{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":561879136,"defaultBranch":"main","name":"wdl-common","ownerLogin":"PacificBiosciences","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2022-11-04T17:43:19.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/999745?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1715129579.0","currentOid":""},"activityList":{"items":[{"before":"0963b2cc571ad61ea9ad3ed886afab33b00444c6","after":"896bc64aa1b037d1ca0c53b5c85a68dc0f49bc37","ref":"refs/heads/feature/wgs-v2","pushedAt":"2024-05-10T22:53:19.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Revert to using pharmcat version tag.","shortMessageHtmlLink":"Revert to using pharmcat version tag."}},{"before":"98d6fbe696a4bcefe0913f4bbf26b4180817184e","after":"0963b2cc571ad61ea9ad3ed886afab33b00444c6","ref":"refs/heads/feature/wgs-v2","pushedAt":"2024-05-09T18:03:04.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Normalize mosdepth output name.","shortMessageHtmlLink":"Normalize mosdepth output name."}},{"before":"d29df22687effede8d9f9ce5f8b01c0232169bce","after":"98d6fbe696a4bcefe0913f4bbf26b4180817184e","ref":"refs/heads/feature/wgs-v2","pushedAt":"2024-05-09T18:02:05.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Normalize mosdepth output name.","shortMessageHtmlLink":"Normalize mosdepth output name."}},{"before":"028f6de4251e557bfaec6f8251953b3d34f8744c","after":"d29df22687effede8d9f9ce5f8b01c0232169bce","ref":"refs/heads/feature/wgs-v2","pushedAt":"2024-05-09T16:33:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Normalize mosdepth output name.","shortMessageHtmlLink":"Normalize mosdepth output name."}},{"before":"3e30e2b5dc11fe49a57aaa55ce4398155fa90f63","after":"028f6de4251e557bfaec6f8251953b3d34f8744c","ref":"refs/heads/feature/wgs-v2","pushedAt":"2024-05-09T01:05:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Remove pangu input from pharmcat inputs.","shortMessageHtmlLink":"Remove pangu input from pharmcat inputs."}},{"before":"092ebf5fce24233a43364d8515416e306a80affc","after":"3e30e2b5dc11fe49a57aaa55ce4398155fa90f63","ref":"refs/heads/feature/wgs-v2","pushedAt":"2024-05-09T01:03:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Correct backend to AWS-OMICS","shortMessageHtmlLink":"Correct backend to AWS-OMICS"}},{"before":"89bacce0580e7b00e4ecc779d326f80053eb0513","after":"092ebf5fce24233a43364d8515416e306a80affc","ref":"refs/heads/feature/wgs-v2","pushedAt":"2024-05-09T00:58:47.000Z","pushType":"push","commitsCount":8,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Backend configuration requires container_registry for AWS-OMICS backend","shortMessageHtmlLink":"Backend configuration requires container_registry for AWS-OMICS backend"}},{"before":"b1dbcfab8f7775530871e86172250aec52bbf724","after":null,"ref":"refs/heads/feature/samtools_reset","pushedAt":"2024-05-08T00:52:59.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"}},{"before":"2523b4d2703859db55eebaa2497ac24a324178cf","after":null,"ref":"refs/heads/feature/hiphase-1.1","pushedAt":"2024-05-08T00:52:41.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"}},{"before":"cc9b52f071f94d2fe827102ccb1af9ba41fabc15","after":"89bacce0580e7b00e4ecc779d326f80053eb0513","ref":"refs/heads/feature/wgs-v2","pushedAt":"2024-05-08T00:51:01.000Z","pushType":"push","commitsCount":14,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"fix threading for bcftools","shortMessageHtmlLink":"fix threading for bcftools"}},{"before":null,"after":"cc9b52f071f94d2fe827102ccb1af9ba41fabc15","ref":"refs/heads/feature/wgs-v2","pushedAt":"2024-04-23T05:46:00.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"feat(GLnexus): Added custom configuration requiring minimum depth of 1. Cleaned up temporary files.","shortMessageHtmlLink":"feat(GLnexus): Added custom configuration requiring minimum depth of …"}},{"before":null,"after":"318fe21076150061bdec8e44258101ba4fad8d1e","ref":"refs/heads/te","pushedAt":"2024-04-09T22:59:09.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"gconcepcion","name":"Greg","path":"/gconcepcion","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4172670?s=80&v=4"},"commit":{"message":"optional inclusion of pangu tsv","shortMessageHtmlLink":"optional inclusion of pangu tsv"}},{"before":null,"after":"91155fa72e38ed427e52c386b08d6cdd70efa1f0","ref":"refs/heads/pharmcat","pushedAt":"2024-04-05T18:29:44.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"gconcepcion","name":"Greg","path":"/gconcepcion","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4172670?s=80&v=4"},"commit":{"message":"I should have added better tests for this","shortMessageHtmlLink":"I should have added better tests for this"}},{"before":null,"after":"e426ef4b24f37fb4dce68f4ff4cf3dc36de2bfa7","ref":"refs/heads/refactor/move-wgs-tasks","pushedAt":"2024-03-26T05:13:16.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"refactor: Move tasks from HiFi-human-WGS-WDL to wdl-common","shortMessageHtmlLink":"refactor: Move tasks from HiFi-human-WGS-WDL to wdl-common"}},{"before":"31c33da7fedb0812f151bfb08bc9d55f90e7cabf","after":"2523b4d2703859db55eebaa2497ac24a324178cf","ref":"refs/heads/feature/hiphase-1.1","pushedAt":"2024-03-09T05:05:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"fix: Clean up large intermediate files.","shortMessageHtmlLink":"fix: Clean up large intermediate files."}},{"before":"b99a04648136eb6d7a125d3dd6cfce8cf2799e8c","after":"31c33da7fedb0812f151bfb08bc9d55f90e7cabf","ref":"refs/heads/feature/hiphase-1.1","pushedAt":"2024-03-09T03:43:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"feat(hiphase): If only one BAM is to be haplotagged, use normalized name sample.ref.","shortMessageHtmlLink":"feat(hiphase): If only one BAM is to be haplotagged, use normalized n…"}},{"before":"994f5a166b3abb84e24fdb17ef19974c8f01e5f4","after":"b99a04648136eb6d7a125d3dd6cfce8cf2799e8c","ref":"refs/heads/feature/hiphase-1.1","pushedAt":"2024-02-17T02:43:01.000Z","pushType":"push","commitsCount":9,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Merge branch 'main' into feature/hiphase-1.1","shortMessageHtmlLink":"Merge branch 'main' into feature/hiphase-1.1"}},{"before":"f4b4e4133e2792fc36dcda3ff4cc607716e29194","after":"994f5a166b3abb84e24fdb17ef19974c8f01e5f4","ref":"refs/heads/feature/hiphase-1.1","pushedAt":"2024-02-17T01:19:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"fix: Reducing mem for pbsv_discover to 10GB. We needed an increase, but an extra 2GB should be enough. No need for 50% increase.","shortMessageHtmlLink":"fix: Reducing mem for pbsv_discover to 10GB. We needed an increase, b…"}},{"before":"e062bfb557a50c724d1e77bacc691752653bd698","after":null,"ref":"refs/heads/hotfix/memory-increases","pushedAt":"2024-01-17T01:23:03.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"}},{"before":"5fffe24715d82765bc5d88ecd16a0e7fe615c64e","after":"f4b4e4133e2792fc36dcda3ff4cc607716e29194","ref":"refs/heads/feature/hiphase-1.1","pushedAt":"2024-01-17T01:22:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"fix: Increased memory for tasks with OOM errors.\n\nSome tasks have been hitting OOM errors in recent testing with various potential causes including tool threading/mem changes, untested platforms, etc.","shortMessageHtmlLink":"fix: Increased memory for tasks with OOM errors."}},{"before":null,"after":"e062bfb557a50c724d1e77bacc691752653bd698","ref":"refs/heads/hotfix/memory-increases","pushedAt":"2024-01-17T01:19:26.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"fix: Increased memory for tasks with OOM errors.\n\nSome tasks have been hitting OOM errors in recent testing with various potential causes including tool threading/mem changes, untested platforms, etc.","shortMessageHtmlLink":"fix: Increased memory for tasks with OOM errors."}},{"before":"ec28a7f674fc382aa13d1b16cc1f4027b695464a","after":null,"ref":"refs/heads/hotfix/deepvariant-1.6.0","pushedAt":"2023-12-15T21:16:35.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"}},{"before":"14688185dd64196a0c52bee8d3b93679d753da2a","after":"7baa139678f470aa38181d59fb4ae664a9b6fa9d","ref":"refs/heads/main","pushedAt":"2023-12-15T21:16:32.000Z","pushType":"pr_merge","commitsCount":4,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Merge pull request #39 from PacificBiosciences/hotfix/deepvariant-1.6.0\n\nfeat: Update to DeepVariant v1.6","shortMessageHtmlLink":"Merge pull request #39 from PacificBiosciences/hotfix/deepvariant-1.6.0"}},{"before":"dd3f63866b9fd1eb8396409ed4ab6f33c822d008","after":"ec28a7f674fc382aa13d1b16cc1f4027b695464a","ref":"refs/heads/hotfix/deepvariant-1.6.0","pushedAt":"2023-12-15T20:10:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Change model directory to writable location.","shortMessageHtmlLink":"Change model directory to writable location."}},{"before":"ab5b669ea508c240d8e7999a6b6b882883d8434b","after":"dd3f63866b9fd1eb8396409ed4ab6f33c822d008","ref":"refs/heads/hotfix/deepvariant-1.6.0","pushedAt":"2023-12-15T18:17:33.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Remove temporary files.\n\nSigned-off-by: William Rowell ","shortMessageHtmlLink":"Remove temporary files."}},{"before":"dd3f63866b9fd1eb8396409ed4ab6f33c822d008","after":null,"ref":"refs/heads/hotfix/deepvariant-1.6.0-temp","pushedAt":"2023-12-15T18:14:26.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"}},{"before":null,"after":"dd3f63866b9fd1eb8396409ed4ab6f33c822d008","ref":"refs/heads/hotfix/deepvariant-1.6.0-temp","pushedAt":"2023-12-15T18:13:22.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Remove temporary files.\n\nSigned-off-by: William Rowell ","shortMessageHtmlLink":"Remove temporary files."}},{"before":null,"after":"a6a9e4d3ff03727f42e032b12c3881443a657212","ref":"refs/heads/feature/deepvariant-gpu","pushedAt":"2023-12-15T06:31:19.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Merge branch 'main' into feature/deepvariant-gpu","shortMessageHtmlLink":"Merge branch 'main' into feature/deepvariant-gpu"}},{"before":"a6a9e4d3ff03727f42e032b12c3881443a657212","after":null,"ref":"refs/heads/feature/deepvariant-gpu","pushedAt":"2023-12-15T06:31:13.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"}},{"before":null,"after":"ab5b669ea508c240d8e7999a6b6b882883d8434b","ref":"refs/heads/hotfix/deepvariant-1.6.0","pushedAt":"2023-12-15T00:44:57.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"williamrowell","name":"Billy Rowell","path":"/williamrowell","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/627365?s=80&v=4"},"commit":{"message":"Update to DeepVariant v1.6\n\nIn DeepVariant 1.6, the number and types of model files have changed, so rather than specify these files individually within a complex struct, I'm moving instead to providing a tarball of the model files.\n\nWe make liberal use of tarballed outputs in this subworkflow, but since we don't remove the original outputs, the storage required multiplies on HPC systems with persistent shared storage. Cleaning up files after they've been compressed/decompressed should help with intermediate storage requirements.\n\nSigned-off-by: William Rowell ","shortMessageHtmlLink":"Update to DeepVariant v1.6"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAERvtQwwA","startCursor":null,"endCursor":null}},"title":"Activity · PacificBiosciences/wdl-common"}