{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":415950509,"defaultBranch":"main","name":"pgsc_calc","ownerLogin":"PGScatalog","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2021-10-11T13:59:45.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/57760981?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1717259171.0","currentOid":""},"activityList":{"items":[{"before":"84009ddaa783edf594938f67f57d05d0e07dc7ae","after":null,"ref":"refs/heads/doc_popsim","pushedAt":"2024-06-01T16:26:11.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"}},{"before":"76fe4a6315809b2d35196e70da2e7fc6d0cd8084","after":null,"ref":"refs/heads/docs","pushedAt":"2024-06-01T16:25:19.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"}},{"before":"c77192b24ea178830946cce6ff07af87acc033bd","after":null,"ref":"refs/heads/2_alpha_5","pushedAt":"2024-06-01T16:25:02.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"}},{"before":"984ebb1d4a04df0144a1ef48168cee6b0ba24a2c","after":"4b18dfb88330759b98dd6869a7a427cf5cf4b52d","ref":"refs/heads/main","pushedAt":"2024-06-01T09:25:42.000Z","pushType":"pr_merge","commitsCount":7,"pusher":{"login":"smlmbrt","name":"Sam Lambert","path":"/smlmbrt","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4139843?s=80&v=4"},"commit":{"message":"Merge pull request #299 from PGScatalog/docs\n\nUpdate containers.rst","shortMessageHtmlLink":"Merge pull request #299 from PGScatalog/docs"}},{"before":"30a34cc84fdf95d52141daa648f480d87cbe7c34","after":"76fe4a6315809b2d35196e70da2e7fc6d0cd8084","ref":"refs/heads/docs","pushedAt":"2024-06-01T09:12:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"smlmbrt","name":"Sam Lambert","path":"/smlmbrt","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4139843?s=80&v=4"},"commit":{"message":"Update main docs with citation","shortMessageHtmlLink":"Update main docs with citation"}},{"before":"279804db68f277776dbcadbe3610880fbcc39cdb","after":"30a34cc84fdf95d52141daa648f480d87cbe7c34","ref":"refs/heads/docs","pushedAt":"2024-06-01T09:07:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"smlmbrt","name":"Sam Lambert","path":"/smlmbrt","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4139843?s=80&v=4"},"commit":{"message":"Update CITATIONS.md with preprint","shortMessageHtmlLink":"Update CITATIONS.md with preprint"}},{"before":"901ded419fcab141220d5db332a7cc4c3078f272","after":"984ebb1d4a04df0144a1ef48168cee6b0ba24a2c","ref":"refs/heads/main","pushedAt":"2024-06-01T09:06:32.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Revert \"Set defaultBranch to v2.0.0-alpha.5 (#306)\"\n\nThis reverts commit 901ded419fcab141220d5db332a7cc4c3078f272.\n\nOdd nextflow behaviour doesn't respect the default branch, I need to investigate further","shortMessageHtmlLink":"Revert \"Set defaultBranch to v2.0.0-alpha.5 (#306)\""}},{"before":"61f20641830dc0ebe4b4724485d209be6e82b2cf","after":"279804db68f277776dbcadbe3610880fbcc39cdb","ref":"refs/heads/docs","pushedAt":"2024-06-01T09:05:43.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"smlmbrt","name":"Sam Lambert","path":"/smlmbrt","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4139843?s=80&v=4"},"commit":{"message":"Add medRxiv to readme","shortMessageHtmlLink":"Add medRxiv to readme"}},{"before":"517a3ae20a19f1ab5cb6555e84648802c43dad92","after":null,"ref":"refs/heads/downgrade-manifest","pushedAt":"2024-06-01T08:53:25.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"}},{"before":"8bdf287d558a7abe1ef86e961337df71d7289d0d","after":"c77192b24ea178830946cce6ff07af87acc033bd","ref":"refs/heads/2_alpha_5","pushedAt":"2024-06-01T08:38:58.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"update defaultBranch","shortMessageHtmlLink":"update defaultBranch"}},{"before":"01980336fcbfc24aafc6553077a1f7c4232ca173","after":"901ded419fcab141220d5db332a7cc4c3078f272","ref":"refs/heads/main","pushedAt":"2024-05-31T16:59:26.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Set defaultBranch to v2.0.0-alpha.5 (#306)\n\ndefaultBranch only supports branches, not tags, so I made a branch with:\r\n\r\n$ git checkout -b 2_alpha_5 v2.0.0-alpha.5","shortMessageHtmlLink":"Set defaultBranch to v2.0.0-alpha.5 (#306)"}},{"before":null,"after":"517a3ae20a19f1ab5cb6555e84648802c43dad92","ref":"refs/heads/downgrade-manifest","pushedAt":"2024-05-30T12:48:03.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Set defaultBranch to v2.0.0-alpha.5\n\ndefaultBranch only supports branches, not tags, so I made a branch with:\r\n\r\n$ git checkout -b 2_alpha_5 v2.0.0-alpha.5","shortMessageHtmlLink":"Set defaultBranch to v2.0.0-alpha.5"}},{"before":null,"after":"8bdf287d558a7abe1ef86e961337df71d7289d0d","ref":"refs/heads/2_alpha_5","pushedAt":"2024-05-30T12:46:39.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Update date in changelog","shortMessageHtmlLink":"Update date in changelog"}},{"before":null,"after":"01980336fcbfc24aafc6553077a1f7c4232ca173","ref":"refs/heads/dev","pushedAt":"2024-05-26T12:05:15.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"smlmbrt","name":"Sam Lambert","path":"/smlmbrt","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4139843?s=80&v=4"},"commit":{"message":"Bump minimum nextflow version to 23.10.0 (#297)\n\n* Update nextflow.config\r\n\r\n* Update README.md\r\n\r\n* Update standard-test.yml\r\n\r\n* Update changelog.rst\r\n\r\n* Update README.md\r\n\r\n* Update standard-test.yml","shortMessageHtmlLink":"Bump minimum nextflow version to 23.10.0 (#297)"}},{"before":"d17c1dbdcb25f4e8dbc1da16ae383ce1e08d1e57","after":"61f20641830dc0ebe4b4724485d209be6e82b2cf","ref":"refs/heads/docs","pushedAt":"2024-05-24T12:54:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"361b27f4a9877fb92bc03394d798f05fc806b0e3","after":"d17c1dbdcb25f4e8dbc1da16ae383ce1e08d1e57","ref":"refs/heads/docs","pushedAt":"2024-05-24T12:44:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Update CITATIONS.md","shortMessageHtmlLink":"Update CITATIONS.md"}},{"before":null,"after":"361b27f4a9877fb92bc03394d798f05fc806b0e3","ref":"refs/heads/docs","pushedAt":"2024-05-24T12:21:50.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Update containers.rst","shortMessageHtmlLink":"Update containers.rst"}},{"before":"4bbf2007ec81078bb1b7bc4f2bdf4a74b7b3cd24","after":null,"ref":"refs/heads/correlation","pushedAt":"2024-05-24T11:11:18.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"}},{"before":"d368a585082a1eb94b060c33d7261e9aeed44993","after":null,"ref":"refs/heads/bump-min-version","pushedAt":"2024-05-24T11:03:40.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"}},{"before":"822e51797e824002df8ead51e8908d36c9aea280","after":"01980336fcbfc24aafc6553077a1f7c4232ca173","ref":"refs/heads/main","pushedAt":"2024-05-24T11:03:36.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Bump minimum nextflow version to 23.10.0 (#297)\n\n* Update nextflow.config\r\n\r\n* Update README.md\r\n\r\n* Update standard-test.yml\r\n\r\n* Update changelog.rst\r\n\r\n* Update README.md\r\n\r\n* Update standard-test.yml","shortMessageHtmlLink":"Bump minimum nextflow version to 23.10.0 (#297)"}},{"before":"732be8c5c29eaf48adcae841ff5c3db1a3a69c78","after":"d368a585082a1eb94b060c33d7261e9aeed44993","ref":"refs/heads/bump-min-version","pushedAt":"2024-05-24T10:40:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Update standard-test.yml","shortMessageHtmlLink":"Update standard-test.yml"}},{"before":"0ad45c41601097af4a3df105a48500d60502d521","after":"732be8c5c29eaf48adcae841ff5c3db1a3a69c78","ref":"refs/heads/bump-min-version","pushedAt":"2024-05-24T10:35:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":"8b5f690eb2dbf8b5ac82e65633b6d04a04ec645c","after":"0ad45c41601097af4a3df105a48500d60502d521","ref":"refs/heads/bump-min-version","pushedAt":"2024-05-24T10:33:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Update changelog.rst","shortMessageHtmlLink":"Update changelog.rst"}},{"before":"c07389a98774bdd9c7a3e72fecc17db3649001c8","after":"8b5f690eb2dbf8b5ac82e65633b6d04a04ec645c","ref":"refs/heads/bump-min-version","pushedAt":"2024-05-24T10:32:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Update standard-test.yml","shortMessageHtmlLink":"Update standard-test.yml"}},{"before":"2a57a143b3632b4b61a969a826cef228a9e852a9","after":"c07389a98774bdd9c7a3e72fecc17db3649001c8","ref":"refs/heads/bump-min-version","pushedAt":"2024-05-24T10:31:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Update README.md","shortMessageHtmlLink":"Update README.md"}},{"before":null,"after":"2a57a143b3632b4b61a969a826cef228a9e852a9","ref":"refs/heads/bump-min-version","pushedAt":"2024-05-24T10:31:04.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Update nextflow.config","shortMessageHtmlLink":"Update nextflow.config"}},{"before":"1321c1ab474f5682da73cdcaf3f74c767ff4e71d","after":"822e51797e824002df8ead51e8908d36c9aea280","ref":"refs/heads/main","pushedAt":"2024-05-24T10:19:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"bump conda minimum version","shortMessageHtmlLink":"bump conda minimum version"}},{"before":"db50fdc5167b03277133a55fb26c1881941a3019","after":null,"ref":"refs/heads/dev","pushedAt":"2024-05-24T09:05:53.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"}},{"before":"8bdf287d558a7abe1ef86e961337df71d7289d0d","after":"1321c1ab474f5682da73cdcaf3f74c767ff4e71d","ref":"refs/heads/main","pushedAt":"2024-05-24T09:05:49.000Z","pushType":"pr_merge","commitsCount":31,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"Merge pull request #274 from PGScatalog/dev\n\n* Check for _ in sampleset names\r\n\r\n* fix samplesheet path to point to VCF\r\n\r\n* drop vcf suffix\r\n\r\n* update tests with removed vcf suffix\r\n\r\n* include inputs when relabelling (geno and sample files are unchanged)\r\n\r\n* add more tests for results structure\r\n\r\n* Expose documentation about switching versions.\r\n\r\n* add cloud / JSON samplesheet docs\r\n\r\n* add multiple chromosomes example\r\n\r\n* add links to JSON samplesheet\r\n\r\n* explicitly set default results to $PWD/results\r\n\r\nthis change affects people running the workflow directly from\r\ngithub, e.g.\r\n\r\n$ nextflow run pgscatalog/pgsc_calc ...\r\n\r\nif --outdir isn't set, then the results folder can be in $NXF_HOME,\r\nwhich is a hidden folder in the home directory by default. not a\r\nhelpful place for results to be!\r\n\r\nthis doesn't affect people running from a cloned repo directly\r\n\r\n* Fix typo in output.rst\r\n\r\n* Add in documentation about popsimilarity file.\r\n\r\n* migrate to pygscatalog utilities (#296)\r\n\r\n* add correlation test\r\n\r\n* add correlation action\r\n\r\n* fix download URL\r\n\r\n* use scoring files from correlation archive\r\n\r\n* get test profile working with pygscatalog\r\n\r\n* integration updates\r\n\r\n* fix correlation scorefile wildcard\r\n\r\n* fix tests\r\n\r\n* update plink2\r\n\r\n* gzip afreq in plink2_vcf\r\n\r\n* update custom scoring files for liftover\r\n\r\n* fix match module test\r\n\r\n* use local files in test suite\r\n\r\n* fix singularity container definition\r\n\r\n* check for environment variables with set -euxo\r\n\r\n* logs are massive, don't upload, debug locally\r\n\r\n* Improve pca (#267)\r\n\r\n* Output allele frequencies along with missingness (for filtering variants)\r\n\r\n* Add afreq to output\r\n\r\n* Add afreq to intersect_variants.nf\r\n\r\n* add afreq to intersect_thinned\r\n\r\n* intersect with new pgscatalog-intersect application\r\n\r\n* rebase\r\n\r\n* Make verbose\r\n\r\n* Remove duplication\r\n\r\n* Use new output of intersect_variants in filtering\r\n\r\n* Use new output of intersect_variants in intersect_variants.nf : keeps memory footprint very low (but higher I/O into tempfiles)\r\n\r\n* Fix column index to PCA_ELIGIBLE (13)\r\n\r\n* Fix awk statement that doesn't work with odd carriage return?\r\n\r\n* Fix awk statement for True/False (not 0/1 as in previous version)\r\n\r\n* Add in variant-based filters\r\n\r\n---------\r\n\r\nCo-authored-by: Benjamin Wingfield \r\n\r\n* remove duplicate container definition (pygscatalog)\r\n\r\n* fix duplicate freq flags\r\n\r\n* bump workflow version\r\n\r\n* don't upload output directory in ancestry tests\r\n\r\n* add docker uid runOption to test config\r\n\r\n* just use working directory as tmpdir\r\n\r\n* drop deprecated docker.userEmulation\r\n\r\n* update upload-artifact to v4\r\n\r\n* fix join failure caused by wrong meta in afreq output (VCF)\r\n\r\n* Superseded by pgscatalog-intersect\r\n\r\n* Update pgscatalog_utils conda environment\r\n\r\n* use stable container tags\r\n\r\n* bump pgscatalog.core version\r\n\r\n---------\r\n\r\nCo-authored-by: Benjamin Wingfield ","shortMessageHtmlLink":"Merge pull request #274 from PGScatalog/dev"}},{"before":"f3f58045869be9ad605f5cf062d1e28c5368402c","after":"db50fdc5167b03277133a55fb26c1881941a3019","ref":"refs/heads/dev","pushedAt":"2024-05-24T08:49:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nebfield","name":"Benjamin Wingfield","path":"/nebfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11425618?s=80&v=4"},"commit":{"message":"docs runthrough","shortMessageHtmlLink":"docs runthrough"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEWc2l-AA","startCursor":null,"endCursor":null}},"title":"Activity ยท PGScatalog/pgsc_calc"}