{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":791275299,"defaultBranch":"main","name":"CAESAR","ownerLogin":"labgem","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2024-04-24T12:24:46.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/50515420?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1726756520.0","currentOid":""},"activityList":{"items":[{"before":"fc4ee973fb5cf87cb7366aec5edf503e483b6c80","after":"1191ffd285fee91763015d3b3fdd1361be990a4d","ref":"refs/heads/main","pushedAt":"2024-09-19T14:24:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"fix: unmasks the --mem option\n\nThe --mem option was hidden for all sub-commands except blastp","shortMessageHtmlLink":"fix: unmasks the --mem option"}},{"before":"5b0400c36baf94ee632e2df4ad38c907b9c99a67","after":"fc4ee973fb5cf87cb7366aec5edf503e483b6c80","ref":"refs/heads/main","pushedAt":"2024-09-19T12:43:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"docs: update README","shortMessageHtmlLink":"docs: update README"}},{"before":"37994afdd80808ba0b21070f8614c148d26709db","after":"5b0400c36baf94ee632e2df4ad38c907b9c99a67","ref":"refs/heads/main","pushedAt":"2024-09-19T07:47:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"feat: adapts the contents of summary file for each subcommand","shortMessageHtmlLink":"feat: adapts the contents of summary file for each subcommand"}},{"before":"d859697d959e30b96a18797fcf6b8098fa165121","after":"37994afdd80808ba0b21070f8614c148d26709db","ref":"refs/heads/main","pushedAt":"2024-09-18T13:03:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"fix: adds error message if no sequences are retained","shortMessageHtmlLink":"fix: adds error message if no sequences are retained"}},{"before":"bff43fac26e7f0169d0018deb95fded601c9235f","after":"d859697d959e30b96a18797fcf6b8098fa165121","ref":"refs/heads/main","pushedAt":"2024-09-18T07:41:16.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"docs: update README.md","shortMessageHtmlLink":"docs: update README.md"}},{"before":"139ae6c055ea022e25ea238aed462b40273391a5","after":"bff43fac26e7f0169d0018deb95fded601c9235f","ref":"refs/heads/main","pushedAt":"2024-09-17T13:27:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"docs: update README.md","shortMessageHtmlLink":"docs: update README.md"}},{"before":"a09d5cb21827812c93805949f169dc930e401fa8","after":"139ae6c055ea022e25ea238aed462b40273391a5","ref":"refs/heads/main","pushedAt":"2024-09-17T13:24:04.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"docs: add CAESAR logo","shortMessageHtmlLink":"docs: add CAESAR logo"}},{"before":"ec5f966b215033624adf25939fe22370fef8571d","after":"a09d5cb21827812c93805949f169dc930e401fa8","ref":"refs/heads/main","pushedAt":"2024-09-17T13:21:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"refactor: update help message","shortMessageHtmlLink":"refactor: update help message"}},{"before":"f8132fa428847ca4d992d9842adb49a6d8c187ac","after":"ec5f966b215033624adf25939fe22370fef8571d","ref":"refs/heads/main","pushedAt":"2024-09-17T13:20:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"feat: can write a hmm score column in all_candidates.tsv","shortMessageHtmlLink":"feat: can write a hmm score column in all_candidates.tsv"}},{"before":"70113d8524cb2141f20dab8890d348a90f54dfd7","after":"f8132fa428847ca4d992d9842adb49a6d8c187ac","ref":"refs/heads/main","pushedAt":"2024-09-17T09:49:48.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"refactor: update hlep message for subcommands","shortMessageHtmlLink":"refactor: update hlep message for subcommands"}},{"before":"e5756c778cc16d4a6737464d76bde17e8b464ed8","after":"70113d8524cb2141f20dab8890d348a90f54dfd7","ref":"refs/heads/main","pushedAt":"2024-09-17T05:56:52.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"refactor: updates help message for --cov option","shortMessageHtmlLink":"refactor: updates help message for --cov option"}},{"before":"afcb20c287635a4dbb66c12a6cb4bc068d0c2303","after":"e5756c778cc16d4a6737464d76bde17e8b464ed8","ref":"refs/heads/main","pushedAt":"2024-09-11T07:54:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"docs: updates of README.md","shortMessageHtmlLink":"docs: updates of README.md"}},{"before":"a0c4da8b3a996b79fdcaca745f59ec1242a9430e","after":"afcb20c287635a4dbb66c12a6cb4bc068d0c2303","ref":"refs/heads/main","pushedAt":"2024-09-11T07:26:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"refactor: replaces --start argument with subcommands\n\nEach subcommand correspond to a starting steps","shortMessageHtmlLink":"refactor: replaces --start argument with subcommands"}},{"before":"346c564c31ed7265bbc34171760ffa49e55b4a82","after":"a0c4da8b3a996b79fdcaca745f59ec1242a9430e","ref":"refs/heads/main","pushedAt":"2024-09-04T08:33:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"docs: update of README.md","shortMessageHtmlLink":"docs: update of README.md"}},{"before":"d4441204970483f376760fd12548ab1af9f745de","after":"346c564c31ed7265bbc34171760ffa49e55b4a82","ref":"refs/heads/main","pushedAt":"2024-09-04T07:32:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"chore: adds a conda recipe\n\nallows the user to create a conda environment with all the necessary Python dependencies and external bioinformatics tools.","shortMessageHtmlLink":"chore: adds a conda recipe"}},{"before":"0550d84fe66eeb69a579c2a449aed1fe5dd3c191","after":"d4441204970483f376760fd12548ab1af9f745de","ref":"refs/heads/main","pushedAt":"2024-09-04T07:25:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"feat: adds the --hmm-score argument\n\nthis is argument is used to set a treshold on the full sequence bit score of hmmsearch results","shortMessageHtmlLink":"feat: adds the --hmm-score argument"}},{"before":"02eb87f03872c669c7e0d0961a1a25d1a5a0eee6","after":"0550d84fe66eeb69a579c2a449aed1fe5dd3c191","ref":"refs/heads/main","pushedAt":"2024-09-04T07:22:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"feat: adds -s argument to set the score treshold","shortMessageHtmlLink":"feat: adds -s argument to set the score treshold"}},{"before":"387280654be743d5d1752804710367bb28e23638","after":"02eb87f03872c669c7e0d0961a1a25d1a5a0eee6","ref":"refs/heads/main","pushedAt":"2024-09-03T14:02:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"feat: adds --hmm-score argument\n\nAllow to use a treshold for the full sequence bit score to filters domain retrieves by hmmsearch","shortMessageHtmlLink":"feat: adds --hmm-score argument"}},{"before":"fb70b5b316a0800f99a092f827fcac765a88f4fa","after":"387280654be743d5d1752804710367bb28e23638","ref":"refs/heads/main","pushedAt":"2024-08-30T06:58:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"refactor: removes useless if block","shortMessageHtmlLink":"refactor: removes useless if block"}},{"before":"21bd367cdbafdfbedc305679f9a5ebb010f3b7cb","after":"fb70b5b316a0800f99a092f827fcac765a88f4fa","ref":"refs/heads/main","pushedAt":"2024-08-30T06:28:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"fix: removes echo","shortMessageHtmlLink":"fix: removes echo"}},{"before":"b83762020d0a22a5aae17fb0494409c2f06e44a5","after":"21bd367cdbafdfbedc305679f9a5ebb010f3b7cb","ref":"refs/heads/main","pushedAt":"2024-08-30T06:27:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"fix: grep pattern to extract the db name","shortMessageHtmlLink":"fix: grep pattern to extract the db name"}},{"before":"f79437c87d4de7cce868d1c43f9963ed2133e8bc","after":"b83762020d0a22a5aae17fb0494409c2f06e44a5","ref":"refs/heads/main","pushedAt":"2024-08-29T14:00:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"fix: sbatch command for the hmmsearch step","shortMessageHtmlLink":"fix: sbatch command for the hmmsearch step"}},{"before":"aa9fb62091b88af3f381fdc1617ed78d697fc205","after":"f79437c87d4de7cce868d1c43f9963ed2133e8bc","ref":"refs/heads/main","pushedAt":"2024-08-29T13:56:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"fix: grep command to extract job_id of blastp and hmmsearch step","shortMessageHtmlLink":"fix: grep command to extract job_id of blastp and hmmsearch step"}},{"before":"a1bd40540f659db5b9b398f1aa9e50638b92a31e","after":"aa9fb62091b88af3f381fdc1617ed78d697fc205","ref":"refs/heads/main","pushedAt":"2024-08-29T13:50:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"fix: setting up the phylogeny stage with --start equals hmmsearch","shortMessageHtmlLink":"fix: setting up the phylogeny stage with --start equals hmmsearch"}},{"before":"6fba405b45f0414f3bdfc629b61e79811872bc01","after":"a1bd40540f659db5b9b398f1aa9e50638b92a31e","ref":"refs/heads/main","pushedAt":"2024-08-29T13:46:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"style: updates of help message","shortMessageHtmlLink":"style: updates of help message"}},{"before":"cbc9673d99baaad69ac4d5c5e39eae316be6ef34","after":"6fba405b45f0414f3bdfc629b61e79811872bc01","ref":"refs/heads/main","pushedAt":"2024-08-29T09:10:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"Fix: correct the job_id in dependency for the filter step\n\nUses a unique variable name to store the job_id of blastp or hmmsearch","shortMessageHtmlLink":"Fix: correct the job_id in dependency for the filter step"}},{"before":"aca61ee69ab4f78065788e8a7f1d5b0a3ec01630","after":"cbc9673d99baaad69ac4d5c5e39eae316be6ef34","ref":"refs/heads/main","pushedAt":"2024-08-29T08:52:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"feat: sets the hmmsearch step with slurm job scheduler","shortMessageHtmlLink":"feat: sets the hmmsearch step with slurm job scheduler"}},{"before":"0b74981b8f289112389b1b3acc940a1df82e3e94","after":"aca61ee69ab4f78065788e8a7f1d5b0a3ec01630","ref":"refs/heads/main","pushedAt":"2024-08-12T10:18:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"refactor: replaces -d with --data in set_candiate_selection","shortMessageHtmlLink":"refactor: replaces -d with --data in set_candiate_selection"}},{"before":"bd29833626093970eaaf407ca6900bd15193cfbb","after":"0b74981b8f289112389b1b3acc940a1df82e3e94","ref":"refs/heads/main","pushedAt":"2024-08-12T10:07:38.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"refactor: replaces --blast-data and --hmm-data with --data\n\nInside the main, the first line of the data file is read to checks the data type","shortMessageHtmlLink":"refactor: replaces --blast-data and --hmm-data with --data"}},{"before":"82a734c7116900fbca1b4a206d37b91b6757d2b6","after":"bd29833626093970eaaf407ca6900bd15193cfbb","ref":"refs/heads/main","pushedAt":"2024-08-08T14:05:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"thomas-bailly","name":null,"path":"/thomas-bailly","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/89846183?s=80&v=4"},"commit":{"message":"fix: adds if block to find the hmmsearch output","shortMessageHtmlLink":"fix: adds if block to find the hmmsearch output"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEuvaBPgA","startCursor":null,"endCursor":null}},"title":"Activity ยท labgem/CAESAR"}