant @jessicaway @tnguyensanger