{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":136971526,"defaultBranch":"master","name":"IGS_dada2_pipeline","ownerLogin":"jbholm","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2018-06-11T19:26:52.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/17168205?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1710356223.0","currentOid":""},"activityList":{"items":[{"before":"8ec904ec84cb60fb7ff5fa0c681b38092e45bdc8","after":"04a2ed9e9ce0d386e242f49b6c9dff5c4721be97","ref":"refs/heads/master","pushedAt":"2024-03-13T18:56:22.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"jonalim","name":"Jonathan Lim","path":"/jonalim","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/32965677?s=80&v=4"},"commit":{"message":"Specify queue when submitting to SGE; informatics patches (v6.2.1)\n\nillumina_dada2.pl\nInclude -q in qsub calls because all.q can't run jobs requesting `-pe thread`.\n\nmake_project_sample_map.py\nInclude path for if no manifest was given.\nRemove ladder from the pooling detail earlier on, since it has text in the\n  \"Sample Description\" field that prevent it from being removed.\n\nSquashed commit of the following from patch/queue_config:\n\ncommit 01530c3d202ba23d598d5ecfe549b4a9974402c0","shortMessageHtmlLink":"Specify queue when submitting to SGE; informatics patches (v6.2.1)"}},{"before":"1ce1b8ac3d7451fdd0c4d65e566178c18ba63457","after":"8ec904ec84cb60fb7ff5fa0c681b38092e45bdc8","ref":"refs/heads/master","pushedAt":"2024-01-31T21:52:42.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"jonalim","name":"Jonathan Lim","path":"/jonalim","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/32965677?s=80&v=4"},"commit":{"message":"Rework project/sample informatics (v6.2.0) (v6.2.0)\n\nFirst join manifest to plate maps, if available. Sometimes the manifest itself\n  will serve as the platemap (rename the columns). Sometimes we receive beads in\n  plates. We extract gDNA and add controls; this means the manfiest sample names\n  are the final sample names (they trump conflicting sample ID's on the gDNA\n  maps) but gDNA map samples NOT on the manifest will get added to the project\n  too.\nThen join this sample map to the pooling detail. This enables to create the\n  names of files and data table rows that will be grabbed from run demux\n  directories.\nThe \"Sample Description\" column of the pooling detail can be used to identify\n  the plate, if gDNA plate ID is N/A. This reflects that at pooling, plates can\n  come from two different sources (they're two different types of plates).\n  I treat them identically, but not everyone does.\nDo some CLI argument validation at the very start.\nKeep the APJR3 barcode map in the repo.\n\nSquashed commit of the following from feature/rework_project_informatics:\n\ncommit be89b3b31eb7b915b674378c51efff613c7739ce\ncommit 81f365a85295c5ce7bb57035e205eaac75c19820","shortMessageHtmlLink":"Rework project/sample informatics (v6.2.0) (v6.2.0)"}},{"before":"c56e0dc8da06b909e311022c9860ae6ac1066533","after":"1ce1b8ac3d7451fdd0c4d65e566178c18ba63457","ref":"refs/heads/master","pushedAt":"2024-01-11T16:49:21.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"jonalim","name":"Jonathan Lim","path":"/jonalim","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/32965677?s=80&v=4"},"commit":{"message":"Make project sample maps for PacBio projects; accommodate plate-format manifests (v6.0.0)\n\nBreaking\n\nscripts/make_project_sample_map.py\n--platform is now required. If the platform is PacBio, this script will not try\n  to get the barcode plate ID's from the pooling detail.\nIf present in the directory, gDNA pooling plates will be used. If not, PacBio\n  demux maps are used.\nPlate-format manifests are now accepted. Format is given via --manifest_format.\n--manifest_tubeid_column (and all other column specifier options) now take\n  column names, not a numeric index.\n--manifest_plateid_column and --manifest_platerow_column can be used to specify\n  the names of the important columns in plate-format manifests.\n--manifest_plate_remap is used to map manifest plates to gDNA plates (or PacBio\n  runs, if there really aren't any gDNA plate maps).\n\nFeatures\n\nResource execution for PacBio QC and denoising has adopted the Nextflow paradigm.\n  part1_pacbio.sh is where the user requests the number of cpus and memory for the\n  task execution. The values of those resources are also passed to pacbio_dada2.R\n  so it can restrict its own resources. This paradigm enables pacbio_dada2.R to be\n  run independently, and also allows us to run the wrapper without needing to\n  understand pacbio_dada2.R's CLI.\nThe wrapper uses the size of the files in the input directory to determine how\n  much memory to request on the grid. This is because I found that memory used by\n  dada2::learnErrors and dada2::dada was a function of dataset size. The number\n  of cpu threads in the qsub request is just arbitrarily defined as 12 (the max #\n  of cpus in the largest nf-core task category) in config.json.\nThread usage for PacBio quality trimming is calculated by pacbio_dada2.R based on\n  dataset size to keep memory usage under the specified amount. This step also\n  respects the --multithread option given in pacbio_dada2.R's CLI.\nWhen combining runs, project maps with illegal characters in the sampleIDs are now\n  acceptable and sanitized. (Because sometimes the user just needs to push through\n  a map that wasn't generated with scripts/make_project_sample_map.py)\n\nQuality-of-life\n\npart1_pacbio.sh also gets the default SGE project from config.json.\npart1_pacbio.sh prints the qsub command to be executed then asks for\n  confirmation.\nPrint the parameters to all of the PacBio processing steps\nWhen combining runs, added informative error message if the project map needs to\n  be processed by dos2unix.\n\nSquashed commit of the following:\n\ncommit f5df7341204181a6bac0cec81eb2f664a3fcb0cb\ncommit 8a787eda1f5bbc6ca8400c3f05e00c124cda4f51\ncommit a1cdc6b5f7fafdda209c0099c51ca6d2bc0b2a2d","shortMessageHtmlLink":"Make project sample maps for PacBio projects; accommodate plate-forma…"}},{"before":"c60510e66aa7b7e2669f6f7c99b1d08472b971a5","after":"c56e0dc8da06b909e311022c9860ae6ac1066533","ref":"refs/heads/master","pushedAt":"2023-06-01T14:47:59.848Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"jonalim","name":"Jonathan Lim","path":"/jonalim","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/32965677?s=80&v=4"},"commit":{"message":"Use updated speciateIT models (v5.3.6)\n\nRenamed speciateIT models once again. The previous time I didn't modify the\n  correct files.\n  BVAB1 -> Candidatus_Lachnocurva_vaginae\n  BVAB3 -> Mageeibacillus_indolicus\nFor future reference, use these commands to modify speciateIT model names:\n  cd /local/projects/grc/devel/jolim/packages/speciateIT/models/v1.0c/V3V4/\n  mv BVAB1.fa Candidatus_Lachnocurva_vaginae.fa\n  echo {error_thlds.txt,MC*Prob,model.tree,modelIds.txt,spp_paths.txt} | \\\n    xargs sed -i 's/BVAB1/Candidatus_Lachnocurva_vaginae/g'\nUpdated valencia centroids to match.\nMoved speciateIT to /local/projects/grc/devel/jolim/packages/ as a frozen GRC\n  version.\n\nChanged default SGE executor to lsadzewicz-grc\n\nDADA2 denoise can now be run with up to 160G mem_free requested, and minimum\n  of 30G.\n\nSquashed commit of the following:\n\ncommit 05c9f7455d7d001b65a87e13a7252e9c95a582c3","shortMessageHtmlLink":"Use updated speciateIT models (v5.3.6)"}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEFNbcFAA","startCursor":null,"endCursor":null}},"title":"Activity · jbholm/IGS_dada2_pipeline"}