{"id":53807,"name":"external/pipeline-Nextflow-module","ecosystem":"submodules","repository_url":null,"issues_count":7,"created_at":"2025-07-22T03:20:16.142Z","updated_at":"2025-07-22T03:20:16.142Z","purl":"pkg:submodules/external/pipeline-Nextflow-module","unique_repositories_count":6,"unique_repositories_count_past_30_days":1,"recent_issues":[{"uuid":"4527629435","node_id":"PR_kwDOREXTis7flRFm","number":6,"state":"closed","title":"Bump the pipeline-submodules group with 2 updates","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":2,"pull_request":true,"closed_at":"2026-05-28T23:41:27.000Z","author_association":null,"state_reason":null,"created_at":"2026-05-26T21:29:09.000Z","updated_at":"2026-05-28T23:41:28.000Z","time_to_close":180738,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","group_name":"pipeline-submodules","update_count":2,"packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`1cfa9fa`","new_version":"`5700f55`","repository_url":"https://github.com/TheBoutrosLab/pipeline-Nextflow-module"},{"name":"external/pipeline-Nextflow-config","old_version":"`4b7b9dd`","new_version":"`f40df6a`","repository_url":"https://github.com/TheBoutrosLab/pipeline-Nextflow-config"}],"path":null,"ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 2 updates: [external/pipeline-Nextflow-module](https://github.com/TheBoutrosLab/pipeline-Nextflow-module) and [external/pipeline-Nextflow-config](https://github.com/TheBoutrosLab/pipeline-Nextflow-config).\n\nUpdates `external/pipeline-Nextflow-module` from `1cfa9fa` to `5700f55`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/5700f55a5a37d098f0579f4d7b0fc78ca830e600\"\u003e\u003ccode\u003e5700f55\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-module/issues/7\"\u003e#7\u003c/a\u003e from TheBoutrosLab/yashpatel-standardize-log-saving\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/4cff5ef1412dda68e8dae4d0419ccb200d1b4369\"\u003e\u003ccode\u003e4cff5ef\u003c/code\u003e\u003c/a\u003e Update CHANGELOG\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/22684d5304b218f24b2d6b2956fd5c6dde89cd34\"\u003e\u003ccode\u003e22684d5\u003c/code\u003e\u003c/a\u003e Standardize log saving in common processes\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/1c9a726b98cc5cc43e04fd6fa0f6759447e0a32a\"\u003e\u003ccode\u003e1c9a726\u003c/code\u003e\u003c/a\u003e Standardize log saving in SAMtools process\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/15ade37395c46d8b1eb67e78c220cee5edca1645\"\u003e\u003ccode\u003e15ade37\u003c/code\u003e\u003c/a\u003e Standardize log saving in PipeVal processes\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/b33d7bcbde42e32cb82a0df989fc585a0826b45a\"\u003e\u003ccode\u003eb33d7bc\u003c/code\u003e\u003c/a\u003e Standardize log saving in BCFtools processes\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/b8cc8cecf67807f78ac9a6d16747fa5dfcf84fca\"\u003e\u003ccode\u003eb8cc8ce\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-module/issues/6\"\u003e#6\u003c/a\u003e from TheBoutrosLab/yashpatel-capture-all-validation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/81bcebff3b11db7c1dd0a40b0f150605bf40cb0d\"\u003e\u003ccode\u003e81bcebf\u003c/code\u003e\u003c/a\u003e Update CHANGELOG\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/1d992d48936b9f1b4a058c1159cebbdbf2afc5f1\"\u003e\u003ccode\u003e1d992d4\u003c/code\u003e\u003c/a\u003e Capture stdout and stderr in validation.txt output\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/f1d38b02c5e047a76bd027d8267e917709ba7e2b\"\u003e\u003ccode\u003ef1d38b0\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-module/issues/5\"\u003e#5\u003c/a\u003e from TheBoutrosLab/yashpatel-syntax-fix\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/compare/1cfa9fa55f043f9dbaad29d5a18d2df25890b715...5700f55a5a37d098f0579f4d7b0fc78ca830e600\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\nUpdates `external/pipeline-Nextflow-config` from `4b7b9dd` to `f40df6a`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/f40df6acc0c61e036b97f49e97a2c6e9df0a495e\"\u003e\u003ccode\u003ef40df6a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-config/issues/9\"\u003e#9\u003c/a\u003e from TheBoutrosLab/yashpatel-assertion-cleanup\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/93d7560f312991a82190d19c7b99122f633a5186\"\u003e\u003ccode\u003e93d7560\u003c/code\u003e\u003c/a\u003e Update CHANGELOG\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/a3bc987a5beb97e9c98e2184cf8680323481e243\"\u003e\u003ccode\u003ea3bc987\u003c/code\u003e\u003c/a\u003e Convert assertion into Exception\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/158d92c778d5ed45c5b387acbfd5110b20bae91d\"\u003e\u003ccode\u003e158d92c\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-config/issues/8\"\u003e#8\u003c/a\u003e from TheBoutrosLab/automation-crawler-update-documentat...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/29ecebbf5a836c1956fff79c2d01fd31dd447265\"\u003e\u003ccode\u003e29ecebb\u003c/code\u003e\u003c/a\u003e Update documentation links\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/89c111e5a9739bab55f95daaedab922fe9aeaeb1\"\u003e\u003ccode\u003e89c111e\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-config/issues/7\"\u003e#7\u003c/a\u003e from TheBoutrosLab/yashpatel-name-static-analysis\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/3f3ad1e293f7c68b26652c56fbcdde2e2a74f157\"\u003e\u003ccode\u003e3f3ad1e\u003c/code\u003e\u003c/a\u003e Normalize static analysis workflow names\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/ffe93b70aa1c07b87575ad0ee554a59cf81e15c4\"\u003e\u003ccode\u003effe93b7\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-config/issues/6\"\u003e#6\u003c/a\u003e from TheBoutrosLab/yashpatel-add-pipeline-workflows\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/3064008b1a06fe543d01e7fc3ae254e5d930522f\"\u003e\u003ccode\u003e3064008\u003c/code\u003e\u003c/a\u003e Delete .github/workflows/PlantUML.yaml\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/831d91a836822771d79e71e53f42cfeaef5917f5\"\u003e\u003ccode\u003e831d91a\u003c/code\u003e\u003c/a\u003e Delete .github/workflows/alias-release.yaml\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/compare/4b7b9dd99f38b71d1559399b456372f8212a0ece...f40df6acc0c61e036b97f49e97a2c6e9df0a495e\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/TheBoutrosLab/pipeline-StableLift/pull/6","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/TheBoutrosLab%2Fpipeline-StableLift/issues/6","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/6/packages"},{"uuid":"3395777859","node_id":"PR_kwDOEcSUoM6nd-Rr","number":356,"state":"open","title":"Bump external/pipeline-Nextflow-module from `1efa9bf` to `4596358` in the pipeline-submodules group","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":2,"pull_request":true,"closed_at":null,"author_association":null,"state_reason":null,"created_at":"2025-09-08T21:18:15.000Z","updated_at":"2025-12-02T01:50:24.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`1efa9bf`","new_version":"`4596358`","repository_url":"https://github.com/uclahs-cds/pipeline-Nextflow-module"}],"path":"the pipeline-submodules group","ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 1 update: [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).\n\nUpdates `external/pipeline-Nextflow-module` from `1efa9bf` to `4596358`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/459635873118e8b8f485a46d92ec2dfd5c5fbd6f\"\u003e\u003ccode\u003e4596358\u003c/code\u003e\u003c/a\u003e Prepare for version \u003ccode\u003e2.0.0\u003c/code\u003e (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/60\"\u003e#60\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/00b3549af130c36f67b6180d37bc907887cc51e6\"\u003e\u003ccode\u003e00b3549\u003c/code\u003e\u003c/a\u003e Remove usage of \u003ccode\u003eaddParams\u003c/code\u003e (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/56\"\u003e#56\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/a4991ccf39a395030755bbdb69392d733e7b4835\"\u003e\u003ccode\u003ea4991cc\u003c/code\u003e\u003c/a\u003e Update CHANGELOG for version \u003ccode\u003e1.0.0\u003c/code\u003e (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/59\"\u003e#59\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/03eb89edb7756b586299b9a41720646ffe35c35d\"\u003e\u003ccode\u003e03eb89e\u003c/code\u003e\u003c/a\u003e Remove version_files input from release workflow (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/58\"\u003e#58\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/088a548d862a79a7d6d78545c68228272bc7992b\"\u003e\u003ccode\u003e088a548\u003c/code\u003e\u003c/a\u003e Add release management workflows (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/57\"\u003e#57\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/compare/1efa9bf4b1e4e31e24603b0fee496eac45ee8e8b...459635873118e8b8f485a46d92ec2dfd5c5fbd6f\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/uclahs-cds/pipeline-call-sSNV/pull/356","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/uclahs-cds%2Fpipeline-call-sSNV/issues/356","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/356/packages"},{"uuid":"2806874423","node_id":"PR_kwDON9cPTc6nTYE3","number":12,"state":"open","title":"Bump external/pipeline-Nextflow-module from `1efa9bf` to `4596358` in the pipeline-submodules group","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-09-08T05:19:14.000Z","updated_at":"2025-09-08T05:19:15.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`1efa9bf`","new_version":"`4596358`","repository_url":"https://github.com/uclahs-cds/pipeline-Nextflow-module"}],"path":"the pipeline-submodules group","ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 1 update: [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).\n\nUpdates `external/pipeline-Nextflow-module` from `1efa9bf` to `4596358`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/459635873118e8b8f485a46d92ec2dfd5c5fbd6f\"\u003e\u003ccode\u003e4596358\u003c/code\u003e\u003c/a\u003e Prepare for version \u003ccode\u003e2.0.0\u003c/code\u003e (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/60\"\u003e#60\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/00b3549af130c36f67b6180d37bc907887cc51e6\"\u003e\u003ccode\u003e00b3549\u003c/code\u003e\u003c/a\u003e Remove usage of \u003ccode\u003eaddParams\u003c/code\u003e (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/56\"\u003e#56\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/a4991ccf39a395030755bbdb69392d733e7b4835\"\u003e\u003ccode\u003ea4991cc\u003c/code\u003e\u003c/a\u003e Update CHANGELOG for version \u003ccode\u003e1.0.0\u003c/code\u003e (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/59\"\u003e#59\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/03eb89edb7756b586299b9a41720646ffe35c35d\"\u003e\u003ccode\u003e03eb89e\u003c/code\u003e\u003c/a\u003e Remove version_files input from release workflow (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/58\"\u003e#58\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/088a548d862a79a7d6d78545c68228272bc7992b\"\u003e\u003ccode\u003e088a548\u003c/code\u003e\u003c/a\u003e Add release management workflows (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/57\"\u003e#57\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/compare/1efa9bf4b1e4e31e24603b0fee496eac45ee8e8b...459635873118e8b8f485a46d92ec2dfd5c5fbd6f\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/uclahs-cds/pipeline-calculate-mtDNA-CopyNumber/pull/12","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/uclahs-cds%2Fpipeline-calculate-mtDNA-CopyNumber/issues/12","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/12/packages"},{"uuid":"3038396690","node_id":"PR_kwDOKc9lI86U3sbh","number":100,"state":"open","title":"Bump external/pipeline-Nextflow-module from `12f28e4` to `1efa9bf` in the pipeline-submodules group","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":null,"author_association":null,"state_reason":null,"created_at":"2025-05-05T01:29:34.000Z","updated_at":"2025-11-17T01:17:27.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`12f28e4`","new_version":"`1efa9bf`","repository_url":"https://github.com/uclahs-cds/pipeline-Nextflow-module"}],"path":"the pipeline-submodules group","ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 1 update: [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).\n\nUpdates `external/pipeline-Nextflow-module` from `12f28e4` to `1efa9bf`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/1efa9bf4b1e4e31e24603b0fee496eac45ee8e8b\"\u003e\u003ccode\u003e1efa9bf\u003c/code\u003e\u003c/a\u003e Update log dir set up in BCF2VCF (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/54\"\u003e#54\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/compare/12f28e4ebfc3e0f9a327c6c0dabf620ed4efe573...1efa9bf4b1e4e31e24603b0fee496eac45ee8e8b\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/uclahs-cds/pipeline-generate-SQC-BAM/pull/100","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/uclahs-cds%2Fpipeline-generate-SQC-BAM/issues/100","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/100/packages"},{"uuid":"2470623339","node_id":"PR_kwDON9cPTc6TQrhr","number":9,"state":"open","title":"Bump external/pipeline-Nextflow-module from `12f28e4` to `1efa9bf` in the pipeline-submodules group","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"NONE","state_reason":null,"created_at":"2025-04-21T06:35:11.000Z","updated_at":"2025-08-05T20:27:31.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`12f28e4`","new_version":"`1efa9bf`","repository_url":"https://github.com/uclahs-cds/pipeline-Nextflow-module"}],"path":"the pipeline-submodules group","ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 1 update: [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).\n\nUpdates `external/pipeline-Nextflow-module` from `12f28e4` to `1efa9bf`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/1efa9bf4b1e4e31e24603b0fee496eac45ee8e8b\"\u003e\u003ccode\u003e1efa9bf\u003c/code\u003e\u003c/a\u003e Update log dir set up in BCF2VCF (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/54\"\u003e#54\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/compare/12f28e4ebfc3e0f9a327c6c0dabf620ed4efe573...1efa9bf4b1e4e31e24603b0fee496eac45ee8e8b\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/uclahs-cds/pipeline-calculate-mtDNA-CopyNumber/pull/9","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/uclahs-cds%2Fpipeline-calculate-mtDNA-CopyNumber/issues/9","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/9/packages"},{"uuid":"2977987671","node_id":"PR_kwDOF1BFn86RsYLT","number":197,"state":"open","title":"Bump external/pipeline-Nextflow-module from `ef40c10` to `12f28e4` in the pipeline-submodules group across 1 directory","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":4,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-04-07T20:59:21.000Z","updated_at":"2025-08-05T21:18:27.706Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`ef40c10`","new_version":"`12f28e4`","repository_url":"https://github.com/uclahs-cds/pipeline-Nextflow-module"}],"path":"the pipeline-submodules group across 1 directory","ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 1 update in the / directory: [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).\n\nUpdates `external/pipeline-Nextflow-module` from `ef40c10` to `12f28e4`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/12f28e4ebfc3e0f9a327c6c0dabf620ed4efe573\"\u003e\u003ccode\u003e12f28e4\u003c/code\u003e\u003c/a\u003e Add bcf2vcf module (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/53\"\u003e#53\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/de9adf95e74bd35fad9f90ca4354ed8f158150c5\"\u003e\u003ccode\u003ede9adf9\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/51\"\u003e#51\u003c/a\u003e from uclahs-cds/kpash-reorganize-process-logs\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/cb51edea42d881961d0ded8f2f0e0bf2d2aac779\"\u003e\u003ccode\u003ecb51ede\u003c/code\u003e\u003c/a\u003e make sample directory\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/d6470939d8bcf8bec09f02ba3bd38747aa1fcd36\"\u003e\u003ccode\u003ed647093\u003c/code\u003e\u003c/a\u003e remove stray replace\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/61890721f059bcdb7a1a33ae2af4aa3e3739159b\"\u003e\u003ccode\u003e6189072\u003c/code\u003e\u003c/a\u003e standardize by removing replace('_','-')\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/b1f2dce4819f70953189e89afaa981455495e86e\"\u003e\u003ccode\u003eb1f2dce\u003c/code\u003e\u003c/a\u003e update process log naming standard to include workflow\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/2413b40be95d102ae2d7359f5719b32e811931e1\"\u003e\u003ccode\u003e2413b40\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/49\"\u003e#49\u003c/a\u003e from uclahs-cds/kpash-fix-process-log\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/3567f9a2e106998b5de0d811a505d7ef7de7ec41\"\u003e\u003ccode\u003e3567f9a\u003c/code\u003e\u003c/a\u003e reorganize repo structure: create modules/SAMtools/* dir\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/cbb56617c671a5ca2b090473b559963de37c8068\"\u003e\u003ccode\u003ecbb5661\u003c/code\u003e\u003c/a\u003e update README\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/67523dc0624a7359a9a04da0b7d872e3795eb5ce\"\u003e\u003ccode\u003e67523dc\u003c/code\u003e\u003c/a\u003e rename enclosing directory to be more descriptive\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/compare/ef40c100005466b7d44f2fd60adb2c60ef451c4f...12f28e4ebfc3e0f9a327c6c0dabf620ed4efe573\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/uclahs-cds/pipeline-call-gSNP/pull/197","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/uclahs-cds%2Fpipeline-call-gSNP/issues/197","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/197/packages"},{"uuid":"2383116368","node_id":"PR_kwDOJugmJM6OC3hQ","number":93,"state":"closed","title":"Bump external/pipeline-Nextflow-module from `de9adf9` to `12f28e4` in the pipeline-submodules group","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":2,"pull_request":true,"closed_at":"2025-08-05T20:26:15.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-03-10T19:27:59.000Z","updated_at":"2025-08-05T20:26:15.000Z","time_to_close":12790696,"merged_at":"2025-08-05T20:26:15.000Z","merged_by":"yashpatel6","closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`de9adf9`","new_version":"`12f28e4`","repository_url":"https://github.com/uclahs-cds/pipeline-Nextflow-module"}],"path":"the pipeline-submodules group","ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 1 update: [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).\n\nUpdates `external/pipeline-Nextflow-module` from `de9adf9` to `12f28e4`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/12f28e4ebfc3e0f9a327c6c0dabf620ed4efe573\"\u003e\u003ccode\u003e12f28e4\u003c/code\u003e\u003c/a\u003e Add bcf2vcf module (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/53\"\u003e#53\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/compare/de9adf95e74bd35fad9f90ca4354ed8f158150c5...12f28e4ebfc3e0f9a327c6c0dabf620ed4efe573\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/uclahs-cds/pipeline-recalibrate-BAM/pull/93","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/uclahs-cds%2Fpipeline-recalibrate-BAM/issues/93","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/93/packages"}],"issue_packages":[{"old_version":"`1cfa9fa`","new_version":"`5700f55`","update_type":null,"path":null,"pr_created_at":"2026-05-26T21:29:09.000Z","version_change":"`1cfa9fa` → `5700f55`","issue":{"uuid":"4527629435","node_id":"PR_kwDOREXTis7flRFm","number":6,"state":"closed","title":"Bump the pipeline-submodules group with 2 updates","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":2,"pull_request":true,"closed_at":"2026-05-28T23:41:27.000Z","author_association":null,"state_reason":null,"created_at":"2026-05-26T21:29:09.000Z","updated_at":"2026-05-28T23:41:28.000Z","time_to_close":180738,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","group_name":"pipeline-submodules","update_count":2,"packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`1cfa9fa`","new_version":"`5700f55`","repository_url":"https://github.com/TheBoutrosLab/pipeline-Nextflow-module"},{"name":"external/pipeline-Nextflow-config","old_version":"`4b7b9dd`","new_version":"`f40df6a`","repository_url":"https://github.com/TheBoutrosLab/pipeline-Nextflow-config"}],"path":null,"ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 2 updates: [external/pipeline-Nextflow-module](https://github.com/TheBoutrosLab/pipeline-Nextflow-module) and [external/pipeline-Nextflow-config](https://github.com/TheBoutrosLab/pipeline-Nextflow-config).\n\nUpdates `external/pipeline-Nextflow-module` from `1cfa9fa` to `5700f55`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/5700f55a5a37d098f0579f4d7b0fc78ca830e600\"\u003e\u003ccode\u003e5700f55\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-module/issues/7\"\u003e#7\u003c/a\u003e from TheBoutrosLab/yashpatel-standardize-log-saving\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/4cff5ef1412dda68e8dae4d0419ccb200d1b4369\"\u003e\u003ccode\u003e4cff5ef\u003c/code\u003e\u003c/a\u003e Update CHANGELOG\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/22684d5304b218f24b2d6b2956fd5c6dde89cd34\"\u003e\u003ccode\u003e22684d5\u003c/code\u003e\u003c/a\u003e Standardize log saving in common processes\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/1c9a726b98cc5cc43e04fd6fa0f6759447e0a32a\"\u003e\u003ccode\u003e1c9a726\u003c/code\u003e\u003c/a\u003e Standardize log saving in SAMtools process\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/15ade37395c46d8b1eb67e78c220cee5edca1645\"\u003e\u003ccode\u003e15ade37\u003c/code\u003e\u003c/a\u003e Standardize log saving in PipeVal processes\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/b33d7bcbde42e32cb82a0df989fc585a0826b45a\"\u003e\u003ccode\u003eb33d7bc\u003c/code\u003e\u003c/a\u003e Standardize log saving in BCFtools processes\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/b8cc8cecf67807f78ac9a6d16747fa5dfcf84fca\"\u003e\u003ccode\u003eb8cc8ce\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-module/issues/6\"\u003e#6\u003c/a\u003e from TheBoutrosLab/yashpatel-capture-all-validation\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/81bcebff3b11db7c1dd0a40b0f150605bf40cb0d\"\u003e\u003ccode\u003e81bcebf\u003c/code\u003e\u003c/a\u003e Update CHANGELOG\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/1d992d48936b9f1b4a058c1159cebbdbf2afc5f1\"\u003e\u003ccode\u003e1d992d4\u003c/code\u003e\u003c/a\u003e Capture stdout and stderr in validation.txt output\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/commit/f1d38b02c5e047a76bd027d8267e917709ba7e2b\"\u003e\u003ccode\u003ef1d38b0\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-module/issues/5\"\u003e#5\u003c/a\u003e from TheBoutrosLab/yashpatel-syntax-fix\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-module/compare/1cfa9fa55f043f9dbaad29d5a18d2df25890b715...5700f55a5a37d098f0579f4d7b0fc78ca830e600\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\nUpdates `external/pipeline-Nextflow-config` from `4b7b9dd` to `f40df6a`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/f40df6acc0c61e036b97f49e97a2c6e9df0a495e\"\u003e\u003ccode\u003ef40df6a\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-config/issues/9\"\u003e#9\u003c/a\u003e from TheBoutrosLab/yashpatel-assertion-cleanup\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/93d7560f312991a82190d19c7b99122f633a5186\"\u003e\u003ccode\u003e93d7560\u003c/code\u003e\u003c/a\u003e Update CHANGELOG\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/a3bc987a5beb97e9c98e2184cf8680323481e243\"\u003e\u003ccode\u003ea3bc987\u003c/code\u003e\u003c/a\u003e Convert assertion into Exception\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/158d92c778d5ed45c5b387acbfd5110b20bae91d\"\u003e\u003ccode\u003e158d92c\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-config/issues/8\"\u003e#8\u003c/a\u003e from TheBoutrosLab/automation-crawler-update-documentat...\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/29ecebbf5a836c1956fff79c2d01fd31dd447265\"\u003e\u003ccode\u003e29ecebb\u003c/code\u003e\u003c/a\u003e Update documentation links\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/89c111e5a9739bab55f95daaedab922fe9aeaeb1\"\u003e\u003ccode\u003e89c111e\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-config/issues/7\"\u003e#7\u003c/a\u003e from TheBoutrosLab/yashpatel-name-static-analysis\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/3f3ad1e293f7c68b26652c56fbcdde2e2a74f157\"\u003e\u003ccode\u003e3f3ad1e\u003c/code\u003e\u003c/a\u003e Normalize static analysis workflow names\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/ffe93b70aa1c07b87575ad0ee554a59cf81e15c4\"\u003e\u003ccode\u003effe93b7\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/TheBoutrosLab/pipeline-Nextflow-config/issues/6\"\u003e#6\u003c/a\u003e from TheBoutrosLab/yashpatel-add-pipeline-workflows\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/3064008b1a06fe543d01e7fc3ae254e5d930522f\"\u003e\u003ccode\u003e3064008\u003c/code\u003e\u003c/a\u003e Delete .github/workflows/PlantUML.yaml\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/commit/831d91a836822771d79e71e53f42cfeaef5917f5\"\u003e\u003ccode\u003e831d91a\u003c/code\u003e\u003c/a\u003e Delete .github/workflows/alias-release.yaml\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/TheBoutrosLab/pipeline-Nextflow-config/compare/4b7b9dd99f38b71d1559399b456372f8212a0ece...f40df6acc0c61e036b97f49e97a2c6e9df0a495e\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/TheBoutrosLab/pipeline-StableLift/pull/6","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/TheBoutrosLab%2Fpipeline-StableLift/issues/6","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/6/packages"}},{"old_version":"`1efa9bf`","new_version":"`4596358`","update_type":null,"path":"the pipeline-submodules group","pr_created_at":"2025-09-08T21:18:15.000Z","version_change":"`1efa9bf` → `4596358`","issue":{"uuid":"3395777859","node_id":"PR_kwDOEcSUoM6nd-Rr","number":356,"state":"open","title":"Bump external/pipeline-Nextflow-module from `1efa9bf` to `4596358` in the pipeline-submodules group","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":2,"pull_request":true,"closed_at":null,"author_association":null,"state_reason":null,"created_at":"2025-09-08T21:18:15.000Z","updated_at":"2025-12-02T01:50:24.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`1efa9bf`","new_version":"`4596358`","repository_url":"https://github.com/uclahs-cds/pipeline-Nextflow-module"}],"path":"the pipeline-submodules group","ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 1 update: [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).\n\nUpdates `external/pipeline-Nextflow-module` from `1efa9bf` to `4596358`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/459635873118e8b8f485a46d92ec2dfd5c5fbd6f\"\u003e\u003ccode\u003e4596358\u003c/code\u003e\u003c/a\u003e Prepare for version \u003ccode\u003e2.0.0\u003c/code\u003e (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/60\"\u003e#60\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/00b3549af130c36f67b6180d37bc907887cc51e6\"\u003e\u003ccode\u003e00b3549\u003c/code\u003e\u003c/a\u003e Remove usage of \u003ccode\u003eaddParams\u003c/code\u003e (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/56\"\u003e#56\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/a4991ccf39a395030755bbdb69392d733e7b4835\"\u003e\u003ccode\u003ea4991cc\u003c/code\u003e\u003c/a\u003e Update CHANGELOG for version \u003ccode\u003e1.0.0\u003c/code\u003e (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/59\"\u003e#59\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/03eb89edb7756b586299b9a41720646ffe35c35d\"\u003e\u003ccode\u003e03eb89e\u003c/code\u003e\u003c/a\u003e Remove version_files input from release workflow (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/58\"\u003e#58\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/088a548d862a79a7d6d78545c68228272bc7992b\"\u003e\u003ccode\u003e088a548\u003c/code\u003e\u003c/a\u003e Add release management workflows (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/57\"\u003e#57\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/compare/1efa9bf4b1e4e31e24603b0fee496eac45ee8e8b...459635873118e8b8f485a46d92ec2dfd5c5fbd6f\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/uclahs-cds/pipeline-call-sSNV/pull/356","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/uclahs-cds%2Fpipeline-call-sSNV/issues/356","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/356/packages"}},{"old_version":"`1efa9bf`","new_version":"`4596358`","update_type":null,"path":"the pipeline-submodules group","pr_created_at":"2025-09-08T05:19:14.000Z","version_change":"`1efa9bf` → `4596358`","issue":{"uuid":"2806874423","node_id":"PR_kwDON9cPTc6nTYE3","number":12,"state":"open","title":"Bump external/pipeline-Nextflow-module from `1efa9bf` to `4596358` in the pipeline-submodules group","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-09-08T05:19:14.000Z","updated_at":"2025-09-08T05:19:15.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`1efa9bf`","new_version":"`4596358`","repository_url":"https://github.com/uclahs-cds/pipeline-Nextflow-module"}],"path":"the pipeline-submodules group","ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 1 update: [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).\n\nUpdates `external/pipeline-Nextflow-module` from `1efa9bf` to `4596358`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/459635873118e8b8f485a46d92ec2dfd5c5fbd6f\"\u003e\u003ccode\u003e4596358\u003c/code\u003e\u003c/a\u003e Prepare for version \u003ccode\u003e2.0.0\u003c/code\u003e (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/60\"\u003e#60\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/00b3549af130c36f67b6180d37bc907887cc51e6\"\u003e\u003ccode\u003e00b3549\u003c/code\u003e\u003c/a\u003e Remove usage of \u003ccode\u003eaddParams\u003c/code\u003e (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/56\"\u003e#56\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/a4991ccf39a395030755bbdb69392d733e7b4835\"\u003e\u003ccode\u003ea4991cc\u003c/code\u003e\u003c/a\u003e Update CHANGELOG for version \u003ccode\u003e1.0.0\u003c/code\u003e (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/59\"\u003e#59\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/03eb89edb7756b586299b9a41720646ffe35c35d\"\u003e\u003ccode\u003e03eb89e\u003c/code\u003e\u003c/a\u003e Remove version_files input from release workflow (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/58\"\u003e#58\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/088a548d862a79a7d6d78545c68228272bc7992b\"\u003e\u003ccode\u003e088a548\u003c/code\u003e\u003c/a\u003e Add release management workflows (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/57\"\u003e#57\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/compare/1efa9bf4b1e4e31e24603b0fee496eac45ee8e8b...459635873118e8b8f485a46d92ec2dfd5c5fbd6f\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/uclahs-cds/pipeline-calculate-mtDNA-CopyNumber/pull/12","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/uclahs-cds%2Fpipeline-calculate-mtDNA-CopyNumber/issues/12","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/12/packages"}},{"old_version":"`12f28e4`","new_version":"`1efa9bf`","update_type":null,"path":"the pipeline-submodules group","pr_created_at":"2025-05-05T01:29:34.000Z","version_change":"`12f28e4` → `1efa9bf`","issue":{"uuid":"3038396690","node_id":"PR_kwDOKc9lI86U3sbh","number":100,"state":"open","title":"Bump external/pipeline-Nextflow-module from `12f28e4` to `1efa9bf` in the pipeline-submodules group","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":1,"pull_request":true,"closed_at":null,"author_association":null,"state_reason":null,"created_at":"2025-05-05T01:29:34.000Z","updated_at":"2025-11-17T01:17:27.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`12f28e4`","new_version":"`1efa9bf`","repository_url":"https://github.com/uclahs-cds/pipeline-Nextflow-module"}],"path":"the pipeline-submodules group","ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 1 update: [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).\n\nUpdates `external/pipeline-Nextflow-module` from `12f28e4` to `1efa9bf`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/1efa9bf4b1e4e31e24603b0fee496eac45ee8e8b\"\u003e\u003ccode\u003e1efa9bf\u003c/code\u003e\u003c/a\u003e Update log dir set up in BCF2VCF (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/54\"\u003e#54\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/compare/12f28e4ebfc3e0f9a327c6c0dabf620ed4efe573...1efa9bf4b1e4e31e24603b0fee496eac45ee8e8b\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/uclahs-cds/pipeline-generate-SQC-BAM/pull/100","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/uclahs-cds%2Fpipeline-generate-SQC-BAM/issues/100","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/100/packages"}},{"old_version":"`12f28e4`","new_version":"`1efa9bf`","update_type":null,"path":"the pipeline-submodules group","pr_created_at":"2025-04-21T06:35:11.000Z","version_change":"`12f28e4` → `1efa9bf`","issue":{"uuid":"2470623339","node_id":"PR_kwDON9cPTc6TQrhr","number":9,"state":"open","title":"Bump external/pipeline-Nextflow-module from `12f28e4` to `1efa9bf` in the pipeline-submodules group","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":0,"pull_request":true,"closed_at":null,"author_association":"NONE","state_reason":null,"created_at":"2025-04-21T06:35:11.000Z","updated_at":"2025-08-05T20:27:31.000Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`12f28e4`","new_version":"`1efa9bf`","repository_url":"https://github.com/uclahs-cds/pipeline-Nextflow-module"}],"path":"the pipeline-submodules group","ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 1 update: [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).\n\nUpdates `external/pipeline-Nextflow-module` from `12f28e4` to `1efa9bf`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/1efa9bf4b1e4e31e24603b0fee496eac45ee8e8b\"\u003e\u003ccode\u003e1efa9bf\u003c/code\u003e\u003c/a\u003e Update log dir set up in BCF2VCF (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/54\"\u003e#54\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/compare/12f28e4ebfc3e0f9a327c6c0dabf620ed4efe573...1efa9bf4b1e4e31e24603b0fee496eac45ee8e8b\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/uclahs-cds/pipeline-calculate-mtDNA-CopyNumber/pull/9","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/uclahs-cds%2Fpipeline-calculate-mtDNA-CopyNumber/issues/9","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/9/packages"}},{"old_version":"`ef40c10`","new_version":"`12f28e4`","update_type":null,"path":"the pipeline-submodules group across 1 directory","pr_created_at":"2025-04-07T20:59:21.000Z","version_change":"`ef40c10` → `12f28e4`","issue":{"uuid":"2977987671","node_id":"PR_kwDOF1BFn86RsYLT","number":197,"state":"open","title":"Bump external/pipeline-Nextflow-module from `ef40c10` to `12f28e4` in the pipeline-submodules group across 1 directory","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":4,"pull_request":true,"closed_at":null,"author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-04-07T20:59:21.000Z","updated_at":"2025-08-05T21:18:27.706Z","time_to_close":null,"merged_at":null,"merged_by":null,"closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`ef40c10`","new_version":"`12f28e4`","repository_url":"https://github.com/uclahs-cds/pipeline-Nextflow-module"}],"path":"the pipeline-submodules group across 1 directory","ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 1 update in the / directory: [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).\n\nUpdates `external/pipeline-Nextflow-module` from `ef40c10` to `12f28e4`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/12f28e4ebfc3e0f9a327c6c0dabf620ed4efe573\"\u003e\u003ccode\u003e12f28e4\u003c/code\u003e\u003c/a\u003e Add bcf2vcf module (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/53\"\u003e#53\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/de9adf95e74bd35fad9f90ca4354ed8f158150c5\"\u003e\u003ccode\u003ede9adf9\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/51\"\u003e#51\u003c/a\u003e from uclahs-cds/kpash-reorganize-process-logs\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/cb51edea42d881961d0ded8f2f0e0bf2d2aac779\"\u003e\u003ccode\u003ecb51ede\u003c/code\u003e\u003c/a\u003e make sample directory\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/d6470939d8bcf8bec09f02ba3bd38747aa1fcd36\"\u003e\u003ccode\u003ed647093\u003c/code\u003e\u003c/a\u003e remove stray replace\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/61890721f059bcdb7a1a33ae2af4aa3e3739159b\"\u003e\u003ccode\u003e6189072\u003c/code\u003e\u003c/a\u003e standardize by removing replace('_','-')\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/b1f2dce4819f70953189e89afaa981455495e86e\"\u003e\u003ccode\u003eb1f2dce\u003c/code\u003e\u003c/a\u003e update process log naming standard to include workflow\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/2413b40be95d102ae2d7359f5719b32e811931e1\"\u003e\u003ccode\u003e2413b40\u003c/code\u003e\u003c/a\u003e Merge pull request \u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/49\"\u003e#49\u003c/a\u003e from uclahs-cds/kpash-fix-process-log\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/3567f9a2e106998b5de0d811a505d7ef7de7ec41\"\u003e\u003ccode\u003e3567f9a\u003c/code\u003e\u003c/a\u003e reorganize repo structure: create modules/SAMtools/* dir\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/cbb56617c671a5ca2b090473b559963de37c8068\"\u003e\u003ccode\u003ecbb5661\u003c/code\u003e\u003c/a\u003e update README\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/67523dc0624a7359a9a04da0b7d872e3795eb5ce\"\u003e\u003ccode\u003e67523dc\u003c/code\u003e\u003c/a\u003e rename enclosing directory to be more descriptive\u003c/li\u003e\n\u003cli\u003eAdditional commits viewable in \u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/compare/ef40c100005466b7d44f2fd60adb2c60ef451c4f...12f28e4ebfc3e0f9a327c6c0dabf620ed4efe573\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/uclahs-cds/pipeline-call-gSNP/pull/197","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/uclahs-cds%2Fpipeline-call-gSNP/issues/197","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/197/packages"}},{"old_version":"`de9adf9`","new_version":"`12f28e4`","update_type":null,"path":"the pipeline-submodules group","pr_created_at":"2025-03-10T19:27:59.000Z","version_change":"`de9adf9` → `12f28e4`","issue":{"uuid":"2383116368","node_id":"PR_kwDOJugmJM6OC3hQ","number":93,"state":"closed","title":"Bump external/pipeline-Nextflow-module from `de9adf9` to `12f28e4` in the pipeline-submodules group","user":"dependabot[bot]","labels":["dependencies","submodules"],"assignees":[],"locked":false,"comments_count":2,"pull_request":true,"closed_at":"2025-08-05T20:26:15.000Z","author_association":"CONTRIBUTOR","state_reason":null,"created_at":"2025-03-10T19:27:59.000Z","updated_at":"2025-08-05T20:26:15.000Z","time_to_close":12790696,"merged_at":"2025-08-05T20:26:15.000Z","merged_by":"yashpatel6","closed_by":null,"dependency_metadata":{"prefix":"Bump","packages":[{"name":"external/pipeline-Nextflow-module","old_version":"`de9adf9`","new_version":"`12f28e4`","repository_url":"https://github.com/uclahs-cds/pipeline-Nextflow-module"}],"path":"the pipeline-submodules group","ecosystem":"submodules"},"body":"Bumps the pipeline-submodules group with 1 update: [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module).\n\nUpdates `external/pipeline-Nextflow-module` from `de9adf9` to `12f28e4`\n\u003cdetails\u003e\n\u003csummary\u003eCommits\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/commit/12f28e4ebfc3e0f9a327c6c0dabf620ed4efe573\"\u003e\u003ccode\u003e12f28e4\u003c/code\u003e\u003c/a\u003e Add bcf2vcf module (\u003ca href=\"https://redirect.github.com/uclahs-cds/pipeline-Nextflow-module/issues/53\"\u003e#53\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003eSee full diff in \u003ca href=\"https://github.com/uclahs-cds/pipeline-Nextflow-module/compare/de9adf95e74bd35fad9f90ca4354ed8f158150c5...12f28e4ebfc3e0f9a327c6c0dabf620ed4efe573\"\u003ecompare view\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/details\u003e\n\u003cbr /\u003e\n\n\nDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.\n\n[//]: # (dependabot-automerge-start)\n[//]: # (dependabot-automerge-end)\n\n---\n\n\u003cdetails\u003e\n\u003csummary\u003eDependabot commands and options\u003c/summary\u003e\n\u003cbr /\u003e\n\nYou can trigger Dependabot actions by commenting on this PR:\n- `@dependabot rebase` will rebase this PR\n- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it\n- `@dependabot merge` will merge this PR after your CI passes on it\n- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it\n- `@dependabot cancel merge` will cancel a previously requested merge and block automerging\n- `@dependabot reopen` will reopen this PR if it is closed\n- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually\n- `@dependabot show \u003cdependency name\u003e ignore conditions` will show all of the ignore conditions of the specified dependency\n- `@dependabot ignore \u003cdependency name\u003e major version` will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e minor version` will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)\n- `@dependabot ignore \u003cdependency name\u003e` will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)\n- `@dependabot unignore \u003cdependency name\u003e` will remove all of the ignore conditions of the specified dependency\n- `@dependabot unignore \u003cdependency name\u003e \u003cignore condition\u003e` will remove the ignore condition of the specified dependency and ignore conditions\n\n\n\u003c/details\u003e","html_url":"https://github.com/uclahs-cds/pipeline-recalibrate-BAM/pull/93","url":"https://dependabot.ecosyste.ms/api/v1/hosts/GitHub/repositories/uclahs-cds%2Fpipeline-recalibrate-BAM/issues/93","packages_url":"https://dependabot.ecosyste.ms/api/v1/issues/93/packages"}}]}