{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":75911147,"defaultBranch":"master","name":"megSAP","ownerLogin":"imgag","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2016-12-08T06:46:58.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/18442622?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1726035265.0","currentOid":""},"activityList":{"items":[{"before":"46d0e1788099c2d1bd3a7dcc278324de47e0741a","after":"dee8a705917f1f96b26b1d0fbd8ba81f8813528f","ref":"refs/heads/master","pushedAt":"2024-09-12T08:14:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marc-sturm","name":"Marc Sturm","path":"/marc-sturm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5638144?s=80&v=4"},"commit":{"message":"Updated ngs-bits version","shortMessageHtmlLink":"Updated ngs-bits version"}},{"before":"76905f2527da80024e22ffe65581898a9689437c","after":"46d0e1788099c2d1bd3a7dcc278324de47e0741a","ref":"refs/heads/master","pushedAt":"2024-09-12T05:46:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marc-sturm","name":"Marc Sturm","path":"/marc-sturm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5638144?s=80&v=4"},"commit":{"message":"merge_gvcf: replaced bcftools by ngs-bits","shortMessageHtmlLink":"merge_gvcf: replaced bcftools by ngs-bits"}},{"before":"db39619473636379a015abf1cdf78859a6f936ef","after":"76905f2527da80024e22ffe65581898a9689437c","ref":"refs/heads/master","pushedAt":"2024-09-12T05:11:42.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marc-sturm","name":"Marc Sturm","path":"/marc-sturm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5638144?s=80&v=4"},"commit":{"message":"REVEL score now has 3 decimal places","shortMessageHtmlLink":"REVEL score now has 3 decimal places"}},{"before":"fba10500d3d4463532790009480bc33ce0cc64e2","after":"0dcd2dee9b0116635a3b3f37afa9b4421e344a9e","ref":"refs/heads/containerize_tools","pushedAt":"2024-09-11T11:49:51.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"KilianIlius","name":null,"path":"/KilianIlius","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/77616357?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'remotes/origin/master' into containerize_tools","shortMessageHtmlLink":"Merge remote-tracking branch 'remotes/origin/master' into containeriz…"}},{"before":"dd842b7ba9b550cf4ed22e21adbfee9b7acf6440","after":"fba10500d3d4463532790009480bc33ce0cc64e2","ref":"refs/heads/containerize_tools","pushedAt":"2024-09-11T11:46:06.000Z","pushType":"push","commitsCount":10,"pusher":{"login":"KilianIlius","name":null,"path":"/KilianIlius","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/77616357?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'remotes/origin/master' into containerize_tools","shortMessageHtmlLink":"Merge remote-tracking branch 'remotes/origin/master' into containeriz…"}},{"before":"69b4ffbd22f77135ff11511beefa656e0b4ad0b3","after":"db39619473636379a015abf1cdf78859a6f936ef","ref":"refs/heads/master","pushedAt":"2024-09-11T10:58:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marc-sturm","name":"Marc Sturm","path":"/marc-sturm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5638144?s=80&v=4"},"commit":{"message":"Updated citing section.","shortMessageHtmlLink":"Updated citing section."}},{"before":"fb9637e59a06a58f49d6f056fd9d31bbd6ec82d6","after":"dd842b7ba9b550cf4ed22e21adbfee9b7acf6440","ref":"refs/heads/containerize_tools","pushedAt":"2024-09-11T10:54:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"KilianIlius","name":null,"path":"/KilianIlius","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/77616357?s=80&v=4"},"commit":{"message":"added samblaster container","shortMessageHtmlLink":"added samblaster container"}},{"before":"5eb4c2a943641dae9c1c7685eaed83bd4ccfa5d9","after":"69b4ffbd22f77135ff11511beefa656e0b4ad0b3","ref":"refs/heads/master","pushedAt":"2024-09-10T19:02:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marc-sturm","name":"Marc Sturm","path":"/marc-sturm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5638144?s=80&v=4"},"commit":{"message":"Added missing reference genome parameters of ngs-bits tools","shortMessageHtmlLink":"Added missing reference genome parameters of ngs-bits tools"}},{"before":"7c2ad046fd6eca9d6e3d47ecc730949c2c8c2540","after":"fb9637e59a06a58f49d6f056fd9d31bbd6ec82d6","ref":"refs/heads/containerize_tools","pushedAt":"2024-09-10T12:56:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"KilianIlius","name":null,"path":"/KilianIlius","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/77616357?s=80&v=4"},"commit":{"message":"added vcflib, gatk, abra2 and clincnv container. Added ngs-bits settings.ini mount functionallity as well as execSingularity command_only option","shortMessageHtmlLink":"added vcflib, gatk, abra2 and clincnv container. Added ngs-bits setti…"}},{"before":"b148ff95014d8a3858a179a39940e72e924c99c7","after":"5eb4c2a943641dae9c1c7685eaed83bd4ccfa5d9","ref":"refs/heads/master","pushedAt":"2024-09-10T10:46:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marc-sturm","name":"Marc Sturm","path":"/marc-sturm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5638144?s=80&v=4"},"commit":{"message":"fixed typos","shortMessageHtmlLink":"fixed typos"}},{"before":"239ac8e1bf2fbe1a218c5c4acff785476e06f73a","after":"b148ff95014d8a3858a179a39940e72e924c99c7","ref":"refs/heads/master","pushedAt":"2024-09-10T07:12:20.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"Ott-Alexander","name":"Alexander Ott","path":"/Ott-Alexander","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/30521779?s=80&v=4"},"commit":{"message":"Merge branch 'master' of https://github.com/imgag/megSAP","shortMessageHtmlLink":"Merge branch 'master' of https://github.com/imgag/megSAP"}},{"before":"02f114f0313670840617f703acce621f1518496d","after":"239ac8e1bf2fbe1a218c5c4acff785476e06f73a","ref":"refs/heads/master","pushedAt":"2024-09-10T06:26:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marc-sturm","name":"Marc Sturm","path":"/marc-sturm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5638144?s=80&v=4"},"commit":{"message":"updated docu for release 2024_09","shortMessageHtmlLink":"updated docu for release 2024_09"}},{"before":"0d724e29dfe91b90b2fca5e456447225db09824e","after":"02f114f0313670840617f703acce621f1518496d","ref":"refs/heads/master","pushedAt":"2024-09-10T06:23:06.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marc-sturm","name":"Marc Sturm","path":"/marc-sturm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5638144?s=80&v=4"},"commit":{"message":"updated db download scripts","shortMessageHtmlLink":"updated db download scripts"}},{"before":"d735ef88d39248ebba49c525cd04f5de5168a2da","after":"0d724e29dfe91b90b2fca5e456447225db09824e","ref":"refs/heads/master","pushedAt":"2024-09-09T13:20:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marc-sturm","name":"Marc Sturm","path":"/marc-sturm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5638144?s=80&v=4"},"commit":{"message":"updated tool download scripts","shortMessageHtmlLink":"updated tool download scripts"}},{"before":"6768396d3ff850da8e9edf26d757ab97ab46b599","after":"d735ef88d39248ebba49c525cd04f5de5168a2da","ref":"refs/heads/master","pushedAt":"2024-09-09T08:18:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leonschuetz","name":"Leon Schütz","path":"/leonschuetz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11536499?s=80&v=4"},"commit":{"message":"data/download_tools_longread.sh: added StraglrOn\n\nsrc/NGS/runqc_parser_ont.php: allow manual exclusion of analysis folders","shortMessageHtmlLink":"data/download_tools_longread.sh: added StraglrOn"}},{"before":"590677537a443bfdba8b9117e031235ed5c01282","after":"6768396d3ff850da8e9edf26d757ab97ab46b599","ref":"refs/heads/master","pushedAt":"2024-09-09T07:35:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marc-sturm","name":"Marc Sturm","path":"/marc-sturm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5638144?s=80&v=4"},"commit":{"message":"CNV analysis: coverage profile is now re-created every time","shortMessageHtmlLink":"CNV analysis: coverage profile is now re-created every time"}},{"before":"3eb3ffdc02657eba015057afe7ec44178e944c13","after":"7c2ad046fd6eca9d6e3d47ecc730949c2c8c2540","ref":"refs/heads/containerize_tools","pushedAt":"2024-09-06T10:27:11.000Z","pushType":"push","commitsCount":75,"pusher":{"login":"KilianIlius","name":null,"path":"/KilianIlius","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/77616357?s=80&v=4"},"commit":{"message":"Merge remote-tracking branch 'remotes/origin/master' into containerize_tools","shortMessageHtmlLink":"Merge remote-tracking branch 'remotes/origin/master' into containeriz…"}},{"before":"c6d50593fb1c2565a2d6be32f6ca27ae79def060","after":"3eb3ffdc02657eba015057afe7ec44178e944c13","ref":"refs/heads/containerize_tools","pushedAt":"2024-09-06T09:58:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"KilianIlius","name":null,"path":"/KilianIlius","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/77616357?s=80&v=4"},"commit":{"message":"built and implemented vep, circos, ClinCNV and ExpansionHunter container","shortMessageHtmlLink":"built and implemented vep, circos, ClinCNV and ExpansionHunter container"}},{"before":"cc1bd7e5cebdff09f92d349ed15fca169b75e013","after":"590677537a443bfdba8b9117e031235ed5c01282","ref":"refs/heads/master","pushedAt":"2024-09-06T09:11:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"Ott-Alexander","name":"Alexander Ott","path":"/Ott-Alexander","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/30521779?s=80&v=4"},"commit":{"message":"update installation from mantis to msisensor-pro","shortMessageHtmlLink":"update installation from mantis to msisensor-pro"}},{"before":"3fe5a00854d7798983c40cd4ed942cc8bd3c73b0","after":"c6d50593fb1c2565a2d6be32f6ca27ae79def060","ref":"refs/heads/containerize_tools","pushedAt":"2024-09-04T12:32:09.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"KilianIlius","name":null,"path":"/KilianIlius","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/77616357?s=80&v=4"},"commit":{"message":"updated bind path handling and implemented bwa-mem2, ngs-bits, umiVar, longphase and freebayes container","shortMessageHtmlLink":"updated bind path handling and implemented bwa-mem2, ngs-bits, umiVar…"}},{"before":"15580989d666c345b3ce105676e7d9eadfe9bdae","after":"cc1bd7e5cebdff09f92d349ed15fca169b75e013","ref":"refs/heads/master","pushedAt":"2024-09-04T12:24:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marc-sturm","name":"Marc Sturm","path":"/marc-sturm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5638144?s=80&v=4"},"commit":{"message":"updated low mappabilty regions: updated genes for WES, genome with masked false duplications for WGS","shortMessageHtmlLink":"updated low mappabilty regions: updated genes for WES, genome with ma…"}},{"before":"0fff80732c92e3fb7946cb27e8e3d81a9f52a098","after":"15580989d666c345b3ce105676e7d9eadfe9bdae","ref":"refs/heads/master","pushedAt":"2024-09-04T11:16:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leonschuetz","name":"Leon Schütz","path":"/leonschuetz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11536499?s=80&v=4"},"commit":{"message":"src/Tools/merge_samples.php: added build parameter (required to get methylation info)","shortMessageHtmlLink":"src/Tools/merge_samples.php: added build parameter (required to get m…"}},{"before":"39d610bbc4fb06cd19b059985bc210dc44aaa3bc","after":"0fff80732c92e3fb7946cb27e8e3d81a9f52a098","ref":"refs/heads/master","pushedAt":"2024-09-04T08:13:37.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"leonschuetz","name":"Leon Schütz","path":"/leonschuetz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11536499?s=80&v=4"},"commit":{"message":"Merge branch 'master' of https://github.com/imgag/megSAP","shortMessageHtmlLink":"Merge branch 'master' of https://github.com/imgag/megSAP"}},{"before":"c50ad05c742cb092277fbcdeed4eb6f8c86aafe7","after":"39d610bbc4fb06cd19b059985bc210dc44aaa3bc","ref":"refs/heads/master","pushedAt":"2024-09-04T07:36:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marc-sturm","name":"Marc Sturm","path":"/marc-sturm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5638144?s=80&v=4"},"commit":{"message":"docu update","shortMessageHtmlLink":"docu update"}},{"before":"b635ded4b68a179c61a1b5f4e9b493cb6ca11419","after":"c50ad05c742cb092277fbcdeed4eb6f8c86aafe7","ref":"refs/heads/master","pushedAt":"2024-09-02T12:27:12.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"leonschuetz","name":"Leon Schütz","path":"/leonschuetz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11536499?s=80&v=4"},"commit":{"message":"src/NGS/vc_sniffles.php: added optional target region\n\ntest/tool_test_vc_sniffles.php: uses target region to speed up tests\n\ntest/data_longread/Makefile: added offset to qcML to fix tests","shortMessageHtmlLink":"src/NGS/vc_sniffles.php: added optional target region"}},{"before":"0d8e5cd584069f3cfebfc6f2bc85ce4e25d393b9","after":"3fe5a00854d7798983c40cd4ed942cc8bd3c73b0","ref":"refs/heads/containerize_tools","pushedAt":"2024-09-02T08:19:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"KilianIlius","name":null,"path":"/KilianIlius","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/77616357?s=80&v=4"},"commit":{"message":"removed scritps_singularity.php duplicates and implemented whatshap in multisample_longread pipeline. Added workdir removel in execSingularity function in ToolBase.php. Changed dirname() to dirname(realpath()) when determining bind paths for input files.","shortMessageHtmlLink":"removed scritps_singularity.php duplicates and implemented whatshap i…"}},{"before":"c8f66b47656fcb3ed1415204247a6b273ab47ad9","after":"b635ded4b68a179c61a1b5f4e9b493cb6ca11419","ref":"refs/heads/master","pushedAt":"2024-08-30T09:31:26.000Z","pushType":"push","commitsCount":7,"pusher":{"login":"Ott-Alexander","name":"Alexander Ott","path":"/Ott-Alexander","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/30521779?s=80&v=4"},"commit":{"message":"Merge branch 'master' of https://github.com/imgag/megSAP","shortMessageHtmlLink":"Merge branch 'master' of https://github.com/imgag/megSAP"}},{"before":"fc16f3c6ebaaf1e03f8aa883d377da844c683734","after":"c8f66b47656fcb3ed1415204247a6b273ab47ad9","ref":"refs/heads/master","pushedAt":"2024-08-29T05:21:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"marc-sturm","name":"Marc Sturm","path":"/marc-sturm","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5638144?s=80&v=4"},"commit":{"message":"added missing model for Clair3","shortMessageHtmlLink":"added missing model for Clair3"}},{"before":"b94c60b968dacf13d9bb58649e08adbc9bee833f","after":"fc16f3c6ebaaf1e03f8aa883d377da844c683734","ref":"refs/heads/master","pushedAt":"2024-08-28T13:03:12.000Z","pushType":"push","commitsCount":12,"pusher":{"login":"Ott-Alexander","name":"Alexander Ott","path":"/Ott-Alexander","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/30521779?s=80&v=4"},"commit":{"message":"Merge branch 'master' of https://github.com/imgag/megSAP","shortMessageHtmlLink":"Merge branch 'master' of https://github.com/imgag/megSAP"}},{"before":null,"after":"0d8e5cd584069f3cfebfc6f2bc85ce4e25d393b9","ref":"refs/heads/containerize_tools","pushedAt":"2024-08-28T09:36:06.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"KilianIlius","name":null,"path":"/KilianIlius","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/77616357?s=80&v=4"},"commit":{"message":"Initial creation of GitHub branch for the containerization of all pipeline tools. New php scripts, tool_tests and test data for: clair3, manta, straglr, strelka2 and minimap2","shortMessageHtmlLink":"Initial creation of GitHub branch for the containerization of all pip…"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEtBncawA","startCursor":null,"endCursor":null}},"title":"Activity · imgag/megSAP"}