{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":235450808,"defaultBranch":"master","name":"motrpac-proteomics-pipeline","ownerLogin":"MoTrPAC","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2020-01-21T22:04:58.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/47675013?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1722937966.0","currentOid":""},"activityList":{"items":[{"before":"7d3edd0e345cec9178bd0e326235a23b03da7bd6","after":"93421c6fa86723efb1f5d356808621f223d8d0a3","ref":"refs/heads/develop","pushedAt":"2024-08-12T15:04:40.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Merge pull request #88 from MoTrPAC/feat/preemptible\n\nfix: unify preemptible attributes","shortMessageHtmlLink":"Merge pull request #88 from MoTrPAC/feat/preemptible"}},{"before":"82d5fb516f66bc3e5318263aea13596640a3e2b2","after":"b8a9488b82340e2a5c45854700c16baf69565964","ref":"refs/heads/feat/preemptible","pushedAt":"2024-08-09T01:35:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mihirsamdarshi","name":"Mihir Samdarshi","path":"/mihirsamdarshi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5462077?s=80&v=4"},"commit":{"message":"refactor: unify preemptible attempt configuration\n\n- Introduced `num_preemptible_attempts` as a new input variable\n- Replaced individual preemptible attempts across tasks with the new unified variable\n- Updated configuration files to use the new unified variable","shortMessageHtmlLink":"refactor: unify preemptible attempt configuration"}},{"before":"b6ca51170a7ff4a2b4686903806f9b51ad309863","after":"06686a6815680b570154137ea2df526e126dd00a","ref":"refs/heads/master","pushedAt":"2024-08-06T09:50:49.000Z","pushType":"pr_merge","commitsCount":4,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Merge pull request #87 from MoTrPAC/develop\n\nProteomics msgfplus v1.1.0","shortMessageHtmlLink":"Merge pull request #87 from MoTrPAC/develop"}},{"before":"efeff7ef762caa3a127e1090879ee723b7790bd6","after":"7d3edd0e345cec9178bd0e326235a23b03da7bd6","ref":"refs/heads/develop","pushedAt":"2024-08-06T09:43:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Proteomics msgfplus v1.1.0\n\nAdd option to run on pre-emptible VMs","shortMessageHtmlLink":"Proteomics msgfplus v1.1.0"}},{"before":"b6ca51170a7ff4a2b4686903806f9b51ad309863","after":"efeff7ef762caa3a127e1090879ee723b7790bd6","ref":"refs/heads/develop","pushedAt":"2024-08-05T18:04:39.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Merge pull request #86 from MoTrPAC/feat/preemptible\n\nAdd option to run on pre-emptible VMs","shortMessageHtmlLink":"Merge pull request #86 from MoTrPAC/feat/preemptible"}},{"before":null,"after":"82d5fb516f66bc3e5318263aea13596640a3e2b2","ref":"refs/heads/feat/preemptible","pushedAt":"2024-08-04T06:58:07.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"mihirsamdarshi","name":"Mihir Samdarshi","path":"/mihirsamdarshi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5462077?s=80&v=4"},"commit":{"message":"feat(wdl): add preemptible runtime attribute to tasks for additional cost savings\n\n- Introduce `preemptible` attribute with default value of two attempts with a pre-emptible VM before falling back to a standard VM.\n- Modify runtime block to include `preemptible` configuration.\n- Update JSON configuration templates to support `preemptible`.\n- Pre-emptible VMs are cost-effective batch computing solutions.","shortMessageHtmlLink":"feat(wdl): add preemptible runtime attribute to tasks for additional …"}},{"before":"88de5a52eab2ff90247ec822acb23263d1388c4e","after":"b6ca51170a7ff4a2b4686903806f9b51ad309863","ref":"refs/heads/develop","pushedAt":"2024-08-04T06:28:23.000Z","pushType":"push","commitsCount":6,"pusher":{"login":"mihirsamdarshi","name":"Mihir Samdarshi","path":"/mihirsamdarshi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5462077?s=80&v=4"},"commit":{"message":"Merge pull request #84 from MoTrPAC/feat/add-helper-script\n\nScript fixes, remove redundant isPTM input parameter","shortMessageHtmlLink":"Merge pull request #84 from MoTrPAC/feat/add-helper-script"}},{"before":"b792ede16ddeb7b35aa6368abcc7b180bb1e2af4","after":"88de5a52eab2ff90247ec822acb23263d1388c4e","ref":"refs/heads/develop","pushedAt":"2024-08-02T08:10:15.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Merge pull request #83 from MoTrPAC/develop\n\nAdd tmt-18 support for msgfplus","shortMessageHtmlLink":"Merge pull request #83 from MoTrPAC/develop"}},{"before":"88de5a52eab2ff90247ec822acb23263d1388c4e","after":"b6ca51170a7ff4a2b4686903806f9b51ad309863","ref":"refs/heads/master","pushedAt":"2024-08-02T07:54:57.000Z","pushType":"pr_merge","commitsCount":6,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Merge pull request #84 from MoTrPAC/feat/add-helper-script\n\nScript fixes, remove redundant isPTM input parameter","shortMessageHtmlLink":"Merge pull request #84 from MoTrPAC/feat/add-helper-script"}},{"before":"f54636fb216b1a0ba01ca1cca7b3894512de5776","after":"fbb9be59fd1c80ee70545dae8ee6eeec78a3df19","ref":"refs/heads/feat/add-helper-script","pushedAt":"2024-07-30T19:36:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mihirsamdarshi","name":"Mihir Samdarshi","path":"/mihirsamdarshi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5462077?s=80&v=4"},"commit":{"message":"fix: automatically set isPTM based on proteomics experiment, sync with OmicsPipelines","shortMessageHtmlLink":"fix: automatically set isPTM based on proteomics experiment, sync wit…"}},{"before":"84a36b84d4aee8cd2527bd818111a33e54e4f1f8","after":"f54636fb216b1a0ba01ca1cca7b3894512de5776","ref":"refs/heads/feat/add-helper-script","pushedAt":"2024-07-29T20:11:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"mihirsamdarshi","name":"Mihir Samdarshi","path":"/mihirsamdarshi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5462077?s=80&v=4"},"commit":{"message":"fix: use correct isPTM filter","shortMessageHtmlLink":"fix: use correct isPTM filter"}},{"before":null,"after":"84a36b84d4aee8cd2527bd818111a33e54e4f1f8","ref":"refs/heads/feat/add-helper-script","pushedAt":"2024-05-24T10:25:59.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"mihirsamdarshi","name":"Mihir Samdarshi","path":"/mihirsamdarshi","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5462077?s=80&v=4"},"commit":{"message":"fix: filter erroneous files from file manifest generation","shortMessageHtmlLink":"fix: filter erroneous files from file manifest generation"}},{"before":"185700da118103bf2b465f2b1157d57692f07c26","after":"88de5a52eab2ff90247ec822acb23263d1388c4e","ref":"refs/heads/master","pushedAt":"2024-05-23T20:26:42.000Z","pushType":"pr_merge","commitsCount":25,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Merge pull request #83 from MoTrPAC/develop\n\nAdd tmt-18 support for msgfplus","shortMessageHtmlLink":"Merge pull request #83 from MoTrPAC/develop"}},{"before":"f72164c43a8545e58e2253299e13660489dfcab3","after":"b792ede16ddeb7b35aa6368abcc7b180bb1e2af4","ref":"refs/heads/develop","pushedAt":"2024-05-23T20:15:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Update readme_msgfplus-details.md","shortMessageHtmlLink":"Update readme_msgfplus-details.md"}},{"before":"58374ef1a616be25b0e753fc3807738cc592adcd","after":"f72164c43a8545e58e2253299e13660489dfcab3","ref":"refs/heads/develop","pushedAt":"2024-05-23T19:18:56.000Z","pushType":"pr_merge","commitsCount":23,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Merge pull request #82 from MoTrPAC/feat-add-redox\n\nSupport for tmt-18 and other improvements","shortMessageHtmlLink":"Merge pull request #82 from MoTrPAC/feat-add-redox"}},{"before":"d71f2b992a03b45a1b84e2b7111ae6e41cf878cf","after":"db9e6212b91d73afab66c3815b7c64151b3ccef9","ref":"refs/heads/feat-add-redox","pushedAt":"2024-05-23T05:21:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Add msgplus templates for tmt-18 PTMs","shortMessageHtmlLink":"Add msgplus templates for tmt-18 PTMs"}},{"before":"7fb027516f912012643f462a000578f9a9834ce4","after":"d71f2b992a03b45a1b84e2b7111ae6e41cf878cf","ref":"refs/heads/feat-add-redox","pushedAt":"2024-05-23T04:50:18.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Config file for redox","shortMessageHtmlLink":"Config file for redox"}},{"before":"5396bdd90382b02adab8000496a48c12e189ef27","after":"7fb027516f912012643f462a000578f9a9834ce4","ref":"refs/heads/feat-add-redox","pushedAt":"2024-05-21T04:18:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"New version of phrp, debian based, and back to previous prot-ppmerror version","shortMessageHtmlLink":"New version of phrp, debian based, and back to previous prot-ppmerror…"}},{"before":"d243ce34de224a2c8b6c1c0505f798cc584f48ce","after":"5396bdd90382b02adab8000496a48c12e189ef27","ref":"refs/heads/feat-add-redox","pushedAt":"2024-05-17T22:52:45.000Z","pushType":"push","commitsCount":5,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Update input templates msgfplus with new software versions","shortMessageHtmlLink":"Update input templates msgfplus with new software versions"}},{"before":"50730f7c5d7e683c7a327aa5f30755b293797b98","after":"d243ce34de224a2c8b6c1c0505f798cc584f48ce","ref":"refs/heads/feat-add-redox","pushedAt":"2024-05-17T00:29:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Update MASIC to support tmt-18","shortMessageHtmlLink":"Update MASIC to support tmt-18"}},{"before":"41d8603a8ed2a9c5e6008a01607b634d0a18ca02","after":"50730f7c5d7e683c7a327aa5f30755b293797b98","ref":"refs/heads/feat-add-redox","pushedAt":"2024-04-26T16:58:03.000Z","pushType":"push","commitsCount":6,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Update copy_pipeline_results.py\n\nminor update","shortMessageHtmlLink":"Update copy_pipeline_results.py"}},{"before":"30655d7980e5d833bf66239e0d905f0aa4083f53","after":"41d8603a8ed2a9c5e6008a01607b634d0a18ca02","ref":"refs/heads/feat-add-redox","pushedAt":"2024-04-26T05:21:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"create_study_design: multiple updates\n\n#81","shortMessageHtmlLink":"create_study_design: multiple updates"}},{"before":"32a5798bfca28c8b5c2e5f89bdf3682b1c3e9273","after":null,"ref":"refs/heads/fix/minor-refactor","pushedAt":"2024-02-05T22:22:51.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"}},{"before":"27c0460ae1331019354c90a2e0b46b28c72b6170","after":null,"ref":"refs/heads/adjustments-outputs","pushedAt":"2024-02-05T22:22:45.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"}},{"before":"9fcc8a909155cebaa99733f147a4e2669db7254f","after":"30655d7980e5d833bf66239e0d905f0aa4083f53","ref":"refs/heads/feat-add-redox","pushedAt":"2023-12-29T20:06:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"create_study_design: refactor the creation of MeasurementName\n\ndplyr is giving errors, using base r","shortMessageHtmlLink":"create_study_design: refactor the creation of MeasurementName"}},{"before":"1003f08990ff2d56326ae0fe520b6df81c75448b","after":"9fcc8a909155cebaa99733f147a4e2669db7254f","ref":"refs/heads/feat-add-redox","pushedAt":"2023-11-09T23:00:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"fix: create study design: read vial_metadata","shortMessageHtmlLink":"fix: create study design: read vial_metadata"}},{"before":"1def4198ab643f317bbe7f3a5c3bf893e6c1fdc1","after":"1003f08990ff2d56326ae0fe520b6df81c75448b","ref":"refs/heads/feat-add-redox","pushedAt":"2023-11-08T23:38:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"Update create_study_design.R: several improvements\n\n- MeasurementName is change for the reference channel based on ReporterAlias, i.e., MeasurementName will be NA only if ReporterAlias is Reference (ref)\n- Other adjustments and cleanings","shortMessageHtmlLink":"Update create_study_design.R: several improvements"}},{"before":"9ca4279c645f75cbdde2489203147dfd569538a4","after":"1def4198ab643f317bbe7f3a5c3bf893e6c1fdc1","ref":"refs/heads/feat-add-redox","pushedAt":"2023-11-06T23:44:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"update create_study_design: minor adjustment","shortMessageHtmlLink":"update create_study_design: minor adjustment"}},{"before":"ad81a752776834543a14a9b61358319e1ff315ff","after":"9ca4279c645f75cbdde2489203147dfd569538a4","ref":"refs/heads/feat-add-redox","pushedAt":"2023-11-06T23:42:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"update create_study_design: add 1 to reference.txt if no Ref is present, improved version","shortMessageHtmlLink":"update create_study_design: add 1 to reference.txt if no Ref is prese…"}},{"before":null,"after":"ad81a752776834543a14a9b61358319e1ff315ff","ref":"refs/heads/feat-add-redox","pushedAt":"2023-11-06T23:02:50.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"biodavidjm","name":"David JM","path":"/biodavidjm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6676074?s=80&v=4"},"commit":{"message":"update create_study_design: add 1 to reference.txt if no Ref is present\n\n#80","shortMessageHtmlLink":"update create_study_design: add 1 to reference.txt if no Ref is present"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEmD-ingA","startCursor":null,"endCursor":null}},"title":"Activity · MoTrPAC/motrpac-proteomics-pipeline"}