{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":419331038,"defaultBranch":"main","name":"SimpleMetaPipeline","ownerLogin":"J-Cos","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2021-10-20T12:59:21.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/72385600?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1715199074.0","currentOid":""},"activityList":{"items":[{"before":"bdfb27c0b7f5d8f91874cc2398ca9ee59735b878","after":"5e5aa3b998bab18594d3c614e84c055b32a147fc","ref":"refs/heads/main","pushedAt":"2024-05-06T21:09:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Update README.md\n\nAdd link to Idtaxa classifiers","shortMessageHtmlLink":"Update README.md"}},{"before":"6d28f85143d2d4b9de6d645c86e92cf2495f8acc","after":"bdfb27c0b7f5d8f91874cc2398ca9ee59735b878","ref":"refs/heads/main","pushedAt":"2024-05-06T20:21:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Coding Style Update\n\nTo follow: https://style.tidyverse.org","shortMessageHtmlLink":"Coding Style Update"}},{"before":"b43dfbe13bd4391707abe10cf3a4ef27a4d0521b","after":"1685fdb897e5817e2a8f69702a856977e3a1e0c1","ref":"refs/heads/dev_futurereef","pushedAt":"2024-02-21T13:38:20.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"update dada2 to fix big in multiple orientation run handling\n\npreviously this didn't work when restarting a run midway through dada. This is because adding number completed runs to run was incorrect.","shortMessageHtmlLink":"update dada2 to fix big in multiple orientation run handling"}},{"before":"6d28f85143d2d4b9de6d645c86e92cf2495f8acc","after":"b43dfbe13bd4391707abe10cf3a4ef27a4d0521b","ref":"refs/heads/dev_futurereef","pushedAt":"2024-02-12T16:44:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Enable combining mixed and unmixed orientation runs\n\nThis change makes the pipeline require a logical vector (of length number of runs) as the argument to MixedOrientation. In other words the mixedorientation-ness of each run must be specified independently, rather than just being specified once for all runs being processed together.","shortMessageHtmlLink":"Enable combining mixed and unmixed orientation runs"}},{"before":null,"after":"6d28f85143d2d4b9de6d645c86e92cf2495f8acc","ref":"refs/heads/dev_futurereef","pushedAt":"2024-02-12T15:40:22.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Merge branch 'main' of https://github.com/J-Cos/SimpleMetaPipeline into main","shortMessageHtmlLink":"Merge branch 'main' of https://github.com/J-Cos/SimpleMetaPipeline in…"}},{"before":"60e74047179070ef13432d71ab56726eb9c982ce","after":"6d28f85143d2d4b9de6d645c86e92cf2495f8acc","ref":"refs/heads/main","pushedAt":"2023-12-19T14:54:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Merge branch 'main' of https://github.com/J-Cos/SimpleMetaPipeline into main","shortMessageHtmlLink":"Merge branch 'main' of https://github.com/J-Cos/SimpleMetaPipeline in…"}},{"before":"7452401d5c20045ef129dc36fa4c4077646b926e","after":"60e74047179070ef13432d71ab56726eb9c982ce","ref":"refs/heads/main","pushedAt":"2023-12-19T14:52:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Update README.md\n\ntypos and clarity","shortMessageHtmlLink":"Update README.md"}},{"before":"a1353d3875b3fbcf43575f4ccabefee52e1012fa","after":"7452401d5c20045ef129dc36fa4c4077646b926e","ref":"refs/heads/main","pushedAt":"2023-12-19T14:41:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Merge branch 'main' of https://github.com/J-Cos/SimpleMetaPipeline into main","shortMessageHtmlLink":"Merge branch 'main' of https://github.com/J-Cos/SimpleMetaPipeline in…"}},{"before":"7067dcbd39539641ece2f4b02632a9a93512d81f","after":"a1353d3875b3fbcf43575f4ccabefee52e1012fa","ref":"refs/heads/main","pushedAt":"2023-12-19T14:39:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Update README.md\n\nTypos and clarity","shortMessageHtmlLink":"Update README.md"}},{"before":"c8d0091b466ef5f13da6e8499124b7c8106155e6","after":"7067dcbd39539641ece2f4b02632a9a93512d81f","ref":"refs/heads/main","pushedAt":"2023-11-29T15:01:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Update ControlScriptExample.r\n\nChange default advice for path","shortMessageHtmlLink":"Update ControlScriptExample.r"}},{"before":"ccca198e1497f7bfe42194c38a7cc8371c480415","after":"c8d0091b466ef5f13da6e8499124b7c8106155e6","ref":"refs/heads/main","pushedAt":"2023-11-27T16:07:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"eb6b11e479c0bac48d3bab82baf28205ad4c81dd","after":"ccca198e1497f7bfe42194c38a7cc8371c480415","ref":"refs/heads/main","pushedAt":"2023-11-20T16:05:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Update README.md\n\nReorder getting started instructions","shortMessageHtmlLink":"Update README.md"}},{"before":"7559d1d23bcb338e1a35111546d27c231f46ac09","after":"eb6b11e479c0bac48d3bab82baf28205ad4c81dd","ref":"refs/heads/main","pushedAt":"2023-11-20T16:00:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Update README.md\n\nAdd warning block quotes around macOS guidance","shortMessageHtmlLink":"Update README.md"}},{"before":"af42a49ea200f100becc284305222856ae32bbc9","after":"7559d1d23bcb338e1a35111546d27c231f46ac09","ref":"refs/heads/main","pushedAt":"2023-11-20T15:50:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Update README.md\n\nAdd instructions and code for installation (including guidance for macOS)","shortMessageHtmlLink":"Update README.md"}},{"before":"089d393ba4c001a503a1d58465794b52a706fc04","after":"af42a49ea200f100becc284305222856ae32bbc9","ref":"refs/heads/main","pushedAt":"2023-11-18T11:14:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Fix runBlast bug","shortMessageHtmlLink":"Fix runBlast bug"}},{"before":"8fe72070b7cdc0ff6e06cde8ae18ad4e68074aa3","after":"089d393ba4c001a503a1d58465794b52a706fc04","ref":"refs/heads/main","pushedAt":"2023-11-17T12:41:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"set standard path in example control script","shortMessageHtmlLink":"set standard path in example control script"}},{"before":"9c4e902ab5878a5a57f53ed903234c011c23767f","after":"8fe72070b7cdc0ff6e06cde8ae18ad4e68074aa3","ref":"refs/heads/main","pushedAt":"2023-11-17T12:32:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"set CreateMatchlistForLulu to maxhits=10","shortMessageHtmlLink":"set CreateMatchlistForLulu to maxhits=10"}},{"before":"94071dc58372813013649bc594be2aad89cf8df8","after":"9c4e902ab5878a5a57f53ed903234c011c23767f","ref":"refs/heads/main","pushedAt":"2023-11-17T12:29:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"update to always start pipeline in BioinformaticPipeline_Env","shortMessageHtmlLink":"update to always start pipeline in BioinformaticPipeline_Env"}},{"before":"5fa3433d89b9c50508329f3020e97b3839d8c6d9","after":"94071dc58372813013649bc594be2aad89cf8df8","ref":"refs/heads/main","pushedAt":"2023-11-17T11:55:54.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"update readme\n\nimprove results guidance","shortMessageHtmlLink":"update readme"}},{"before":"38dc15e9f25df1395cbfa1f7eba01d29592cf1cc","after":"5fa3433d89b9c50508329f3020e97b3839d8c6d9","ref":"refs/heads/main","pushedAt":"2023-11-17T11:18:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"update readme\n\nCorrect directory structure presentation","shortMessageHtmlLink":"update readme"}},{"before":"576230ac5e8f71ce2454e9bab294dd875170b0b7","after":"38dc15e9f25df1395cbfa1f7eba01d29592cf1cc","ref":"refs/heads/main","pushedAt":"2023-11-17T11:15:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Improve guidance","shortMessageHtmlLink":"Improve guidance"}},{"before":"eff0722a59c16961b183889ebcf51e692eff6984","after":"576230ac5e8f71ce2454e9bab294dd875170b0b7","ref":"refs/heads/main","pushedAt":"2023-11-17T10:51:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"remove HPC argument","shortMessageHtmlLink":"remove HPC argument"}},{"before":"d1dfaccb93e3a006b421e2d5153c7e4259b0db56","after":"eff0722a59c16961b183889ebcf51e692eff6984","ref":"refs/heads/main","pushedAt":"2023-11-17T10:28:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Update README.md\n\nAlways singular \"BioinformaticPipeline\"","shortMessageHtmlLink":"Update README.md"}},{"before":"4741635e3a5eb30d8029cb4ffa3ddbd86516e414","after":"d1dfaccb93e3a006b421e2d5153c7e4259b0db56","ref":"refs/heads/main","pushedAt":"2023-11-17T10:25:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Merge branch 'main' of https://github.com/J-Cos/SimpleMetaPipeline into main","shortMessageHtmlLink":"Merge branch 'main' of https://github.com/J-Cos/SimpleMetaPipeline in…"}},{"before":"76b95b17be7737f9fa6648cebba9c3430ae14bc2","after":"4741635e3a5eb30d8029cb4ffa3ddbd86516e414","ref":"refs/heads/main","pushedAt":"2023-11-17T10:20:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"fd682fc156b1e3cd80ab00f8ac0036d4a45bf4aa","after":"76b95b17be7737f9fa6648cebba9c3430ae14bc2","ref":"refs/heads/main","pushedAt":"2023-11-17T10:18:37.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"a9706959118b5d064dae0b731ac1da3ed72b047e","after":"fd682fc156b1e3cd80ab00f8ac0036d4a45bf4aa","ref":"refs/heads/main","pushedAt":"2023-11-17T10:10:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Update README.md\n\nfix code presentation","shortMessageHtmlLink":"Update README.md"}},{"before":"ded6d9116ce0d3ea7c555132e5364887251056cc","after":"a9706959118b5d064dae0b731ac1da3ed72b047e","ref":"refs/heads/main","pushedAt":"2023-11-17T10:06:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Adjust pipeline installation for conda environment.yml","shortMessageHtmlLink":"Adjust pipeline installation for conda environment.yml"}},{"before":"6cad2a2851eb8249410fc11b4c072475624a369e","after":"ded6d9116ce0d3ea7c555132e5364887251056cc","ref":"refs/heads/main","pushedAt":"2023-10-05T09:21:10.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Add option to locate fastqs externally\n\nenables use of RDS on an HPC or an external storage device for large datasets. Also remove loadFastq function, recognised to be no longer needed.","shortMessageHtmlLink":"Add option to locate fastqs externally"}},{"before":"53a89e6bd19ef8078e976ac4dd01d83f15bdd404","after":"6cad2a2851eb8249410fc11b4c072475624a369e","ref":"refs/heads/main","pushedAt":"2023-09-19T13:59:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"J-Cos","name":"Jake Williams","path":"/J-Cos","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/72385600?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEQvGPxQA","startCursor":null,"endCursor":null}},"title":"Activity · J-Cos/SimpleMetaPipeline"}