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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file. See standard-version for commit guidelines.

1.6.0 (2022-12-28)

Features

  • Add ARM support for CLI build (#569) (f002a3d)
  • added verbose logging to workflow run (#480) (5bec60a)
  • reduce permissions related to APIGateway for recommended user role (#538) (fd9e230)
  • Support and use Toil 5.8's WES task output (#501) (a5e52b5)
  • support for PRIVATE API Gateway endpoints (#507) (357d545)

Bug Fixes

  • bump nextflow version to 22.04.1 (#450) (ec9c02c), closes #387
  • Install script output name (def4335)
  • update go version to fix bug with go test -race in OSX Monterey (#505) (c918e97)
  • update nextflow version environment variable (b8ea514)

1.5.2 (2022-10-18)

Security fixes

  • Updates CDK and VM2 versions to include the latest releases to fix the following dependabot issues (#10) (#11)

1.5.1 (2022-09-08)

Bug Fixes

1.5.0 (2022-05-25)

Bug Fixes

  • enforce GO111MODULE=on for the build (#457) (412eff7)

1.4.0 (2022-04-15)

Features

  • add "public subnet" mode for lower ongoing costs (#283) (d6a67f9)
  • Add optionsFile flag (#352) (884308f)
  • allow engine logs of specific cromwell workflows using run-id (#389) (ef8c6a3)
  • Download and report WES run log files (#319) (2a8fab0)
  • Engine logs for specific workflow runs (#379) (8bda674)
  • ensures vpcId is recalled (if available) on account_activate (#365) (f056026)
  • Record command run and show in agc workflow status (#353) (45fac3a)

Bug Fixes

  • Add safety checks in optional manifest fields (#403) (c084782)
  • Converts WDL log exit_code from string to int32 per WES spec (#380) (2b93a2c)
  • do not set WorkflowEngineParameters when empty (#402) (3260d73)
  • ensure workflow engines can and do terminate child tasks when the engine task is stopped by AGC (#391) (68861e1)
  • miniwdl wdl1.1support (#370) (7bcfd8f)
  • nextflow wes adapter can retrieve more than 100 task logs (#377) (a1c2d30)
  • remove temp directory prefix from input URI (#405) (3933d7a)
  • Revert change to WDL version for this workflow (#378) (75603a8)
  • updates cromwell exit_code (#398) (9f6480d)
  • updates workflow engine parameters for key, val pairing (#407) (7a27122)

1.3.0 (2022-03-04)

Features

  • add a global --silent flag (#219) (eed4189)
  • add a global --silent flag (#219) (#285) (388533b)
  • Add AGC version tag to AWS resources (#243) (fc6cad7)
  • Add JSON as a CLI output format (#215) (#309) (2d6ad0c)
  • Add snakemake wes adapter + cdk + example workflow (#304) (6357b47)
  • Add WES API endpoint information to agc context describe output (#253) (6145db3)
  • Added output file creation snakemake + copying efs files to s3 (#316) (bb4a42f)
  • Bootstrap CDK during Account Activation (#272) (5228492)
  • Bootstrap CDK during Account Activation (#272) (219596e)
  • context destroy --force flag (#118) (4282093)
  • don't use ebs auto scale for minidl (#300) (225d139)
  • Enable hosting assets in AWS commercial regions (#240) (2eb5007)
  • Explain a bit more about S3 errors (#318) (fa41fa8)
  • Implement EFS IOPs specification in Project YAML (#313) (c1af22b)
  • Improve context stack deployment speed (#150) (f7d6c7f)
  • Improve inputs JSON handling via --inputsFile flag (#335) (#336) (2f24c28)
  • improve reliability of provision scripts (#308) (16eff36)
  • Improved Workflow logs (#156) (f71231c)
  • Initial infrastructure for MiniWdl support (#125) (387393a)
  • Introducing AWS Lambda based WES Adapter for running the workflows (#155) (bd90f47)
  • release extras along with the agc package (b83edd4)
  • release extras along with the agc package (d4891e7)
  • release extras along with the agc package (b350ca4)
  • stop discarding un-actionable deployment errors (#270) (2c7fbcb)
  • Tag infrastructure with custom tags to prevent automatic deletion (#254) (#282) (f4d7aaf)

Bug Fixes

  • Add AGC assets bucket to project read list (#247) (2019b6a)
  • add build wes adapter step to run dev script and readme (#307) (466ea69)
  • Adds a message when new logs aren't shown to the user immediately (#131) (54349d2)
  • Allow home directory path in workflow project config (#137) (760ed3c)
  • Asserts order deterministically (#153) (c4299e8)
  • container validation check with the correct region from user profile (#310) (c36a1f0)
  • correctly handle missing return code from Cromwell executions (#276) (3c61735)
  • correctly link to core app (#133) (ce103b2)
  • Delete bootstrap bucket on account deactivate (#306) (a81710b)
  • deploy wes adapter code as cdk asset (#321) (cbaa38c)
  • Deregionalize min permissions (#128) (c4dc96b)
  • Fix project data path prefix and docs (#315) (69a6bb4)
  • fixed arg validation for format (#198) (0b68019)
  • Fixes how inputs are processed in AGC via Manifest (#277) (be5c684)
  • Fixes how users interact with the context commands (#115) (ffb3bb6)
  • Fixes the mechanism for copying the directory contents (#311) (29f8e9e)
  • fixing monocdk imports (#190) (9c94fd8)
  • force use node v14 in cdk package (d67a18c)
  • function for default config (#201) (e6983ae)
  • Handle errors from CDK command (#245) (99d9378)
  • improve contrast in docs (#149) (beb10f4)
  • Increasing WES adapter lambda timeout (#180) (20cd77d)
  • invalid AWS Health url (#130) (1aef83b)
  • miniwdl interpolation workaround (27f4bf5)
  • nest batch artifacts and disable bucket clean up (#262) (73bb98d)
  • Nextflow workflow logs unmarshal number (#286) (1ddf67c)
  • Nextflow workflow logs unmarshal number (#286) (f739f03)
  • Pass engine endpoint directly the wes adapter (#122) (81ed484)
  • Pinned running of rnaseq to version 3.4 (5386a3c)
  • progress bar doesn't show any progress (#166) (9dd17ae)
  • Remove Chdir when looking for project files (#228) (3564d6f)
  • rename unassigned variable (#329) (a3c26a8)
  • Respect maxVCpus in miniwdl contexts (#202) (e4ad17e)
  • Return timezone information in RunLog (#174) (118e1e2)
  • Revert add a global --silent flag (#219) (#279) (a6cc990), closes #274
  • Revert shrinkwrap upgrade (#298) (9dd6806)
  • Scope down batch role permissions (#230) (14a5aca)
  • show logs for workflows with more than 100 tasks (#114) (4e54c3b)
  • show warning when user choose ARM based instance type in verbose mode during context deployment (3967b81)
  • Shows the relevant error if the workflow logs can't be retrieved (#103) (2051b95)
  • switch from a progress bar to a spinner (#203) (1ae9c8a)
  • temporary folder potential leak in some error scenarios. unit test for cdk command execution (#140) (c50608e)
  • Typo in documentation (#255) (db57703)
  • unique project name (#171) (2cb4303)
  • update go dependency versions (#284) (55f9bed)
  • update go dependency versions (#284) (5925da5)
  • updates context describe to be consistent with context destroy (#143) (bb7667b)
  • updates how the logs are shown from cloudwatch (#142) (1502578)
  • Use correct context name (#132) (c1516b6)
  • use fixed python 3.9 in wes adapter (f88a69e)
  • use proper assertion in order to avoid sporadic unit test failures (#167) (a836f20)
  • use proper go tags for windows build (#117) (7dfa94a)
  • Using shrinkwrap and ci to install set NPM dependencies (#193) (27f456e)
  • Workflow status now ignores unqueryable stacks (#138) (cf817a8)
  • workflows from demo-wdl-project should run without errors out of the box (#108) (6960eac)

1.2.0 (2022-02-17)

Features

  • add a global --silent flag (#219) (eed4189)
  • Add AGC version tag to AWS resources (#243) (fc6cad7)
  • Add snakemake wes adapter + cdk + example workflow (#304) (6357b47)
  • Add WES API endpoint information to agc context describe output (#253) (6145db3)
  • Bootstrap CDK during Account Activation (#272) (5228492)
  • Bootstrap CDK during Account Activation (#272) (219596e)
  • context destroy --force flag (#118) (4282093)
  • don't use ebs auto scale for minidl (#300) (225d139)
  • Enable hosting assets in AWS commercial regions (#240) (2eb5007)
  • Improve context stack deployment speed (#150) (f7d6c7f)
  • improve reliability of provision scripts (#308) (16eff36)
  • Improved Workflow logs (#156) (f71231c)
  • Initial infrastructure for MiniWdl support (#125) (387393a)
  • Introducing AWS Lambda based WES Adapter for running the workflows (#155) (bd90f47)

Bug Fixes

  • Add AGC assets bucket to project read list (#247) (2019b6a)
  • add build wes adapter step to run dev script and readme (#307) (466ea69)
  • Adds a message when new logs aren't shown to the user immediately (#131) (54349d2)
  • Allow home directory path in workflow project config (#137) (760ed3c)
  • Asserts order deterministically (#153) (c4299e8)
  • container validation check with the correct region from user profile (#310) (c36a1f0)
  • correctly handle missing return code from Cromwell executions (#276) (3c61735)
  • correctly link to core app (#133) (ce103b2)
  • Delete bootstrap bucket on account deactivate (#306) (a81710b)
  • deploy wes adapter code as cdk asset (#321) (cbaa38c)
  • Deregionalize min permissions (#128) (c4dc96b)
  • Fix project data path prefix and docs (#315) (69a6bb4)
  • fixed arg validation for format (#198) (0b68019)
  • Fixes how inputs are processed in AGC via Manifest (#277) (be5c684)
  • Fixes how users interact with the context commands (#115) (ffb3bb6)
  • Fixes the mechanism for copying the directory contents (#311) (29f8e9e)
  • fixing monocdk imports (#190) (9c94fd8)
  • force use node v14 in cdk package (d67a18c)
  • function for default config (#201) (e6983ae)
  • Handle errors from CDK command (#245) (99d9378)
  • improve contrast in docs (#149) (beb10f4)
  • Increasing WES adapter lambda timeout (#180) (20cd77d)
  • invalid AWS Health url (#130) (1aef83b)
  • miniwdl interpolation workaround (27f4bf5)
  • nest batch artifacts and disable bucket clean up (#262) (73bb98d)
  • Nextflow workflow logs unmarshal number (#286) (1ddf67c)
  • Nextflow workflow logs unmarshal number (#286) (f739f03)
  • Pass engine endpoint directly the wes adapter (#122) (81ed484)
  • Pinned running of rnaseq to version 3.4 (5386a3c)
  • progress bar doesn't show any progress (#166) (9dd17ae)
  • Remove Chdir when looking for project files (#228) (3564d6f)
  • rename unassigned variable (#329) (a3c26a8)
  • Respect maxVCpus in miniwdl contexts (#202) (e4ad17e)
  • Return timezone information in RunLog (#174) (118e1e2)
  • Revert add a global --silent flag (#219) (#279) (a6cc990), closes #274
  • Revert shrinkwrap upgrade (#298) (9dd6806)
  • Scope down batch role permissions (#230) (14a5aca)
  • show logs for workflows with more than 100 tasks (#114) (4e54c3b)
  • show warning when user choose ARM based instance type in verbose mode during context deployment (3967b81)
  • Shows the relevant error if the workflow logs can't be retrieved (#103) (2051b95)
  • switch from a progress bar to a spinner (#203) (1ae9c8a)
  • temporary folder potential leak in some error scenarios. unit test for cdk command execution (#140) (c50608e)
  • Typo in documentation (#255) (db57703)
  • unique project name (#171) (2cb4303)
  • update go dependency versions (#284) (55f9bed)
  • update go dependency versions (#284) (5925da5)
  • updates context describe to be consistent with context destroy (#143) (bb7667b)
  • updates how the logs are shown from cloudwatch (#142) (1502578)
  • Use correct context name (#132) (c1516b6)
  • use fixed python 3.9 in wes adapter (f88a69e)
  • use proper assertion in order to avoid sporadic unit test failures (#167) (a836f20)
  • use proper go tags for windows build (#117) (7dfa94a)
  • Using shrinkwrap and ci to install set NPM dependencies (#193) (27f456e)
  • Workflow status now ignores unqueryable stacks (#138) (cf817a8)
  • workflows from demo-wdl-project should run without errors out of the box (#108) (6960eac)

1.1.2 (2021-11-24)

Bug Fixes

1.1.1 (2021-11-15)

Bug Fixes

1.1.0 (2021-11-11)

Features

  • context destroy --force flag (#118) (4282093)
  • Initial infrastructure for MiniWdl support (#125) (387393a)
  • Introducing AWS Lambda based WES Adapter for running the workflows (#155) (bd90f47)

Bug Fixes

  • Adds a message when new logs aren't shown to the user immediately (#131) (54349d2)
  • Asserts order deterministically (#153) (c4299e8)
  • correctly link to core app (#133) (ce103b2)
  • Deregionalize min permissions (#128) (c4dc96b)
  • Fixes how users interact with the context commands (#115) (ffb3bb6)
  • improve contrast in docs (#149) (beb10f4)
  • invalid AWS Health url (#130) (1aef83b)
  • miniwdl interpolation workaround (27f4bf5)
  • Pass engine endpoint directly the wes adapter (#122) (81ed484)
  • show logs for workflows with more than 100 tasks (#114) (4e54c3b)
  • Shows the relevant error if the workflow logs can't be retrieved (#103) (2051b95)
  • temporary folder potential leak in some error scenarios. unit test for cdk command execution (#140) (c50608e)
  • updates context describe to be consistent with context destroy (#143) (bb7667b)
  • updates how the logs are shown from cloudwatch (#142) (1502578)
  • Use correct context name (#132) (c1516b6)
  • use proper go tags for windows build (#117) (7dfa94a)
  • Workflow status now ignores unqueryable stacks (#138) (cf817a8)
  • workflows from demo-wdl-project should run without errors out of the box (#108) (6960eac)

1.0.1 (2021-10-01)

Bug Fixes

  • Updated documentation
  • Scoped down engine IAM permissions
  • Improved error messages

1.0.0 (2021-09-26)

Features

  • First release!