v0.11.14

Overview 🌀

This release updates GCP Batch support and improves existing integration tests!

1. Install

➜ curl -sSL https://calypr.org/tools/funnel/install.sh | bash -s -- v0.11.14

➜ which funnel
$HOME/.local/bin/funnel

➜ funnel version
git commit:   2e54ad74
git branch:   v0.11.14
git upstream: https://github.com/calypr/funnel
build date:   2026-06-11T21:28:40Z
version:      0.11.14

2. Run Server

➜ funnel server run

What's Changed

• fix: Add support for single-element/single-quote shell commands by @lbeckman314 in #1411
• Gen3-Funnel integration tests by @paulineribeyre in #1404
• chore: Remove MinIO v6 dep in favor of MinIO v7 by @lbeckman314 in #1415
• fix: Use underscores in Docker image tags for branches by @lbeckman314 in #1417
• fix: report EXECUTOR_ERROR when output upload fails after executor failure by @lbeckman314 in #1416
• fix: Remove hugo.yaml in favor of single publish source by @lbeckman314 in #1424
• fix: Resolve ServiceAccount deletion race condition (thanks @nss10!) by @lbeckman314 in #1421
• feat: Update GCP Batch support (v0.11.14) by @lbeckman314 in #1419
• fix: Remove /tmp volume from being automatically added to commands by @lbeckman314 in #1425
• hotfix: Update Helm repo chart URL by @lbeckman314 in #1418
• fix: Update Funnel resource cleanup all K8s resources (including Worker + Executor jobs) by @lbeckman314 in #1423
• feature/integration-tests → develop by @lbeckman314 in #1263
• chore(deps): Bump the npm_and_yarn group across 1 directory with 5 updates by @dependabot[bot] in #1426
• feat: Add initial support for cleaning orphaned jobs by @lbeckman314 in #1427
• feat: Re-add reconcile support for GCP Batch by @lbeckman314 in #1430
• fix: Improve K8s error diagnostics (CreateContainerConfigError + BackoffLimit) by @lbeckman314 in #1413
• feat: Add workflow_dispatch trigger to release workflow by @lbeckman314 in #1431

Full Changelog: v0.11.13...v0.11.14

v0.11.14-rc.4

Changelog

v0.11.14-rc.2

Changelog

• b5b06bd feature/integration-tests → develop (#1263)
• 1fba5f8 chore(deps): Bump the npm_and_yarn group across 1 directory with 5 updates (#1426)
• 9d04b1d feat: Update GCP Batch support (#1419)
• 1a72779 fix: Remove /tmp volume from being automatically added to commands (#1425)
• 697026d fix: Remove hugo.yaml in favor of single publish source (#1424)
• 89af0db fix: Resolve ServiceAccount deletion race condition (thanks @nss10!) (#1421)
• 2896399 fix: Update Funnel resource cleanup all K8s resources (including Worker + Executor jobs) (#1423)
• 9d1ea9f hotfix: Update Helm repo chart URL (#1418)

v0.11.14-rc.1

Changelog

• b0cf088 Empty commit to trigger CI
• 42c47b7 Gen3-Funnel integration tests
• 7190405 Merge branch 'calypr:develop' into develop
• 332564c Merge pull request #1404 from paulineribeyre/develop
• a7cf0a9 Modify test repo and helm branch settings
• 5cfa87e Pin tests to more-tes-err-logs
• 900f634 Remove branch pins from integration tests workflow
• 9327d61 Update Helm repository URL for ohsu
• ffae4f8 chore: Remove MinIO v6 dep in favor of MinIO v7 (#1415)
• 00ab0c4 feat: Update GCP Batch support
• b433b6a fix: Use underscores in Docker image tags for branches (#1417)

v0.11.13-rc.1

Changelog

• ab83f5b Add PV deletion logic and include namespace in DeletePV
• 34cf6c1 Add clean orphaned resources at the end of reconcile run
• cf044cb Add the indent function during template rendering
• 590bb7c Cleanup logs and comments
• e4244e2 Merge branch 'develop' into chore/fix_file_mapper
• da20892 Merge branch 'develop' into chore/fix_resource_cleanup
• 51b0cf0 Merge branch 'develop' into chore/fix_resource_cleanup
• 9a88891 Merge pull request #1407 from uc-cdis/chore/fix_resource_cleanup
• f3a2f15 Merge pull request #1408 from calypr/chore/fix_file_mapper
• c1aa202 Pring configmap log
• 8b2db55 Re-Add conditional k8s resource creation
• e9d5da5 Remove WIP code -- related to reconcile_modular
• 2d18d7b Responding to PR comments
• e105eab Revert quay repo path
• f56c27a Service account deletion only if the pod is active.
• 4803397 Update ServiceAccount deletion logic to handle user based serviceAccounts without creating orphan resources
• e9ea03d Update cleanOrphanedResources invocation localtion
• 2440ec4 Update compute/kubernetes/resources/pv.go
• 14e2426 Verify why volumeMounts gets duplicate path
• b5c6c03 chore: Fix file mapper duplicated input/output error
• c1ee4c7 feat: Use mvdan.cc/sh for shell parsing in Kubernetes backend
• 15c4238 feat: Use mvdan.cc/sh for shell parsing in Kubernetes backend
• 4103475 hotfix: Update GitHub org in install script (#1406)

v0.11.12

Changelog

• 1717d43 Merge pull request #1400 from calypr/fix/compliance-tests
• 233dff1 chore: Remove branch restrictions for compliance test workflow
• e84f99f chore: Remove tmate session setup from k8s workflow
• 1b84a76 debug: GA
• 386a7c1 debug: GA
• 0619e46 debug: GA
• b09cf3f debug: GA
• 6edd64e debug: GitHub Actions
• e68020f debug: GitHub Actions
• 4fa2f27 debug: GitHub Actions
• 3e87a17 debug: GitHub Actions
• 3855fca debug: GitHub Actions
• 7f5a7e5 debug: GitHub Actions
• 89fff2c fix: Compliance tests

v0.11.12-rc.3

Changelog

• 1717d43 Merge pull request #1400 from calypr/fix/compliance-tests
• 233dff1 chore: Remove branch restrictions for compliance test workflow
• e84f99f chore: Remove tmate session setup from k8s workflow
• 1b84a76 debug: GA
• 386a7c1 debug: GA
• 0619e46 debug: GA
• b09cf3f debug: GA
• 6edd64e debug: GitHub Actions
• e68020f debug: GitHub Actions
• 4fa2f27 debug: GitHub Actions
• 3e87a17 debug: GitHub Actions
• 3855fca debug: GitHub Actions
• 7f5a7e5 debug: GitHub Actions
• 89fff2c fix: Compliance tests

v0.11.12-rc.2

Changelog

• 597c86f Merge branch 'develop' into feat/k8s-ovh-improvements
• 39b024b Merge branch 'develop' into feat/k8s-ovh-improvements
• ef5c430 Merge branch 'develop' into feat/k8s-ovh-improvements
• 818a6a5 Merge branch 'feat/k8s-ovh-improvements' into develop
• bf7c0d1 Merge pull request #1357 from geertvandeweyer/feat/k8s-ovh-improvements
• b2cae45 Merge pull request #1386 from calypr/dependabot/npm_and_yarn/webdash/npm_and_yarn-85af2c71bb
• 3ffaaf4 Merge pull request #1388 from calypr/dependabot/npm_and_yarn/webdash/develop/npm-deps-961301b6ab
• 148ad78 Merge pull request #1390 from calypr/dependabot/go_modules/develop/dependabot-c79b2ea96a
• 70cc2bc Revert "fix(kubernetes): make GenericS3 config optional for PV/PVC creation"
• eab5842 build(deps): bump follow-redirects
• 8dc209f build(deps): bump react-router-dom in /webdash in the npm-deps group
• fe36609 build(deps): bump the dependabot group across 1 directory with 10 updates
• 2fa41e0 build: add build-and-push.sh for develop-branch multiarch image
• aef16a8 build: support DOCKERHUB_USER/PASS env vars for non-interactive Docker Hub login
• 2341f5e chore: Delete dependabot.yaml (deps) in favor of security updates
• 60a91c9 chore: Delete dependabot.yaml (deps) in favor of security updates
• 07ff1e2 feat: port OVH/K8s improvements from main to develop
• 0c6f67a fix(kubernetes): make GenericS3 config optional for PV/PVC creation
• 55efca5 fix(kubernetes): make GenericS3 config optional for PV/PVC creation
• 4e06ae9 fix(kubernetes): make per-task ConfigMap creation optional via ConfigMapTemplate
• b10877f fix(kubernetes): skip per-task SA/Role/RoleBinding when templates not configured
• c590523 fix(kubernetes): use text/template instead of html/template for YAML rendering
• 888713f fix/set TTL for finished tasks if missing, to prevent piling of completed pods on nodes
• 01796d6 fix: Add context to resource creation in K8s backend
• b663ea7 fix: Minor linting errors
• 317bc7c fix: Unit tests + linting (#1398)
• 0e729ba fix: Unit tests + linting (#1398)
• 5adeac1 fix: Update ConfigMap template and related code
• 0b5bd70 hotfix: Revert ConfigMap creation update
• 5b95fa0 refactor(worker): replace Readonly-as-classifier with InputVolumes field
• c4f253f remove accidentally committed build-and-push.sh
• 16e0f45 tests: merge unit tests into kubernetes_test.go

v0.11.12-rc.1

Tip

Issue #1239

PR #1360

Overview 🌀

This release adds support for null tags in Task definitions, which appears to be the default/expected behavior from Cromwell workflows.

Previously Funnel would throw a 400 error (invalid value for string field value: null") resulting in a CromwellFatalException error.

With this release Funnel now accepts null tags (via the new normalizeNilTagValues function) and simply removes tags with null values returning the task payload.

Important

Tags with null keys will be removed from the TES Task request body and not included in any command execution or environment!

We previously experimented with simply setting the null key to an empty string, but determined that removing both the tag key + value would be the cleanest approach...

1. Install

➜ curl -fsSL https://ohsu-comp-bio.github.io/funnel/install.sh | bash -s -- v0.11.12-rc.1

➜ which funnel
$HOME/.local/bin/funnel

➜ funnel version
git commit:   f39e4436
git branch:   v0.11.12-rc.1
git upstream: https://github.com/ohsu-comp-bio/funnel
version:      0.11.12-rc.1

2. Run Server

➜ funnel server run

3. Submit WDL Workflow

➜ java -Dconfig.file=./cromwell.conf -jar cromwell-92.jar run example.wdl
Workflow myWorkflow complete. Final Outputs:
{
  "myWorkflow.myTask.out": "hello world"
}

4. Verify Task

Tip

Using the latest submitted task for here...

➜ funnel task get <TASK ID>
{
  "executors":  [
    {
      "command":  [
        "/bin/bash",
        "/cromwell-executions/myWorkflow/<WORKFLOW ID>/call-myTask/execution/script"
      ],
      "image":  "ubuntu@sha256:186072b...",  }
  ],
  "id":  "<TASK ID>",
  "logs":  [
    {
      "logs":  [
        {
          "stdout":  "hello world\n"
        }
      ],
    }
  ],
  "name":  "myWorkflow.myTask",
  "state":  "COMPLETE",
  "tags":  {
    "root_workflow_id":  "<ROOT WORKFLOW ID>",
    "workflow_id":  "<WORKFLOW ID>"
  }
}

Changelog

• 2afbf70 Apply suggestions from code review
• f39e443 Merge pull request #1360 from ohsu-comp-bio/feat/support-nil-tags
• 43fea28 build(deps): bump flatted from 3.2.7 to 3.4.2 in /webdash (#1358)
• 0437144 build(deps): bump google.golang.org/grpc from 1.79.2 to 1.79.3 (#1355)
• 8a85e55 build(deps): bump picomatch from 2.3.1 to 2.3.2 in /webdash (#1364)
• fb99904 build(deps): bump react-router-dom in /webdash in the npm-deps group (#1361)
• 6a4c57b build(deps): bump the dependabot group across 1 directory with 15 updates (#1365)
• 802a775 build(deps): bump the npm_and_yarn group across 1 directory with 14 updates (#1366)
• 40cfc44 build(deps): bump yaml in /webdash (#1362)
• ee34c27 chore: Clean up npm files
• a026c63 feat: Support nil tags in TES tasks (via custom JSON marshaler)
• c7a8b1f fix: Re-enable unit tests
• 6bb9438 tests: Add tests for nil tags

v0.11.11

Changelog

• 88b2e28 fix: latest Docker tag