v1.6.0

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)

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)

v1.5.2

Security fixes

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

v1.5.1

Bug Fixes

• updated CDK packages (#511) (1140da1)
• bump nextflow version to 22.04.1 (#450) (4296ee7), closes #387

v1.5.0

Features

• CWL support with Toil #422, #431, #423, #424, #425, #426, #439, #441, #460, #464, #465
• BYO VPC can use selected subnets #436
• Specify a default custom AMIs for all contexts on activation #451
• Use token provider for MFA profiles #231

Bug Fixes

• Input files should be resolved as relative to the location of the inputs JSON file #429
• Re-activation of an activated account deletes VPC #432
• UX regressions where CDK logs show when --verbose flag is not used #447
• Enforce GO111MODULE=on for the build #457
• Removed duplicate example "haplotype" from wdl examples #427
• Improve examples stability #419
• Update words with vowels to have the same "shape" as haplotype caller #438
• Add nextflow port of demo words-with-vowels workflow #440

Documentation

• Added details about workflow filesystems #372
• Update CLI reference generation instructions #417
• Update docs on VPC endpoints #437
• Typos #428

Full Changelog: v1.4.0...v1.5.0

v1.4.0

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)

v1.3.0

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](20cd77dac1...

v1.2.0

If upgrading to AGC version 1.2.0 please do the following:

1. $ agc context destroy
2. $ agc account deactivate
3. download and install the new release of agc
4. $ agc account activate
5. re-deploy contexts as needed

Features

• Add AGC version tag to AWS resources (#243) (fc6cad7)
• Add WES API endpoint information to agc context describe output (#253) (6145db3)
• Bootstrap CDK during Account Activation (#272) (5228492)
• 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 shrinkwrap upgrade (#298) (9dd6806)
• Scope down batch role permissions (#230) ([14a5aca](14a5acaf3f931cb...

[DEPRECATED] nightly build

The latest nightly build can be accessed here:
s3://healthai-public-assets-us-east-1/amazon-genomics-cli/nightly-build/amazon-genomics-cli.zip

The nightly build can be downloaded using this command:
aws s3api get-object --bucket healthai-public-assets-us-east-1 --key amazon-genomics-cli/nightly-build/amazon-genomics-cli.zip amazon-genomics-cli.zip

v1.1.2

Bug Fixes

• fixing monocdk imports (#190) (6e4b295)

v1.1.1

Bug Fixes

• Correcting MiniWDL output location (#173) (8e6f3fd)
• fix for installation.md (#161) (72ee50c)
• progress bar doesn't show any progress (#166) (5b4a5b4)
• Return timezone information in RunLog (#174) (37b33a7)
• unique project name (#171) (a464f81)
• Increasing WES adapter lambda timeout (#180) (20cd77d)