{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":48076947,"defaultBranch":"master","name":"rnaseq-pipeline","ownerLogin":"PavlidisLab","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2015-12-16T00:28:05.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/25695421?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1724097278.0","currentOid":""},"activityList":{"items":[{"before":"67570e91435807026a0f9691411784ae0b6cd36b","after":"8e71bc41c070a5b6b48bae87168fe517eee054b2","ref":"refs/heads/master","pushedAt":"2024-09-03T22:30:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Pass --rerun to GenerateReportForExperiment in SubmitExperimentReportToGemma","shortMessageHtmlLink":"Pass --rerun to GenerateReportForExperiment in SubmitExperimentReport…"}},{"before":"eeae8beebbd74050da1eaaa4c9644db07964cfd0","after":"67570e91435807026a0f9691411784ae0b6cd36b","ref":"refs/heads/master","pushedAt":"2024-09-03T20:48:13.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Increase max SRA size to 100G","shortMessageHtmlLink":"Increase max SRA size to 100G"}},{"before":"ebde490c734a42bbd13440fb096bf8988582951a","after":"eeae8beebbd74050da1eaaa4c9644db07964cfd0","ref":"refs/heads/master","pushedAt":"2024-08-30T22:51:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Revert \"Add a priority to GenerateReportForExperiment\"\n\nThis reverts commit ebde490c734a42bbd13440fb096bf8988582951a.","shortMessageHtmlLink":"Revert \"Add a priority to GenerateReportForExperiment\""}},{"before":"298d2019131ca7019bda19c75df400cd04290b8d","after":"ebde490c734a42bbd13440fb096bf8988582951a","ref":"refs/heads/master","pushedAt":"2024-08-30T22:22:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Add a priority to GenerateReportForExperiment","shortMessageHtmlLink":"Add a priority to GenerateReportForExperiment"}},{"before":"dddefeeb41a4cf739d6524fc1455c53716575836","after":"298d2019131ca7019bda19c75df400cd04290b8d","ref":"refs/heads/master","pushedAt":"2024-08-26T18:32:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Add perl to the dependencies for RSEM","shortMessageHtmlLink":"Add perl to the dependencies for RSEM"}},{"before":"ddafd0c2f87de54975b721a124d69728ba89c089","after":"dddefeeb41a4cf739d6524fc1455c53716575836","ref":"refs/heads/master","pushedAt":"2024-08-23T17:10:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Include webviewer templates in the package data","shortMessageHtmlLink":"Include webviewer templates in the package data"}},{"before":null,"after":"2daeb3d86c77a3ab1790aca45a8cfa16829f9e01","ref":"refs/heads/features/fastqdump_splitting","pushedAt":"2024-08-19T19:54:38.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"variable name update","shortMessageHtmlLink":"variable name update"}},{"before":null,"after":"8123bc4447096b8d32a65521c988b85488f5a7d1","ref":"refs/heads/wip/cwl","pushedAt":"2024-08-19T19:54:38.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Generate a CWL workflow (WIP)","shortMessageHtmlLink":"Generate a CWL workflow (WIP)"}},{"before":"632542d58baf1ae8a03fb4f4321285c894399111","after":"ddafd0c2f87de54975b721a124d69728ba89c089","ref":"refs/heads/master","pushedAt":"2024-08-19T18:43:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Add a Makefile","shortMessageHtmlLink":"Add a Makefile"}},{"before":"bbaf421f242ae99bfad783e7a0832cda531b5ed9","after":"632542d58baf1ae8a03fb4f4321285c894399111","ref":"refs/heads/master","pushedAt":"2024-08-19T18:31:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Use Python 3.9 on the CI","shortMessageHtmlLink":"Use Python 3.9 on the CI"}},{"before":"16f249dfcfd7674756d64a5a97ed541697ee422c","after":"bbaf421f242ae99bfad783e7a0832cda531b5ed9","ref":"refs/heads/master","pushedAt":"2024-08-19T17:37:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Add a check for validity of GEO metadata","shortMessageHtmlLink":"Add a check for validity of GEO metadata"}},{"before":"ae02f56272d17475d7cbaa0cac0e6a407bcd22ab","after":"16f249dfcfd7674756d64a5a97ed541697ee422c","ref":"refs/heads/master","pushedAt":"2024-08-13T19:24:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Avoid overriding metadata in DownloadGeoSample and DownloadSraExperiment","shortMessageHtmlLink":"Avoid overriding metadata in DownloadGeoSample and DownloadSraExperiment"}},{"before":"fed06f52ce8f0e89705af272911279a0302edea5","after":"ae02f56272d17475d7cbaa0cac0e6a407bcd22ab","ref":"refs/heads/master","pushedAt":"2024-08-13T17:43:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Make SubmitExperimentReportToGemma rerunnable","shortMessageHtmlLink":"Make SubmitExperimentReportToGemma rerunnable"}},{"before":"7ba68a144143613b68d7ee24656eea5e5b5bfa46","after":"fed06f52ce8f0e89705af272911279a0302edea5","ref":"refs/heads/master","pushedAt":"2024-08-13T17:43:09.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Drop the paired_read_expeirments option and simplify pairedness check","shortMessageHtmlLink":"Drop the paired_read_expeirments option and simplify pairedness check"}},{"before":"1a660ede4c3f8cc71df41f9badf8249f7befd26f","after":"7ba68a144143613b68d7ee24656eea5e5b5bfa46","ref":"refs/heads/master","pushedAt":"2024-08-13T17:21:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Add a 2 hours walltime limit for prefetch tasks","shortMessageHtmlLink":"Add a 2 hours walltime limit for prefetch tasks"}},{"before":"b626a413c69bbc07be18fadf9cc96db1370493ee","after":"1a660ede4c3f8cc71df41f9badf8249f7befd26f","ref":"refs/heads/master","pushedAt":"2024-07-03T17:49:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Improve logic for detecting bulk RNA-Seq datasets","shortMessageHtmlLink":"Improve logic for detecting bulk RNA-Seq datasets"}},{"before":"51d58745d57abc8627bbeac0b1aff3f24b2d73bf","after":"b626a413c69bbc07be18fadf9cc96db1370493ee","ref":"refs/heads/master","pushedAt":"2024-06-25T19:23:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Addresses missing spots_with_mates column in SRA runinfo (fix #93)","shortMessageHtmlLink":"Addresses missing spots_with_mates column in SRA runinfo (fix #93)"}},{"before":"a34826af87de4afcb9891df6819523f3a5c9b9ed","after":"51d58745d57abc8627bbeac0b1aff3f24b2d73bf","ref":"refs/heads/master","pushedAt":"2024-06-14T21:43:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Remove -f flag when calling fillBatchInfo","shortMessageHtmlLink":"Remove -f flag when calling fillBatchInfo"}},{"before":"56984af49598c4e52f375228f97627b6078659f5","after":"a34826af87de4afcb9891df6819523f3a5c9b9ed","ref":"refs/heads/master","pushedAt":"2024-06-07T19:40:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Bump min requirement for bioluigi to 0.3.4","shortMessageHtmlLink":"Bump min requirement for bioluigi to 0.3.4"}},{"before":"fb399fadab10a591b4d7b0f99e5bf12cf788c8c5","after":"56984af49598c4e52f375228f97627b6078659f5","ref":"refs/heads/master","pushedAt":"2024-06-07T19:38:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Perform sample renaming for the MultiQC report","shortMessageHtmlLink":"Perform sample renaming for the MultiQC report"}},{"before":"4352fec8098bb9bc48382822ff849fc73d600d9d","after":"fb399fadab10a591b4d7b0f99e5bf12cf788c8c5","ref":"refs/heads/master","pushedAt":"2024-05-23T23:32:01.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Add a systemd unit for running the pipeline and use conda run","shortMessageHtmlLink":"Add a systemd unit for running the pipeline and use conda run"}},{"before":"cdbe165dd5743d7b5fe41b01f9083b6c39f43490","after":"4352fec8098bb9bc48382822ff849fc73d600d9d","ref":"refs/heads/master","pushedAt":"2024-05-21T23:14:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Add ssRNA-seq to the list of supported strategies","shortMessageHtmlLink":"Add ssRNA-seq to the list of supported strategies"}},{"before":"ab6b567f1b9077f646a0db96f80a08fea00c0827","after":"cdbe165dd5743d7b5fe41b01f9083b6c39f43490","ref":"refs/heads/master","pushedAt":"2024-05-21T20:40:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Fix rename of GemmaTask to GemmaTaskMixin and GemmaCliTask","shortMessageHtmlLink":"Fix rename of GemmaTask to GemmaTaskMixin and GemmaCliTask"}},{"before":"ac1da2aeb32412c2014d20605ba885f5bb1701e4","after":"ab6b567f1b9077f646a0db96f80a08fea00c0827","ref":"refs/heads/master","pushedAt":"2024-05-21T20:40:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Relocate Gemma-specific configuration under [rnaseq_pipeline.gemma]","shortMessageHtmlLink":"Relocate Gemma-specific configuration under [rnaseq_pipeline.gemma]"}},{"before":"acf0e8405bccfc174fc920e19acb25b85591997b","after":"ac1da2aeb32412c2014d20605ba885f5bb1701e4","ref":"refs/heads/master","pushedAt":"2024-05-21T20:39:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Make Gemma's appdata directory configurable","shortMessageHtmlLink":"Make Gemma's appdata directory configurable"}},{"before":"31f8199b638555323246347ff26112cb02023671","after":"acf0e8405bccfc174fc920e19acb25b85591997b","ref":"refs/heads/master","pushedAt":"2024-05-17T17:50:14.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Remove unused STAR_CLEANUP_SCRIPT config","shortMessageHtmlLink":"Remove unused STAR_CLEANUP_SCRIPT config"}},{"before":"533d237e7387528516482089f69bf927055ac448","after":"31f8199b638555323246347ff26112cb02023671","ref":"refs/heads/master","pushedAt":"2024-05-09T22:55:39.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Add a script for synchronizing the MultiQC reports","shortMessageHtmlLink":"Add a script for synchronizing the MultiQC reports"}},{"before":"71c02479d0db050e7ece2a97c3bfb6ef3da608a3","after":"533d237e7387528516482089f69bf927055ac448","ref":"refs/heads/master","pushedAt":"2024-03-20T17:20:42.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Few fixes for the webviewer","shortMessageHtmlLink":"Few fixes for the webviewer"}},{"before":"b9ff1d871cd679e5aad67a8bbfef8c998d2612c0","after":"71c02479d0db050e7ece2a97c3bfb6ef3da608a3","ref":"refs/heads/master","pushedAt":"2024-03-13T21:56:21.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Fix duplicated keys in metadata dict","shortMessageHtmlLink":"Fix duplicated keys in metadata dict"}},{"before":"20a570d149a0cd6f16659023129ed27bd341b6d6","after":"b9ff1d871cd679e5aad67a8bbfef8c998d2612c0","ref":"refs/heads/master","pushedAt":"2024-03-13T21:56:05.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"arteymix","name":"Guillaume Poirier-Morency","path":"/arteymix","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1318477?s=80&v=4"},"commit":{"message":"Fix duplicated keys in metadata dict","shortMessageHtmlLink":"Fix duplicated keys in metadata dict"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0wM1QyMjozMDo0My4wMDAwMDBazwAAAASsFJcV","startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0wM1QyMjozMDo0My4wMDAwMDBazwAAAASsFJcV","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wMy0xM1QyMTo1NjowNS4wMDAwMDBazwAAAAQU-VBk"}},"title":"Activity · PavlidisLab/rnaseq-pipeline"}