{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":337089503,"defaultBranch":"master","name":"mga2","ownerLogin":"crukci-bioinformatics","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2021-02-08T13:43:57.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/5804406?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1710512312.0","currentOid":""},"activityList":{"items":[{"before":"0310c68ddda81158323086791d3773c7b0bd0447","after":"4b74c140e786ba9e9e59ce12c61720d32c079196","ref":"refs/heads/master","pushedAt":"2024-05-21T11:07:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Increase default memory allocation for bowtie process.","shortMessageHtmlLink":"Increase default memory allocation for bowtie process."}},{"before":"eb03f521189c3425b1894e8b997a70bcb5436578","after":"0310c68ddda81158323086791d3773c7b0bd0447","ref":"refs/heads/master","pushedAt":"2024-03-15T14:24:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Updated version numbers to 2.1.0-snapshot.","shortMessageHtmlLink":"Updated version numbers to 2.1.0-snapshot."}},{"before":"fb5da62c7d20887fdfd5c7167e19df05d8fe2bf0","after":"eb03f521189c3425b1894e8b997a70bcb5436578","ref":"refs/heads/master","pushedAt":"2024-03-15T14:16:31.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Updated version number to 2.0.7","shortMessageHtmlLink":"Updated version number to 2.0.7"}},{"before":"6b3389e67a4a2aeb6db0a24caf131be537f4b8ba","after":"fb5da62c7d20887fdfd5c7167e19df05d8fe2bf0","ref":"refs/heads/master","pushedAt":"2024-03-15T14:15:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Fixed typo in changes for release 2.0.7","shortMessageHtmlLink":"Fixed typo in changes for release 2.0.7"}},{"before":"c47aba107a39b22725569a63ccb9d04a739e0960","after":"6b3389e67a4a2aeb6db0a24caf131be537f4b8ba","ref":"refs/heads/master","pushedAt":"2024-03-15T14:15:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Added changes for release version 2.0.7","shortMessageHtmlLink":"Added changes for release version 2.0.7"}},{"before":"dca6e59e3e5529785730ba35093e4e1b7968bbee","after":"c47aba107a39b22725569a63ccb9d04a739e0960","ref":"refs/heads/master","pushedAt":"2024-03-14T18:20:05.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Changed the split alignments script to get the sample ids from the sample sheet instead of the FASTA file to better handle situations where there are no sampled reads for one or more samples; updated the split_genome_alignments_by_sample and split_adapter_alignments_by_sample processes and the workflow accordingly.","shortMessageHtmlLink":"Changed the split alignments script to get the sample ids from the sa…"}},{"before":"33aa830f763e089bd500e146b081093dcd452831","after":"dca6e59e3e5529785730ba35093e4e1b7968bbee","ref":"refs/heads/master","pushedAt":"2024-03-08T14:59:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Use copy mode instead of move when publishing the compressed alignment files and the bar chart; this avoids re-running the task unnecessarily when resuming a run.","shortMessageHtmlLink":"Use copy mode instead of move when publishing the compressed alignmen…"}},{"before":"232e2271e98441ab0f09d2b15e71b943007756ee","after":"33aa830f763e089bd500e146b081093dcd452831","ref":"refs/heads/master","pushedAt":"2024-03-08T14:01:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Changed name of collected genome and adapter alignment files to avoid clash with outputs from split_genome_alignments_by_sample and split_adapter_alignments_by_sample tasks, that caused an issue when resuming a run that had already completed these split tasks and the collectFile operations.","shortMessageHtmlLink":"Changed name of collected genome and adapter alignment files to avoid…"}},{"before":"0634354a56d825f796833c2634a62842743a0140","after":"232e2271e98441ab0f09d2b15e71b943007756ee","ref":"refs/heads/master","pushedAt":"2024-02-15T17:05:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Convert the id in the fastq channel to a character string to ensure it joins to the id read from the sample sheet using splitCsv.","shortMessageHtmlLink":"Convert the id in the fastq channel to a character string to ensure i…"}},{"before":"289ec579845e1396bd94cb67abf6e4053a3ba979","after":"0634354a56d825f796833c2634a62842743a0140","ref":"refs/heads/master","pushedAt":"2024-02-15T15:23:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Updated version to 2.1.0-snapshot","shortMessageHtmlLink":"Updated version to 2.1.0-snapshot"}},{"before":"b957ac81de3805ab57cade4dc98747efd538f6ad","after":"289ec579845e1396bd94cb67abf6e4053a3ba979","ref":"refs/heads/master","pushedAt":"2024-02-15T15:14:31.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Updated version number to 2.0.6","shortMessageHtmlLink":"Updated version number to 2.0.6"}},{"before":"3e8ecfea60d9e35079e8884969ae5ea79a1bd66f","after":"b957ac81de3805ab57cade4dc98747efd538f6ad","ref":"refs/heads/master","pushedAt":"2024-02-15T14:55:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Add user id to fastq channel so that this can be used in the sample_fastq tag.","shortMessageHtmlLink":"Add user id to fastq channel so that this can be used in the sample_f…"}},{"before":"5902ba651eb7c0a4e91f5a4a631e59491d580f2b","after":"3e8ecfea60d9e35079e8884969ae5ea79a1bd66f","ref":"refs/heads/master","pushedAt":"2024-02-14T12:18:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Name the outputs from the inner workflow","shortMessageHtmlLink":"Name the outputs from the inner workflow"}},{"before":"eb9c0f74f10e525675acf15e3d4b386d9f892b2b","after":"5902ba651eb7c0a4e91f5a4a631e59491d580f2b","ref":"refs/heads/master","pushedAt":"2024-02-13T17:08:10.000Z","pushType":"push","commitsCount":7,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Updated to rename the id column to user_id prior to creating a numeric id column for consistency with other scripts and parts of the overall workflow","shortMessageHtmlLink":"Updated to rename the id column to user_id prior to creating a numeri…"}},{"before":"af9454da2d13ddd421e0693059c57dcf02bc472b","after":"eb9c0f74f10e525675acf15e3d4b386d9f892b2b","ref":"refs/heads/master","pushedAt":"2024-02-13T12:35:44.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Clone mga2 repository to src directory so that the R scripts in the bin directory don't take precedence on the path (inconvenient during development and testing)","shortMessageHtmlLink":"Clone mga2 repository to src directory so that the R scripts in the b…"}},{"before":"2d433f7349ad2021270e09a578dae65b8dbf2c35","after":"af9454da2d13ddd421e0693059c57dcf02bc472b","ref":"refs/heads/master","pushedAt":"2024-02-12T10:38:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Removed execute permission/mode.","shortMessageHtmlLink":"Removed execute permission/mode."}},{"before":"c49afed9086b037c092baecd5ff0d1ffccd09ec8","after":"2d433f7349ad2021270e09a578dae65b8dbf2c35","ref":"refs/heads/master","pushedAt":"2024-02-09T11:43:10.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Moved the process definitions from mga2.nf to a separate file, processes.nf, so that these can be more easily used in a modified MGA2 workflow as part of the CRUK-CI automated data processing pipeline; use of val inputs instead of parameters in these process definitions.","shortMessageHtmlLink":"Moved the process definitions from mga2.nf to a separate file, proces…"}},{"before":"6a7b8f2ffc66fa81ad068c471166d5cc02a10921","after":"c49afed9086b037c092baecd5ff0d1ffccd09ec8","ref":"refs/heads/master","pushedAt":"2023-08-31T08:50:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"rich7409","name":"Richard Bowers","path":"/rich7409","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7525281?s=80&v=4"},"commit":{"message":"Change case of '10X' to '10x'.","shortMessageHtmlLink":"Change case of '10X' to '10x'."}},{"before":"93ac7dccc72707dad7549f972cfb5d16d1e3b5c8","after":"6a7b8f2ffc66fa81ad068c471166d5cc02a10921","ref":"refs/heads/master","pushedAt":"2023-08-07T10:33:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Added release instructions file","shortMessageHtmlLink":"Added release instructions file"}},{"before":"55936748515acf9642a3562be05b17157663e089","after":"93ac7dccc72707dad7549f972cfb5d16d1e3b5c8","ref":"refs/heads/master","pushedAt":"2023-08-07T10:27:23.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Merge branch 'master' of https://github.com/crukci-bioinformatics/mga2","shortMessageHtmlLink":"Merge branch 'master' of https://github.com/crukci-bioinformatics/mga2"}},{"before":"34f66ff9ad25532b66ffdb52a6ac141afe6963e8","after":"55936748515acf9642a3562be05b17157663e089","ref":"refs/heads/master","pushedAt":"2023-08-07T10:26:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Removed test sample sheet checked in by mistake","shortMessageHtmlLink":"Removed test sample sheet checked in by mistake"}},{"before":"29e291e99c7da28c308291ca20e2d79081866968","after":"34f66ff9ad25532b66ffdb52a6ac141afe6963e8","ref":"refs/heads/master","pushedAt":"2023-08-07T10:21:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Updated version to 2.1.0-snapshot","shortMessageHtmlLink":"Updated version to 2.1.0-snapshot"}},{"before":"0a0696ad262307e9e0a9a495fe88d8138d6fcb09","after":"29e291e99c7da28c308291ca20e2d79081866968","ref":"refs/heads/master","pushedAt":"2023-08-07T10:06:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Fixed minor typo in 2.0.5 release notes","shortMessageHtmlLink":"Fixed minor typo in 2.0.5 release notes"}},{"before":"1e585c90af42fa00b26356f67a5d98d538c9e8c7","after":"0a0696ad262307e9e0a9a495fe88d8138d6fcb09","ref":"refs/heads/master","pushedAt":"2023-08-07T10:04:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Added release notes for 2.0.5","shortMessageHtmlLink":"Added release notes for 2.0.5"}},{"before":"1027f8864d9effdbdd750e021fd7e8d642c472e0","after":"1e585c90af42fa00b26356f67a5d98d538c9e8c7","ref":"refs/heads/master","pushedAt":"2023-08-07T10:04:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Updated version number to 2.0.5.","shortMessageHtmlLink":"Updated version number to 2.0.5."}},{"before":"35ec2230c15aac36b071e0ef932b54e758187445","after":"1027f8864d9effdbdd750e021fd7e8d642c472e0","ref":"refs/heads/master","pushedAt":"2023-08-07T10:01:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Replaced non-breaking space character","shortMessageHtmlLink":"Replaced non-breaking space character"}},{"before":"a829ae03a882c0b654af33ce6c3ea84de623eab6","after":"35ec2230c15aac36b071e0ef932b54e758187445","ref":"refs/heads/master","pushedAt":"2023-03-15T17:09:35.170Z","pushType":"push","commitsCount":2,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Added process for compressing the final alignment files","shortMessageHtmlLink":"Added process for compressing the final alignment files"}},{"before":"f6913967c451a1f8a865fdc148a85913df265d12","after":"a829ae03a882c0b654af33ce6c3ea84de623eab6","ref":"refs/heads/master","pushedAt":"2023-03-14T21:14:31.603Z","pushType":"push","commitsCount":2,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Updated for change to default output prefix.","shortMessageHtmlLink":"Updated for change to default output prefix."}},{"before":"e8eebee66e33257d0831c68b403da5499c11c853","after":"f6913967c451a1f8a865fdc148a85913df265d12","ref":"refs/heads/master","pushedAt":"2023-03-14T19:42:34.251Z","pushType":"push","commitsCount":1,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Updated to tidyverse v2.0.0","shortMessageHtmlLink":"Updated to tidyverse v2.0.0"}},{"before":"d254e3d7f1cc12a9a19ed6806c9aaa99575d225e","after":"e8eebee66e33257d0831c68b403da5499c11c853","ref":"refs/heads/master","pushedAt":"2023-03-14T19:25:42.996Z","pushType":"push","commitsCount":5,"pusher":{"login":"eldrid01","name":"Matt Eldridge","path":"/eldrid01","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/5559069?s=80&v=4"},"commit":{"message":"Explicit options for output image files","shortMessageHtmlLink":"Explicit options for output image files"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAET8CUOAA","startCursor":null,"endCursor":null}},"title":"Activity · crukci-bioinformatics/mga2"}