{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":645789299,"defaultBranch":"main","name":"laava","ownerLogin":"formbio","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2023-05-26T12:44:13.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/84826452?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1722962088.0","currentOid":""},"activityList":{"items":[{"before":"a44ac803c15673ac3eb5f2d1362305867eff9407","after":"d7c8991eb736985f781193354cc1d9b7140c56b3","ref":"refs/heads/schema3-tsv","pushedAt":"2024-09-09T15:48:24.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Makefile: also execute local test jobs with \"make all\"","shortMessageHtmlLink":"Makefile: also execute local test jobs with \"make all\""}},{"before":"0e8f1cf6f52fc6170fdfba9c4d8fe7c0ee4e5a61","after":"a44ac803c15673ac3eb5f2d1362305867eff9407","ref":"refs/heads/schema3-tsv","pushedAt":"2024-09-08T19:30:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"report: update definitions, titles and section order\n\n- Fix ordering of table rows and plot categories\n- Streamline flip/flop code; unstack the bar plot","shortMessageHtmlLink":"report: update definitions, titles and section order"}},{"before":"a6c6b0580516b83c9c35c7a336b147563024af0c","after":"0e8f1cf6f52fc6170fdfba9c4d8fe7c0ee4e5a61","ref":"refs/heads/schema3-tsv","pushedAt":"2024-09-06T17:58:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Classify left/right-snapback under ssAAV\n\nAlso in ssAAV context:\n- Classify partial in + and - strands as other-vector:snapback (for now)\n- Classify other +/- orientation not otherwise accounted for as\n \"unclassified\"","shortMessageHtmlLink":"Classify left/right-snapback under ssAAV"}},{"before":"9b2b7c03a74f5819545f430e2734543846f1a378","after":"a6c6b0580516b83c9c35c7a336b147563024af0c","ref":"refs/heads/schema3-tsv","pushedAt":"2024-09-06T17:41:15.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Compress alignments.tsv and per_read.tsv with gzip (closes #56)\n\nRename nonmatch_stat.tsv.gz to nonmatch.tsv.gz","shortMessageHtmlLink":"Compress alignments.tsv and per_read.tsv with gzip (closes #56)"}},{"before":"90626734468a5031c943832e8ad9bd1a727f7ea2","after":"9b2b7c03a74f5819545f430e2734543846f1a378","ref":"refs/heads/schema3-tsv","pushedAt":"2024-09-05T22:15:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Compress alignments.tsv and per_read.tsv with gzip (closes #56)\n\nRename nonmatch_stat.tsv.gz to nonmatch.tsv.gz","shortMessageHtmlLink":"Compress alignments.tsv and per_read.tsv with gzip (closes #56)"}},{"before":"05a7918b6c76f799bef14dc7a8fbd694f3deaab9","after":"90626734468a5031c943832e8ad9bd1a727f7ea2","ref":"refs/heads/schema3-tsv","pushedAt":"2024-09-05T16:49:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Add \"strand\" column to alignments.tsv (closes #32)","shortMessageHtmlLink":"Add \"strand\" column to alignments.tsv (closes #32)"}},{"before":"f369155978464577c62d1e588f628c418dd83c3e","after":"05a7918b6c76f799bef14dc7a8fbd694f3deaab9","ref":"refs/heads/schema3-tsv","pushedAt":"2024-09-03T23:27:01.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"summarize_alignment: emit subset BAMs based on given vector_type\n\ni.e. don't emit \"ssAAV\" subset BAMs for a scAAV vector; they'll always\nbe empty.","shortMessageHtmlLink":"summarize_alignment: emit subset BAMs based on given vector_type"}},{"before":"039f75351a12b53211e0449dcb08b2de42ee242f","after":"f369155978464577c62d1e588f628c418dd83c3e","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-29T23:38:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Pass through unlabeled reference names to the report\n\nPreviously they were left out of annotation.txt and therefore dropped by\nthe scripts that relied on it for reference names/labels.","shortMessageHtmlLink":"Pass through unlabeled reference names to the report"}},{"before":"4e7f179c6e16b0f68ef2cc0002be3297e293e790","after":"039f75351a12b53211e0449dcb08b2de42ee242f","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-28T00:34:39.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"summary.tsv: Rename column \"read_ref_label\" to \"reference_label\"","shortMessageHtmlLink":"summary.tsv: Rename column \"read_ref_label\" to \"reference_label\""}},{"before":"0d9bdbb1df1c3992d8280b5abccc5281ebe131fc","after":"4e7f179c6e16b0f68ef2cc0002be3297e293e790","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-23T21:57:07.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"report: fix type/subtype tables and plots\n\n- Sort Table 1 by reference label, then frequency (so all vectors are\n together)\n- Show Figure 1 as a stacked bar chart, stacking by assigned type\n- Show all subtypes in a single line plot","shortMessageHtmlLink":"report: fix type/subtype tables and plots"}},{"before":"e8835cea055fdb8fdf55f40e0e1c73fcb4cc4bfe","after":"0d9bdbb1df1c3992d8280b5abccc5281ebe131fc","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-23T20:32:02.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"report: fix type/subtype tables and plots","shortMessageHtmlLink":"report: fix type/subtype tables and plots"}},{"before":"60d19d471814bc335a58b0795a6ee78ae7df9884","after":"e8835cea055fdb8fdf55f40e0e1c73fcb4cc4bfe","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-23T16:03:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Makefile: add deployment command \"make formbio\"","shortMessageHtmlLink":"Makefile: add deployment command \"make formbio\""}},{"before":"cabce62eaa78c1380390e4722075659d5d8956b9","after":"60d19d471814bc335a58b0795a6ee78ae7df9884","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-22T20:06:49.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Makefile: don't clean test/build, that's another Makefile's job","shortMessageHtmlLink":"Makefile: don't clean test/build, that's another Makefile's job"}},{"before":"1c2006f260c963a7090552d427ee59c01ad9f518","after":"cabce62eaa78c1380390e4722075659d5d8956b9","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-20T22:13:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Implement new read classification scheme; remove readsummary.tsv\n\nalignments.tsv changes:\n- Rename column 'map_type' to 'map_ref_label'\n- Rename column 'map_subtype' to 'map_target_overlap'\n\nper_read.tsv changes:\n- Add columns 'read_ref_label' and 'read_target_overlap'\n- Repurpose columns 'assigned_type' and 'assigned_subtype' to use the\n more detailed new nomenclature, which depends on the given\n `vector_type`\n\nUpdate calculate_rdata.R and report.Rmd to handle the new TSV columns\nsomewhat. Further report changes will be needed to display the new\nclassification scheme more effectively.","shortMessageHtmlLink":"Implement new read classification scheme; remove readsummary.tsv"}},{"before":"e767fc09a51521cd0e13c42e688c9a9740b9faf8","after":"1c2006f260c963a7090552d427ee59c01ad9f518","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-16T20:21:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"test: also check TSV line counts with 'make test'","shortMessageHtmlLink":"test: also check TSV line counts with 'make test'"}},{"before":"ca9964aab88c103d692df5e1e86f59daf16858f1","after":"e767fc09a51521cd0e13c42e688c9a9740b9faf8","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-16T04:46:46.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Remove summary.tsv output and write alignments.tsv from Python\n\nTSV schema changes from the original alignments.tsv:\n- Rename \"SampleID\" to \"sample_id\"\n- Don't add columns \"start\" and \"end\"; they're identical to the existing\n \"start0\" and \"end1\"","shortMessageHtmlLink":"Remove summary.tsv output and write alignments.tsv from Python"}},{"before":"2c59d318d98defc797abfd102e859ca89e4747dd","after":"ca9964aab88c103d692df5e1e86f59daf16858f1","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-14T00:26:44.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"calculate_rdata: group code by output TSVs","shortMessageHtmlLink":"calculate_rdata: group code by output TSVs"}},{"before":"cce972446c55d1ebcd9ce5ebcf21caa45e199f9e","after":"2c59d318d98defc797abfd102e859ca89e4747dd","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-14T00:20:07.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"calculate_rdata: group code by output TSVs","shortMessageHtmlLink":"calculate_rdata: group code by output TSVs"}},{"before":"9b90a5b2d5fd504f79403b241acec511e43050cf","after":"cce972446c55d1ebcd9ce5ebcf21caa45e199f9e","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-14T00:19:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Fix handling of seq_folder_input","shortMessageHtmlLink":"Fix handling of seq_folder_input"}},{"before":"addba3b11ca9c6a9d06fbab9944130209bc0ec9b","after":"9b90a5b2d5fd504f79403b241acec511e43050cf","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-13T23:57:56.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"calculate_rdata: group code by output TSVs","shortMessageHtmlLink":"calculate_rdata: group code by output TSVs"}},{"before":"25eea70778e3738f7162c065aa48c26341b1d984","after":"addba3b11ca9c6a9d06fbab9944130209bc0ec9b","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-13T23:53:48.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"calculate_rdata: group code by output TSVs","shortMessageHtmlLink":"calculate_rdata: group code by output TSVs"}},{"before":"ab844efca9fa3472514065cc43dea76b55177c71","after":"25eea70778e3738f7162c065aa48c26341b1d984","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-09T15:23:19.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"workflow.json: auto-populate input metadata from folder contents\n\nTake the stem of each filename in the selected folder as the sample\nunique ID for the input metadata TSV. The user can then copy that column\nto the sample display name, if they like.","shortMessageHtmlLink":"workflow.json: auto-populate input metadata from folder contents"}},{"before":null,"after":"ab844efca9fa3472514065cc43dea76b55177c71","ref":"refs/heads/schema3-tsv","pushedAt":"2024-08-06T16:34:48.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Merge pull request #50 from formbio/schema3\n\nRevise input fields and metadata I/O","shortMessageHtmlLink":"Merge pull request #50 from formbio/schema3"}},{"before":"56e0ed4ebf11c6e1fd285c2936a0d604a2b88807","after":null,"ref":"refs/heads/schema3","pushedAt":"2024-08-06T14:55:31.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"}},{"before":"f4fc1b5e7d4aaa210e762d9fcb838f9fd3660a86","after":"ab844efca9fa3472514065cc43dea76b55177c71","ref":"refs/heads/main","pushedAt":"2024-08-06T14:55:27.000Z","pushType":"pr_merge","commitsCount":13,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Merge pull request #50 from formbio/schema3\n\nRevise input fields and metadata I/O","shortMessageHtmlLink":"Merge pull request #50 from formbio/schema3"}},{"before":"4943b7933ac371550dc5d071095244e403c9c302","after":"56e0ed4ebf11c6e1fd285c2936a0d604a2b88807","ref":"refs/heads/schema3","pushedAt":"2024-07-31T17:50:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"prepare_annotation: update docstring to reflect ITR vs 'vector'","shortMessageHtmlLink":"prepare_annotation: update docstring to reflect ITR vs 'vector'"}},{"before":"0c3ed25ea1099ee653d057cb9835a26f29125873","after":"4943b7933ac371550dc5d071095244e403c9c302","ref":"refs/heads/schema3","pushedAt":"2024-07-31T17:43:16.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Update workflow input documentation","shortMessageHtmlLink":"Update workflow input documentation"}},{"before":"5e38d16bbbad140a1476530a8554fcce9f13e59b","after":"0c3ed25ea1099ee653d057cb9835a26f29125873","ref":"refs/heads/schema3","pushedAt":"2024-07-31T15:30:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Update workflow input documentation","shortMessageHtmlLink":"Update workflow input documentation"}},{"before":"fe9a234b397a4ec32a94df66e49eab799f261eb2","after":"5e38d16bbbad140a1476530a8554fcce9f13e59b","ref":"refs/heads/schema3","pushedAt":"2024-07-31T05:39:38.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"Use get_reference_names.py in Nextflow; fix issues (#47; closes #31)","shortMessageHtmlLink":"Use get_reference_names.py in Nextflow; fix issues (#47; closes #31)"}},{"before":"6e1447522fe2123f7e76bff800d5c23f6ee08af6","after":"fe9a234b397a4ec32a94df66e49eab799f261eb2","ref":"refs/heads/schema3","pushedAt":"2024-07-30T00:38:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"etal","name":"Eric Talevich","path":"/etal","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/52723?s=80&v=4"},"commit":{"message":"prepare_annotation: Take and use input ITR labels","shortMessageHtmlLink":"prepare_annotation: Take and use input ITR labels"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEsRc9iAA","startCursor":null,"endCursor":null}},"title":"Activity ยท formbio/laava"}