1.0.0

First initial tagged release

What's Changed

• Add draft CI workflow by @BrunoGrandePhD in #1
• Create S3 bucket for storing CloudFormation templates by @BrunoGrandePhD in #2
• Add NextFlow service account policy and user by @tthyer in #4
• Create initial draft for contribution guidelines by @BrunoGrandePhD in #3
• Add launch policy for NextFlow service user by @tthyer in #6
• CICD refactor by @tthyer in #7
• Revert "CICD refactor" by @tthyer in #8
• Revert "Revert "CICD refactor"" by @tthyer in #9
• Fix CICD refactor issues by @tthyer in #10
• Add VPCs by @tthyer in #11
• IT-1223: Add routes to VPN and update Sceptre action by @xschildw in #14
• Provision service user for accessing S3 data by @BrunoGrandePhD in #12
• Add an AWS Aurora cluster required for NextFlow Tower app by @tthyer in #15
• Add lambda to bootstrap tower database by @tthyer in #16
• Use -O option for storing wget output to avoid caching by @BrunoGrandePhD in #17
• WORKFLOWS-25: support sceptre resolvers in build by @tthyer in #19
• WORKFLOWS-21: Add ECS cluster stack by @tthyer in #18
• Add KMS keys for workflows-specific infrastructure by @tthyer in #22
• Update Nextflow IAM Forge Policy by @daisyhan97 in #24
• WORKFLOWS-17: Enable Aurora DB logging via CloudWatch by @BrunoGrandePhD in #21
• Add stack that produces SMTP credentials by @tthyer in #35
• IT-1373: Add hosted zones by @xschildw in #38
• WORKFLOWS-36 use custom keys by @tthyer in #37
• Workflows-22 ECS task definition by @tthyer in #39
• Remove VPC peering by @tthyer in #40
• KMS key for bootstrapping must be in same stack with Lambda by @tthyer in #41
• Add ACM certificates for subdomains by @tthyer in #42
• Update VPC template version to the v0.3.0 tag by @tthyer in #43
• Update prod config for nextflow-aurora-mysql template changes by @tthyer in #44
• WORKFLOWS-20: Custom S3 Bucket Template by @daisyhan97 in #36
• Nextflow ECS Service and ALB by @tthyer in #48
• Happiness is a private subnet by @tthyer in #49
• System to mount Nextflow Tower configuration by @tthyer in #51
• [WORKFLOWS-43] Create comprehensive stack for compute environments by @BrunoGrandePhD in #50
• [WORKFLOWS-34] Onboarding Documentation by @BrunoGrandePhD in #52
• [WORKFLOWS-44] Add Managed Scaling by @tthyer in #53
• [WORKFLOWS-38] Encrypt EFS file system by @tthyer in #55
• [WORKFLOWS-44] Enable metrics collection for autoscaling group by @tthyer in #56
• Restrict KMS key access to project-specific roles and admins by @BrunoGrandePhD in #54
• [WORKFLOWS-51] Switch from GitHub to Google for IdP by @BrunoGrandePhD in #57
• add in challenge project by @thomasyu888 in #58
• [WORKFLOWS-42] Send tower container logs to Cloudwatch by @BrunoGrandePhD in #60
• [WORKFLOW-42] TESTING by @thomasyu888 in #63
• [WORKFLOWS-39] Parametrize IAM resources rather than hard-coding by @BrunoGrandePhD in #59
• [WORKFLOWS-52] Create post-launch hook script for Tower projects by @BrunoGrandePhD in #62
• [WORKFLOWS-60] Integrate configure-tower-project.py into CI by @BrunoGrandePhD in #64
• [WORKFLOWS-15/34] Create README with onboarding docs by @BrunoGrandePhD in #46
• Create jhu-biobank-nf Tower project by @BrunoGrandePhD in #61
• Create imcore Tower project by @BrunoGrandePhD in #66
• [WORKFLOWS-65] Create VPC gateway endpoints for S3 by @BrunoGrandePhD in #67
• Prevent public IPs being assigned to private EC2s by @BrunoGrandePhD in #68
• Require inbound ECS traffic to originate from VPC by @BrunoGrandePhD in #69
• add amp-ad project by @wpoehlm in #71
• [WORKFLOWS-67] Create more granular budget alerts by @BrunoGrandePhD in #73
• [WORKFLOWS-70] Create public buckets for iGenomes reference files by @BrunoGrandePhD in #74
• Add HTAN project by @adamjtaylor in #75
• [WORKFLOWS-66] Allow S3 object indexing by Synapse by @BrunoGrandePhD in #76
• [WORKFLOWS-68] Use Sceptre template handlers for remote templates by @BrunoGrandePhD in #72
• Migrate important info to Confluence wiki page with watchers by @BrunoGrandePhD in #78
• [WORKFLOWS-62 | WORKFLOWS-76] Add CostCenter tags by @BrunoGrandePhD in #77
• Ensure that iGenomes reference files are public by @BrunoGrandePhD in #81
• [WORKFLOWS-55 | WORKFLOWS-96] Upgrade Nextflow Tower to v21.06.4 by @BrunoGrandePhD in #80
• [WORKFLOWS-84] Provide default GitHub credentials by @BrunoGrandePhD in #83
• [WORKFLOWS-99] Switch to BucketOwnerEnforced object ownership setting by @BrunoGrandePhD in #82
• Bump s3 permission by @thomasyu888 in #86
• Create INCLUDE Tower project by @BrunoGrandePhD in #87
• [WORKFLOWS-85] Prototype Tower project in separate account by @BrunoGrandePhD in #84
• Fix dependency paths after re-organizing configs by @BrunoGrandePhD in #88
• Create the production AMP-AD Tower project in the STRIDES AWS account by @BrunoGrandePhD in #89
• Minor docs changes by @allaway in #90
• Create cNF cell line processing Tower project by @allaway in #91
• [WORKFLOWS-93] Create Tower project for project GENIE by @BrunoGrandePhD in #92
• Fix CostCenter tags values based on latest list by @BrunoGrandePhD in #93
• Create ucf-dod-nf2-project.yaml by @allaway in #94
• [WORKFLOWS-181] Create and add teams to Tower workspaces by @BrunoGrandePhD in #96
• [WORKFLOWS-181] Ensure shorter team names due to length limit by @BrunoGrandePhD in #97
• [WORKFLOWS-181] Add support for paged requests by @BrunoGrandePhD in #98
• Create nfri-ctf-nf1-project.yaml by @allaway in #95
• Ensure that database migration completes before launching other containers by @BrunoGrandePhD in #99
• [WORKFLOWS-155] Enable secrets and OIDC token import in Tower-Dev by @BrunoGrandePhD in #100
• Add script for emptying an AWS Batch queue by @BrunoGrandePhD in #102
• Update link to valid program codes by @BrunoGrandePhD in #105
• [WORKFLOWS-187] Add scratch buckets for each Tower project by @BrunoGrandePhD in #103
• [WORKFLOWS-222 ] Update compute environment configuration by @BrunoGrandePhD in #101
• [WORKFLOWS-210] Configure Synapse OIDC as an authentication option by @BrunoGrandePhD in #104
• Create ntap-gdp5-project stack by @BrunoGrandePhD in #106
• [IT-1781] Clean up AWS resources (security tweaks) by @BrunoGrandePhD in #107
• [WORKFLOWS-53] Fix auto-scaling for Tower ECS service by @BrunoGrandePhD in #108
• [WORKFLOWS-233] Upgrade Nextflow Tower to v22.1.0 by @BrunoGrandePhD in #109
• Update maintenance stack with longer cron duration by @BrunoGrandePhD in #110
• Disable private Tower workspaces per user by @BrunoGrandePhD in #111
• Consolidate and update Tower version by @BrunoGrandePhD in #112
• Create ctf-swnts-project.yaml by @ajs3nj in #113
• [WORKFLOWS-258] Block all public access on S3 buckets by @BrunoGrandePhD in #114
• Refine budget limits per account by @BrunoGrandePhD in #115
• [WORKFLOWS-293] Mitigate issue with orphaned EBS volumes (and upgrade Tower) by @BrunoGrandePhD in #116
• Refine budgets again based on notifications by @BrunoGrandePhD in #117
• Add Bruno to STRIDES AMP-AD project by @BrunoGrandePhD in #118
• [WORKFLOWS-410] Disable Tower Fusion in light of persistent issues by @BrunoGrandePhD in #119
• Added configuration files to onboard new users by @wpoehlm in #120
• Create robert-allaway-project by @allaway in #121
• Offboard Haley from GENIE by @thomasyu888 in #122
• Revert "Offboard Haley from GENIE" by @BrunoGrandePhD in #123
• Offboard Haley from GENIE by @BrunoGrandePhD in #124
• Create nf-ntap-biobank-jineta project by @jaybee84 in #126
• Fix pre-commit issues by @thomasyu888 in #127
• Rename robert-allaway-project to robert-allaway-project.yaml by @allaway in #128
• [WORKFLOWS-394] Add TowerViewer roles ahead of sandbox deprecation by @BrunoGrandePhD in #125
• Add chelsea nayan to GENIE read only by @thomasyu888 in #129
• Shell script for configuring SSH via SSM by @BrunoGrandePhD in #130
• Add project for MC2 MCMICRO work by @adamjtaylor in #131
• Change permissions for Chelsea by @thomasyu888 in #133
• Add external HMS collaborators to mc2-mcmicro-project by @BrunoGrandePhD in #134
• Deploy Lambda function to auto-delete orphaned EBS volumes by @BrunoGrandePhD in #135
• Update external user ARN by @adamjtaylor in #136
• WORKFLOWS-454 - Adds Brad access for HTAN by @BWMac in #137
• [ORCA-71] Migrate TowerClient to sagetasks by @BrunoGrandePhD in #138
• remove Tess Thyer, add Jared Hendrickson project S3 read access to st… by @wpoehlm in #139
• Add Sasha to ntap-add5-project.yaml by @ajs3nj in #140
• [WORKFLOWS-455] Harden separation in S3 access between Tower projects by @BrunoGrandePhD in #141
• [WORKFLOWS-461] Clean up Tower workspaces by @BrunoGrandePhD in #142
• [WORKFLOWS-481] Parametrize TowerViewer assumed-role ARN prefix by @BrunoGrandePhD in #143
• [IBCDPE-404] Remove unlisted participants in each workspace by @BrunoGrandePhD in #144
• Bump cryptography from 38.0.1 to 38.0.3 by @dependabot in #145
• IBCDPE-389/agora tower project by @BWMac in #147
• [ORCA-105] Create orca-dev-project Tower project by @BrunoGrandePhD in #148
• [WORKFLOWS-479] Update README for new support process by @BrunoGrandePhD in #146
• [WORKFLOWS-472] Add Rixing with read/write access to genie-bpc-project by @rxu17 in #149
• Add ARN for htan-dev external account by @adamjtaylor in #151
• [WORKFLOWS-497] Only return non-duplicated emails by @thomasyu888 in #152
• Bump certifi from 2022.9.24 to 2022.12.7 by @dependabot in #150
• Add Brad to example-project by @BrunoGrandePhD in #154
• [IBCSPRT-132] Ensure that MC2 external users are added to Tower by @BrunoGrandePhD in #155
• Bump cryptography from 38.0.4 to 39.0.1 by @dependabot in #156
• [WORKFLOWS-420] - Updates tower projects to transition files after 14 days, adds rules … by @BWMac in #153
• [IT-2366] Upgrade Tower to release 22.4.1 by @BrunoGrandePhD in #159
• [IBCDPE-431] iAtlas workspace by @BWMac in #157
• Create dev project for MC2/MCMICRO by @adamjtaylor in #160
• [IT-2364] Improve allocation strategy and instance types by @BrunoGrandePhD in #161
• [WORKFLOWS-515] Limit to cheaper 8xlarge instance types by @BrunoGrandePhD in #162
• [WORKFLOWS-517] Switch to BEST_FIT for smaller instances by @BrunoGrandePhD in #164
• Optimize ECS config by @BrunoGrandePhD in #165
• [IBCSPRT-159] Add shorter data expiration lifecycle rules by @BrunoGrandePhD in #166
• [ORCA-171] Create container registry credentials for Wave service by @BrunoGrandePhD in #167
• [WORKFLOWS-521] Check Redis append-only file first by @BrunoGrandePhD in #174
• [ORCA-143] Enable Wave for Nextflow Tower by @BWMac in #173
• [IT-2357] Test on pull requests by @zaro0508 in #172
• Update sceptre template_path by @zaro0508 in #169
• Bump starlette from 0.22.0 to 0.25.0 by @dependabot in #158
• Bump markdown-it-py from 2.1.0 to 2.2.0 by @dependabot in #163
• [IT-2376] Switch from LaunchConfiguration to LaunchTemplate by @zaro0508 in #170
• [IT-2376] Remove LaunchConfiguration by @zaro0508 in #171
• [IT-2357] Setup dependent pipelines by @zaro0508 in #176
• Update the kms key template by @zaro0508 in #178
• ignore jetbrains folder by @zaro0508 in #179
• Bump AMP-AD budgets by @thomasyu888 in #182
• Add Nextflow dev resource for dan to test by @thomasyu888 in #183
• [IBCDPE-523] Add UNC collaborators to iAtlas project by @BWMac in #175
• [IT-2790] Change release workflow by @zaro0508 in #184
• Test by @thomasyu888 in #185
• [IT-2793] Fix pipenv cache in GH action by @zaro0508 in #186
• install pipenv and dependencies in reusable workflow by @zaro0508 in #188
• Re-commit the env changes by @thomasyu888 in #189
• Update pre-commit linters by @zaro0508 in #187
• Parameterize notifications_email for budgets by @BrunoGrandePhD in #190

New Contributors

• @tthyer made their first contribution in #4
• @xschildw made their first contribution in #14
• @daisyhan97 made their first contribution in #24
• @thomasyu888 made their first contribution in #58
• @wpoehlm made their first contribution in #71
• @adamjtaylor made their first contribution in #75
• @allaway made their first contribution in #90
• @ajs3nj made their first contribution in #113
• @jaybee84 made their first contribution in #126
• @BWMac made their first contribution in #137
• @dependabot made their first contribution in #145
• @rxu17 made their first contribution in #149
• @zaro0508 made their first contribution in #172

Full Changelog: https://github.com/Sage-Bionetworks-Workflows/nextflow-infra/commits/1.0.0