{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":227841530,"defaultBranch":"hl","name":"MIRACUM-Pipe","ownerLogin":"buschlab","currentUserCanPush":false,"isFork":true,"isEmpty":false,"createdAt":"2019-12-13T13:02:10.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/41995646?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1727093064.0","currentOid":""},"activityList":{"items":[{"before":null,"after":"3cd3a40768fd6e39d856ecfbac843829cedfe420","ref":"refs/heads/hl","pushedAt":"2024-09-23T12:04:24.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"don\"t use soft clipped bases for calling and fix possible vep crash","shortMessageHtmlLink":"don\"t use soft clipped bases for calling and fix possible vep crash"}},{"before":"392c3c6887f982bf2940c5e4b4f887e24a90d8a4","after":"3cd3a40768fd6e39d856ecfbac843829cedfe420","ref":"refs/heads/removeVarScan","pushedAt":"2024-07-15T12:11:17.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"don\"t use soft clipped bases for calling and fix possible vep crash","shortMessageHtmlLink":"don\"t use soft clipped bases for calling and fix possible vep crash"}},{"before":"033c3a40c0bfb2e93f7d02ec6a5ca3fdef5ac142","after":"392c3c6887f982bf2940c5e4b4f887e24a90d8a4","ref":"refs/heads/removeVarScan","pushedAt":"2024-07-08T16:00:15.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"fix report if no cnvs found","shortMessageHtmlLink":"fix report if no cnvs found"}},{"before":"012e378a71642980368e65d32a01aa9cc1aa956b","after":"033c3a40c0bfb2e93f7d02ec6a5ca3fdef5ac142","ref":"refs/heads/removeVarScan","pushedAt":"2024-06-10T13:37:26.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"use up to date gene names","shortMessageHtmlLink":"use up to date gene names"}},{"before":"3ca63aa0a04a36a2fd797166268c5fe19eaf7423","after":"012e378a71642980368e65d32a01aa9cc1aa956b","ref":"refs/heads/removeVarScan","pushedAt":"2024-05-31T14:28:00.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"cleanup","shortMessageHtmlLink":"cleanup"}},{"before":"0b1bb8e5d507a5a40f3966675f0fdc690158f752","after":"3ca63aa0a04a36a2fd797166268c5fe19eaf7423","ref":"refs/heads/removeVarScan","pushedAt":"2024-05-29T12:44:18.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"prec 2 on vaf","shortMessageHtmlLink":"prec 2 on vaf"}},{"before":"fa056528979ebd6a330ab3080a12ecc13028c775","after":"0b1bb8e5d507a5a40f3966675f0fdc690158f752","ref":"refs/heads/removeVarScan","pushedAt":"2024-05-28T07:37:34.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"fix genotyping","shortMessageHtmlLink":"fix genotyping"}},{"before":"90ba6354222328b0f179fbe5c34824ea394010d4","after":"fa056528979ebd6a330ab3080a12ecc13028c775","ref":"refs/heads/removeVarScan","pushedAt":"2024-05-14T11:18:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"fix germline calling","shortMessageHtmlLink":"fix germline calling"}},{"before":"82f3eda718f950b25eae3c2386d706c2e93ecfbf","after":"90ba6354222328b0f179fbe5c34824ea394010d4","ref":"refs/heads/removeVarScan","pushedAt":"2024-05-02T07:03:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"remove pileup files after cnv","shortMessageHtmlLink":"remove pileup files after cnv"}},{"before":"ac323425aba0faf4c140b2c2c6ba97d4d0b3452c","after":"82f3eda718f950b25eae3c2386d706c2e93ecfbf","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-30T08:40:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"fix loh maf","shortMessageHtmlLink":"fix loh maf"}},{"before":"b5e56c499761e32b3669f48ced321e9140153f73","after":"ac323425aba0faf4c140b2c2c6ba97d4d0b3452c","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-29T15:26:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"fix panel report generation","shortMessageHtmlLink":"fix panel report generation"}},{"before":"b6d7e3dbde7d776ed73238d723fb6d961128dcbb","after":"b5e56c499761e32b3669f48ced321e9140153f73","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-29T08:43:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"fix merge in panel pipeline","shortMessageHtmlLink":"fix merge in panel pipeline"}},{"before":"97a5e50c4dca1e07ed7680ed765f259f973aad40","after":"b6d7e3dbde7d776ed73238d723fb6d961128dcbb","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-25T21:12:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"fix tumorOnly and panel pdf report","shortMessageHtmlLink":"fix tumorOnly and panel pdf report"}},{"before":"2fb5bfcb32a7bc0404cd4d0435934d528b5bd286","after":"97a5e50c4dca1e07ed7680ed765f259f973aad40","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-25T08:43:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"fix GetPileupSummaries in panel and tumorOnly","shortMessageHtmlLink":"fix GetPileupSummaries in panel and tumorOnly"}},{"before":"08df6e4b56ba40f2a0148500c4dea1208f7ac9b6","after":"2fb5bfcb32a7bc0404cd4d0435934d528b5bd286","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-24T17:37:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"cleanup output of r scripts","shortMessageHtmlLink":"cleanup output of r scripts"}},{"before":"a2da9ea70202fc796e150b821d2e8a068f6f6a27","after":"08df6e4b56ba40f2a0148500c4dea1208f7ac9b6","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-24T15:57:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"apply filter learning to tumoronly and panel","shortMessageHtmlLink":"apply filter learning to tumoronly and panel"}},{"before":"3c849f29f98520f0029077d28f3d63ff03bb26b9","after":"a2da9ea70202fc796e150b821d2e8a068f6f6a27","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-24T15:08:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"remove mane","shortMessageHtmlLink":"remove mane"}},{"before":"dd0b7eeeef1a76460fbf9bba7c06e294e8755dd8","after":"3c849f29f98520f0029077d28f3d63ff03bb26b9","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-24T12:25:41.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"cleanup","shortMessageHtmlLink":"cleanup"}},{"before":"adf30baa20bfc6112f37f207832538e8f346cfbf","after":"dd0b7eeeef1a76460fbf9bba7c06e294e8755dd8","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-24T12:25:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"more mutect filtering","shortMessageHtmlLink":"more mutect filtering"}},{"before":"b30dcb94b55728b1fe23a1365cb09753892ece36","after":"adf30baa20bfc6112f37f207832538e8f346cfbf","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-24T07:53:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"fix xls import","shortMessageHtmlLink":"fix xls import"}},{"before":"4615b713ae41f378c17f99c56be34335323f60fd","after":"b30dcb94b55728b1fe23a1365cb09753892ece36","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-23T13:16:59.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"fix python packages for bam-matcher","shortMessageHtmlLink":"fix python packages for bam-matcher"}},{"before":"55d2d499752d69e4bcaf2ad3681e816b75e198de","after":"4615b713ae41f378c17f99c56be34335323f60fd","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-23T09:12:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"deactivate conda","shortMessageHtmlLink":"deactivate conda"}},{"before":"61cfba135b433f25d8e6c915d3c45dd35f9f15e5","after":"55d2d499752d69e4bcaf2ad3681e816b75e198de","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-23T05:45:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"fix sequenza for python 3.11","shortMessageHtmlLink":"fix sequenza for python 3.11"}},{"before":"9d7883a11627ccc2f2c7d9bfc53759b00cac1448","after":"61cfba135b433f25d8e6c915d3c45dd35f9f15e5","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-22T16:33:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"fix python call for gatk4","shortMessageHtmlLink":"fix python call for gatk4"}},{"before":"f20582aa65d73ed5dc05706c0b600c5cd4c8580d","after":"9d7883a11627ccc2f2c7d9bfc53759b00cac1448","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-22T16:23:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"select correct transcript in vcf2maf","shortMessageHtmlLink":"select correct transcript in vcf2maf"}},{"before":"82038f341b4089b945db188fd5298df31882a7d0","after":"f20582aa65d73ed5dc05706c0b600c5cd4c8580d","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-22T10:07:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"happy python3","shortMessageHtmlLink":"happy python3"}},{"before":"c0839ae4ce12463dc2631304f0fb7e231ab98bea","after":"82038f341b4089b945db188fd5298df31882a7d0","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-22T09:59:35.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"remove python2","shortMessageHtmlLink":"remove python2"}},{"before":"956fc6b3712c0cc0abd4a30a65457f3330395b63","after":"c0839ae4ce12463dc2631304f0fb7e231ab98bea","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-22T09:56:04.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"remove python2","shortMessageHtmlLink":"remove python2"}},{"before":"714639537014bf632f7a622dd1fbf170c468002d","after":"956fc6b3712c0cc0abd4a30a65457f3330395b63","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-22T09:50:38.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"use fastqcr for stats","shortMessageHtmlLink":"use fastqcr for stats"}},{"before":"c76ecaa8e376ccebad8141e12624b97856961fea","after":"714639537014bf632f7a622dd1fbf170c468002d","ref":"refs/heads/removeVarScan","pushedAt":"2024-04-21T16:19:28.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"nr23730","name":"Niklas Reimer","path":"/nr23730","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/20756025?s=80&v=4"},"commit":{"message":"downgrade picard","shortMessageHtmlLink":"downgrade picard"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0yM1QxMjowNDoyNC4wMDAwMDBazwAAAAS96mGw","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wNC0yMVQxNjoxOToyOC4wMDAwMDBazwAAAAQ2V6ba"}},"title":"Activity ยท buschlab/MIRACUM-Pipe"}