OpenScientificCodeRegistry/Database

1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/gagneurlab/drop",4 "url": "https://github.com/gagneurlab/drop",5 "host": "github.com",6 "commit": "41cf4e282d6c0254cb3799de180f43d28c8efe24",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "ad901e737e450064129260dd8dfc67c67f16aa5061821bcaeb4840c69c40c228",14   "language": "License",15   "lines": 21,16   "truncated": false,17   "block": 11,18   "row": 1429319  },20  {21   "path": "MISO/run_miso.sh",22   "sha256": "0571b487b2901adcce3a10ba68e4a3ccff7e9f743537c97928722a323a2fb350",23   "language": "Shell",24   "lines": 8,25   "truncated": false,26   "block": 13,27   "row": 434228  },29  {30   "path": "README.md",31   "sha256": "da3f7d86c41cfaf01f3edea1a0a7774009f87c11417abd3de8a1b8139fa5c0e1",32   "language": "Text",33   "lines": 128,34   "truncated": false,35   "block": 13,36   "row": 693437  },38  {39   "path": "docs/source/conf.py",40   "sha256": "8d2cf8911d0ad3c01d6753ce91fc4342b6df0e5b17fd52334475cd826b57ac2c",41   "language": "Python",42   "lines": 61,43   "truncated": false,44   "block": 12,45   "row": 841046  },47  {48   "path": "drop/__init__.py",49   "sha256": "c7ac7917d51ed4ad6f9671b8b1dcad2ea50f653b7152d4b84585b00b8bb7066f",50   "language": "Python",51   "lines": 8,52   "truncated": false,53   "block": 12,54   "row": 337555  },56  {57   "path": "drop/cli.py",58   "sha256": "fca391b649580ab18ef5c84a54614d84777a71470ab501525b1df0df6c37f7ad",59   "language": "Python",60   "lines": 195,61   "truncated": false,62   "block": 12,63   "row": 1658764  },65  {66   "path": "drop/config/DropConfig.py",67   "sha256": "0b36d14c3d193ac397080b96f4069329a1ce37301fc361a4ec7dbc1fdc7260e7",68   "language": "Python",69   "lines": 199,70   "truncated": false,71   "block": 12,72   "row": 1609573  },74  {75   "path": "drop/config/ExportCounts.py",76   "sha256": "e56983487696fd763af2f04b103212d40c9d9ef911fc8572183a48de2d5d3707",77   "language": "Python",78   "lines": 109,79   "truncated": false,80   "block": 12,81   "row": 1252582  },83  {84   "path": "drop/config/Genome.py",85   "sha256": "c6382f4d4b3ce18d234098a9f3688562e2a2f20c7d311b0e4535fb23189d7384",86   "language": "Python",87   "lines": 78,88   "truncated": false,89   "block": 12,90   "row": 931891  },92  {93   "path": "drop/config/SampleAnnotation.py",94   "sha256": "bed56165a06f9e5550576fff5790b8d685fe7f756be20ede191f40eb61f2b550",95   "language": "Python",96   "lines": 341,97   "truncated": false,98   "block": 12,99   "row": 19676100  },101  {102   "path": "drop/config/SampleParams.py",103   "sha256": "80794e4db0a11d8eb308011aadf0b9ea58904e6a0499afaea07ef06eec8a3351",104   "language": "Python",105   "lines": 259,106   "truncated": false,107   "block": 12,108   "row": 19054109  },110  {111   "path": "drop/config/__init__.py",112   "sha256": "e264c0817e81a5f0de254eea32e151c3163f84cc82cd81f6e4337edfb94c9e80",113   "language": "Python",114   "lines": 7,115   "truncated": false,116   "block": 12,117   "row": 3895118  },119  {120   "path": "drop/config/submodules/AberrantExpression.py",121   "sha256": "ff2798543ea573fc2e4fc44027ddc7f31a77dfd24dacdf78f2c663a7e30c304e",122   "language": "Python",123   "lines": 103,124   "truncated": false,125   "block": 12,126   "row": 13624127  },128  {129   "path": "drop/config/submodules/AberrantSplicing.py",130   "sha256": "ee83ddf996af1fb3cda4e6b9e4fa910383f914b9ce78e0693f3d59c530f8d9b0",131   "language": "Python",132   "lines": 126,133   "truncated": false,134   "block": 12,135   "row": 14731136  },137  {138   "path": "drop/config/submodules/MonoallelicExpression.py",139   "sha256": "eabed4a3c2c4ff4f5af43197e4570ef50d75216b08c091f35b9a83cf666922ca",140   "language": "Python",141   "lines": 187,142   "truncated": false,143   "block": 12,144   "row": 16748145  },146  {147   "path": "drop/config/submodules/RNAVariantCalling.py",148   "sha256": "5120305c04103257745c22a823c46a70cb2dd0146acc3f6a8fd7704035c10243",149   "language": "Python",150   "lines": 78,151   "truncated": false,152   "block": 12,153   "row": 11574154  },155  {156   "path": "drop/config/submodules/Submodules.py",157   "sha256": "566ac24b2232ab90a84085426b74a4a983b8fdcb1d63b03915a5c3a86a5ca7ae",158   "language": "Python",159   "lines": 162,160   "truncated": false,161   "block": 12,162   "row": 15861163  },164  {165   "path": "drop/config/submodules/__init__.py",166   "sha256": "e509decaf845fb2212368fdc870736e3d9d9bb9542e66b7f62b2aaa3a930aae6",167   "language": "Python",168   "lines": 6,169   "truncated": false,170   "block": 12,171   "row": 3470172  },173  {174   "path": "drop/demo/__init__.py",175   "sha256": "9545838b10813deadebb867629a6e732d1c24d760eae529b59c029dd53ea7288",176   "language": "Python",177   "lines": 1,178   "truncated": false,179   "block": 12,180   "row": 3020181  },182  {183   "path": "drop/demo/fixPaths.py",184   "sha256": "be1c3db42029b1db470936a5270172d97786a92ce7fe92ca9d0f12b4df02e319",185   "language": "Python",186   "lines": 54,187   "truncated": false,188   "block": 12,189   "row": 8195190  },191  {192   "path": "drop/download_data.sh",193   "sha256": "26401ad8f686569d5566173c00364c77a8fd3b60f0d2c49f115c9b052b3597a4",194   "language": "Shell",195   "lines": 20,196   "truncated": false,197   "block": 13,198   "row": 4546199  },200  {201   "path": "drop/installRPackages.R",202   "sha256": "2e9cc8f88fc177b047cec7cebe497e2b7b213afddfeba8f38152db0248583d49",203   "language": "R",204   "lines": 51,205   "truncated": false,206   "block": 13,207   "row": 1283208  },209  {210   "path": "drop/modules/aberrant-expression-pipeline/Counting/Datasets.R",211   "sha256": "9db517b6efac9b16c73ee254cfc4d5d4ff7e6294d78a5056059d3d524b4b9466",212   "language": "R",213   "lines": 33,214   "truncated": false,215   "block": 13,216   "row": 1056217  },218  {219   "path": "drop/modules/aberrant-expression-pipeline/Counting/Summary.R",220   "sha256": "63378606ff860fe83422fd4779a9094b7e93826904b610d5a427ddbbcb542290",221   "language": "R",222   "lines": 256,223   "truncated": false,224   "block": 13,225   "row": 2701226  },227  {228   "path": "drop/modules/aberrant-expression-pipeline/Counting/countReads.R",229   "sha256": "72195db122c32e74a54dfd738821530dcdfc4ca9d591fd8076b3f5db978de06f",230   "language": "R",231   "lines": 129,232   "truncated": false,233   "block": 13,234   "row": 1973235  },236  {237   "path": "drop/modules/aberrant-expression-pipeline/Counting/exportCounts.R",238   "sha256": "3471a638a01a667c17d03796d78778d7614a92bb8ae61b4c2c332a6d120d39a6",239   "language": "R",240   "lines": 27,241   "truncated": false,242   "block": 13,243   "row": 995244  },245  {246   "path": "drop/modules/aberrant-expression-pipeline/Counting/filterCounts.R",247   "sha256": "cc7d45ec5a4a851ee6f14b27cfa99a052e0b41ea4f4e4743b2e28b3c1b7a10e4",248   "language": "R",249   "lines": 58,250   "truncated": false,251   "block": 13,252   "row": 1361253  },254  {255   "path": "drop/modules/aberrant-expression-pipeline/Counting/mergeCounts.R",256   "sha256": "01e743bb53a95beec871f9fbadc71cc0a381f845f39786499d3bf3a3571d7300",257   "language": "R",258   "lines": 77,259   "truncated": false,260   "block": 13,261   "row": 1594262  },263  {264   "path": "drop/modules/aberrant-expression-pipeline/OUTRIDER/Datasets.R",265   "sha256": "16bf1c263a7ac2a73cec5093a5d49546c7f45d47351d1fbe68ccd6c5e8ad4119",266   "language": "R",267   "lines": 33,268   "truncated": false,269   "block": 13,270   "row": 1054271  },272  {273   "path": "drop/modules/aberrant-expression-pipeline/OUTRIDER/Summary.R",274   "sha256": "2699e45b7343e1f340b97a701ef543470da5811d3a43bfbcbbce4841b57cdaf1",275   "language": "R",276   "lines": 150,277   "truncated": false,278   "block": 13,279   "row": 2114280  },281  {282   "path": "drop/modules/aberrant-expression-pipeline/OUTRIDER/pvalsOutrider.R",283   "sha256": "884c6d9b8b2125ff9b7ce3de36eaac4c56cb440106162569657ca427ec479bfb",284   "language": "R",285   "lines": 56,286   "truncated": false,287   "block": 13,288   "row": 1373289  },290  {291   "path": "drop/modules/aberrant-expression-pipeline/OUTRIDER/results.R",292   "sha256": "b383a98fc22929f0ab2d0728e48813aaa62fb9e184f223ecd8de8af9d51214c2",293   "language": "R",294   "lines": 66,295   "truncated": false,296   "block": 13,297   "row": 1518298  },299  {300   "path": "drop/modules/aberrant-expression-pipeline/OUTRIDER/runOutrider.R",301   "sha256": "3659bc5fe552b920a9f716b29bd5d429c5137b28bb151744e1def9746b035bd4",302   "language": "R",303   "lines": 95,304   "truncated": false,305   "block": 13,306   "row": 1567307  },308  {309   "path": "drop/modules/aberrant-splicing-pipeline/Counting/00_define_datasets_from_anno.R",310   "sha256": "f3f29594c0c3be786bef96ce91ed6129dbbb7462b196312a110b6d98932f8f5a",311   "language": "R",312   "lines": 59,313   "truncated": false,314   "block": 13,315   "row": 1290316  },317  {318   "path": "drop/modules/aberrant-splicing-pipeline/Counting/01_0_countRNA_init.R",319   "sha256": "0be38be7b89eb2bbc4127c37368e95b9aac9e0f753f140f06fe9b8e43ce9a338",320   "language": "R",321   "lines": 47,322   "truncated": false,323   "block": 13,324   "row": 1248325  },326  {327   "path": "drop/modules/aberrant-splicing-pipeline/Counting/01_1_countRNA_splitReads_samplewise.R",328   "sha256": "3a944727a76a86833c8935660228e511a2502f32e60f2e95af7e8afdca96f381",329   "language": "R",330   "lines": 55,331   "truncated": false,332   "block": 13,333   "row": 1357334  },335  {336   "path": "drop/modules/aberrant-splicing-pipeline/Counting/01_2_countRNA_splitReads_merge.R",337   "sha256": "2aa72407adce445ee0f14f6c77a475b149dbf94b0917b100dd085ba380c6d27a",338   "language": "R",339   "lines": 78,340   "truncated": false,341   "block": 13,342   "row": 1665343  },344  {345   "path": "drop/modules/aberrant-splicing-pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R",346   "sha256": "12ce987a45a929dce01d3d9dffcd9f043d176d2b010217eeea0066307753bf21",347   "language": "R",348   "lines": 53,349   "truncated": false,350   "block": 13,351   "row": 1367352  },353  {354   "path": "drop/modules/aberrant-splicing-pipeline/Counting/01_4_countRNA_nonSplitReads_merge.R",355   "sha256": "e563431d92dae48ef0b69aded714d6a6118008fbc65521d5aa022a881d8191ea",356   "language": "R",357   "lines": 61,358   "truncated": false,359   "block": 13,360   "row": 1483361  },362  {363   "path": "drop/modules/aberrant-splicing-pipeline/Counting/01_5_countRNA_collect.R",364   "sha256": "5fe2d5a3873052aead6abd9dd8d1e1f59931daaba02520147f031d09858b7843",365   "language": "R",366   "lines": 58,367   "truncated": false,368   "block": 13,369   "row": 1458370  },371  {372   "path": "drop/modules/aberrant-splicing-pipeline/Counting/02_psi_value_calculation_FraseR.R",373   "sha256": "f92b9f297678f3a6950bb3c4d9a6fd7aa658c59ad3a8d90a5d2ff3a456ecd2fd",374   "language": "R",375   "lines": 38,376   "truncated": false,377   "block": 13,378   "row": 1180379  },380  {381   "path": "drop/modules/aberrant-splicing-pipeline/Counting/03_filter_expression_FraseR.R",382   "sha256": "5c0db2b94d008bb087146c114dd4df469f453a3f728e3e71802ab15581664ac6",383   "language": "R",384   "lines": 112,385   "truncated": false,386   "block": 13,387   "row": 1979388  },389  {390   "path": "drop/modules/aberrant-splicing-pipeline/Counting/DatasetsF.R",391   "sha256": "4a2ca376664892d01bc5dbcf876bbcfd08fa1ed749488c71f1356fee4c1a2aad",392   "language": "R",393   "lines": 26,394   "truncated": false,395   "block": 13,396   "row": 957397  },398  {399   "path": "drop/modules/aberrant-splicing-pipeline/Counting/Summary.R",400   "sha256": "6561bc507a7723e3ba3d85c63fddbcb1de8f4d408fbe80feeaae970c99be938d",401   "language": "R",402   "lines": 116,403   "truncated": false,404   "block": 13,405   "row": 2077406  },407  {408   "path": "drop/modules/aberrant-splicing-pipeline/Counting/exportCounts.R",409   "sha256": "38b2b1235438dc03ba8b00b89891cace6c2fc2f0f6558f66a2fe84d60e324e73",410   "language": "R",411   "lines": 69,412   "truncated": false,413   "block": 13,414   "row": 1520415  },416  {417   "path": "drop/modules/aberrant-splicing-pipeline/FRASER/04_fit_hyperparameters_FraseR.R",418   "sha256": "d587398d43afdb642a28143147350bd3f0cab4c5a2e7165ac4694ef23aba745a",419   "language": "R",420   "lines": 87,421   "truncated": false,422   "block": 13,423   "row": 1603424  },425  {426   "path": "drop/modules/aberrant-splicing-pipeline/FRASER/05_fit_autoencoder_FraseR.R",427   "sha256": "50d7898ebfcd4e66ec3182228e4fd235342eb076a688c258816ebde068941f23",428   "language": "R",429   "lines": 51,430   "truncated": false,431   "block": 13,432   "row": 1322433  },434  {435   "path": "drop/modules/aberrant-splicing-pipeline/FRASER/06_annotate_genes.R",436   "sha256": "05867e36250921ce4e8e40aca0bfc443da4e803cc1f61623be778cd955fda467",437   "language": "R",438   "lines": 74,439   "truncated": false,440   "block": 13,441   "row": 1630442  },443  {444   "path": "drop/modules/aberrant-splicing-pipeline/FRASER/07_calculation_stats_FraseR.R",445   "sha256": "9ac717332340f22fc3225694b89703bac294c310893864e9097de9c5d3bc4d91",446   "language": "R",447   "lines": 66,448   "truncated": false,449   "block": 13,450   "row": 1502451  },452  {453   "path": "drop/modules/aberrant-splicing-pipeline/FRASER/08_extract_results_FraseR.R",454   "sha256": "0bf09971a09e6de5c0714b199c43673243997bcc24555214d22bcf04ec9969f7",455   "language": "R",456   "lines": 132,457   "truncated": false,458   "block": 13,459   "row": 2227460  },461  {462   "path": "drop/modules/aberrant-splicing-pipeline/FRASER/Datasets.R",463   "sha256": "800ffd6801b163653058e7a3a224aaee7232c8a07097fa37f06b7ce34f3bca36",464   "language": "R",465   "lines": 30,466   "truncated": false,467   "block": 13,468   "row": 1048469  },470  {471   "path": "drop/modules/aberrant-splicing-pipeline/FRASER/Summary.R",472   "sha256": "ec3dc1418de04831444bdcc8b1632489ffecd65fd695d86086269deeecdf2fac",473   "language": "R",474   "lines": 130,475   "truncated": false,476   "block": 13,477   "row": 1893478  },479  {480   "path": "drop/modules/aberrant-splicing-pipeline/config.R",481   "sha256": "bef2a3dce9b6a208a266f19ad3574f3a3dac1ee0a2a5276e4cec60f510bbc9a2",482   "language": "R",483   "lines": 45,484   "truncated": false,485   "block": 13,486   "row": 1081487  },488  {489   "path": "drop/modules/helpers/add_HPO_cols.R",490   "sha256": "7f053c31b3ce8d6b57fd32759b2575bf4d8493e5638bd7bc7b1e80ccb1552796",491   "language": "R",492   "lines": 42,493   "truncated": false,494   "block": 13,495   "row": 1289496  },497  {498   "path": "drop/modules/helpers/parse_subsets_for_FDR.R",499   "sha256": "76d4eacc80a5a2be00193e9901cfe9c84a1e5972c5a8f44cece388e9468aab30",500   "language": "R",501   "lines": 66,502   "truncated": false,503   "block": 13,504   "row": 1427505  },506  {507   "path": "drop/modules/mae-pipeline/MAE/ASEReadCounter.sh",508   "sha256": "500d377f53e6e7277b62fe0ecb8b48de23cd96b710c5983b519e97197181c0be",509   "language": "Shell",510   "lines": 105,511   "truncated": false,512   "block": 13,513   "row": 5557514  },515  {516   "path": "drop/modules/mae-pipeline/MAE/Datasets.R",517   "sha256": "5777c0ca422bc6a7304be7c8d8b8adf96e0c0c49cb4ee3d9fa2c74b13c6ff533",518   "language": "R",519   "lines": 32,520   "truncated": false,521   "block": 13,522   "row": 1023523  },524  {525   "path": "drop/modules/mae-pipeline/MAE/Results.R",526   "sha256": "9526355e2f11eca44ffe88b22e6bb550eec2a9b9e781bfc1e4340e5f402f124a",527   "language": "R",528   "lines": 181,529   "truncated": false,530   "block": 13,531   "row": 2353532  },533  {534   "path": "drop/modules/mae-pipeline/MAE/deseq_mae.R",535   "sha256": "cb94a6cfbc200e9e2f0155032796aec0009818e795057eb7c1c9b5681e1be0f6",536   "language": "R",537   "lines": 50,538   "truncated": false,539   "block": 13,540   "row": 1233541  },542  {543   "path": "drop/modules/mae-pipeline/MAE/filterSNVs.sh",544   "sha256": "75fbaf1b3506bb17bf801a527be6b1db4b65ec3cbec9898715e4befb187a8b17",545   "language": "Shell",546   "lines": 106,547   "truncated": false,548   "block": 13,549   "row": 5565550  },551  {552   "path": "drop/modules/mae-pipeline/MAE/gene_name_mapping.R",553   "sha256": "571c9e4e3483ef5254ef487c87474e8e8c9c96e5ef3bd9f2f895f2469d5c6e88",554   "language": "R",555   "lines": 37,556   "truncated": false,557   "block": 13,558   "row": 1087559  },560  {561   "path": "drop/modules/mae-pipeline/QC/DNA_RNA_matrix_plot.R",562   "sha256": "d74d5cefe85cc6bd297acf9fbe41591e10c9752c632b29f25a0e78de9948615f",563   "language": "R",564   "lines": 154,565   "truncated": false,566   "block": 13,567   "row": 2292568  },569  {570   "path": "drop/modules/mae-pipeline/QC/Datasets.R",571   "sha256": "b3fe3bd9395c95bba6435c77966fd810782b9c65afeb051f2251b6d8f07a68a7",572   "language": "R",573   "lines": 29,574   "truncated": false,575   "block": 13,576   "row": 960577  },578  {579   "path": "drop/modules/mae-pipeline/QC/create_matrix_dna_rna_cor.R",580   "sha256": "0773dd5043f64d4741f014a9e026c17be4daacc39cc68658dd81659e4a650b97",581   "language": "R",582   "lines": 126,583   "truncated": false,584   "block": 13,585   "row": 1828586  },587  {588   "path": "drop/modules/mae-pipeline/QC/deseq_qc.R",589   "sha256": "6d17710159c3707161cf056b7513cc41017ed902d52a5b27cbb852f408f5eed9",590   "language": "R",591   "lines": 38,592   "truncated": false,593   "block": 13,594   "row": 1071595  },596  {597   "path": "drop/modules/rvc-pipeline/GATK_BASH/bqsr.sh",598   "sha256": "8cfad73f80e566110534123327179a1736db889636f8fb64efca9a9832acdaea",599   "language": "Shell",600   "lines": 71,601   "truncated": false,602   "block": 13,603   "row": 5431604  },605  {606   "path": "drop/modules/rvc-pipeline/GATK_BASH/changeHeader.sh",607   "sha256": "e21424665ed51d90858467103e952dc630bb92a0dc46a71dcc571a86606c4a25",608   "language": "Shell",609   "lines": 67,610   "truncated": false,611   "block": 13,612   "row": 5460613  },614  {615   "path": "drop/modules/rvc-pipeline/GATK_BASH/haplotypeCaller.sh",616   "sha256": "cb46a46f12f71568d5d2391f35db4a7dfa58d9b46b5e922f5d4ab7b992a502bd",617   "language": "Shell",618   "lines": 57,619   "truncated": false,620   "block": 13,621   "row": 5296622  },623  {624   "path": "drop/modules/rvc-pipeline/GATK_BASH/maskSingleVCF.sh",625   "sha256": "5b68501f4c2ecc8f799a92710fdb5c02b137a0779784e4937dd8f9527087077c",626   "language": "Shell",627   "lines": 42,628   "truncated": false,629   "block": 13,630   "row": 5046631  },632  {633   "path": "drop/modules/rvc-pipeline/GATK_BASH/simpleAnnotation.sh",634   "sha256": "5f23c9139247291490431dfc16d1635c5a8e0de647666831a56feea1ece90af4",635   "language": "Shell",636   "lines": 44,637   "truncated": false,638   "block": 13,639   "row": 5107640  },641  {642   "path": "drop/modules/rvc-pipeline/countVariants/Datasets.R",643   "sha256": "eea567c9e3a614ae6c18d92476f8e388a10a1507e398a2a3eccb7c7e7d20d9f7",644   "language": "R",645   "lines": 33,646   "truncated": false,647   "block": 13,648   "row": 1046649  },650  {651   "path": "drop/modules/rvc-pipeline/countVariants/Results.R",652   "sha256": "a76116e3b5058ce8c57771947765b570a8e753d26a21c0c1588d28e0b14c0c54",653   "language": "R",654   "lines": 93,655   "truncated": false,656   "block": 13,657   "row": 1731658  },659  {660   "path": "drop/modules/rvc-pipeline/countVariants/batch_data_table.R",661   "sha256": "335fff3e54db011914a424fbd63d8c5dc4aa0237ae35a5ebda242fa0facad7bf",662   "language": "R",663   "lines": 108,664   "truncated": false,665   "block": 13,666   "row": 1891667  },668  {669   "path": "drop/setupDrop.py",670   "sha256": "e814a31997164012c6d9081bb484793853714a1fda6fcc5bf5d7123b1d1016e4",671   "language": "Python",672   "lines": 69,673   "truncated": false,674   "block": 12,675   "row": 9501676  },677  {678   "path": "drop/template/Scripts/AberrantExpression/Overview.R",679   "sha256": "c838d9b9b7feb12231de90d82313b05ad85546e3bcaadb247004d3a6ab3a1892",680   "language": "R",681   "lines": 108,682   "truncated": false,683   "block": 13,684   "row": 1808685  },686  {687   "path": "drop/template/Scripts/AberrantSplicing/Overview.R",688   "sha256": "dce530dd6c76d861382d2cd0e74a4ebc3bc611062b29a70566d1bd5978c7e392",689   "language": "R",690   "lines": 108,691   "truncated": false,692   "block": 13,693   "row": 1783694  },695  {696   "path": "drop/template/Scripts/MonoallelicExpression/Overview.R",697   "sha256": "000638bc6f899358e617e8ddca7431cd77d0ba71cb0effebda8ae47dbe7ef863",698   "language": "R",699   "lines": 108,700   "truncated": false,701   "block": 13,702   "row": 1843703  },704  {705   "path": "drop/template/Scripts/Pipeline/SampleAnnotation.R",706   "sha256": "e9791b5f4599fc390c5d9c3a8d467d8039e32966e983fd3a8491fc882788a0a9",707   "language": "R",708   "lines": 101,709   "truncated": false,710   "block": 13,711   "row": 1593712  },713  {714   "path": "drop/template/Scripts/Pipeline/exportCountsMeta.py",715   "sha256": "8b3ef3d2ae9ae5c8a5cced7a6477567c8f358688aa4b020f7ab70ae6c6fb8bfc",716   "language": "Python",717   "lines": 89,718   "truncated": false,719   "block": 12,720   "row": 10379721  },722  {723   "path": "drop/template/Scripts/Pipeline/preprocessGeneAnnotation.R",724   "sha256": "43fa75d5416194b98e246b40f64352e63bfd14209deed0e71e4839eb42372a33",725   "language": "R",726   "lines": 61,727   "truncated": false,728   "block": 13,729   "row": 1354730  },731  {732   "path": "drop/template/Scripts/html_functions.R",733   "sha256": "f5c4edac9f8c8e97f4f6c49866164455943b545c57327cf0095256943df2cdb2",734   "language": "R",735   "lines": 22,736   "truncated": false,737   "block": 13,738   "row": 921739  },740  {741   "path": "drop/template/Scripts/rnaVariantCalling/Overview.R",742   "sha256": "7473043ebb6dcc2667c748daa13dc05269001b8a39e8d0f01e873bf274094853",743   "language": "R",744   "lines": 55,745   "truncated": false,746   "block": 13,747   "row": 1378748  },749  {750   "path": "drop/utils.py",751   "sha256": "b432cdb9ade2014edb653d602508df1116baa1927c193bcd0819bc256f542e5d",752   "language": "Python",753   "lines": 117,754   "truncated": false,755   "block": 12,756   "row": 11943757  },758  {759   "path": "setup.py",760   "sha256": "d646427983dada887f7ebcf088415ae6fb2169f4781f55e4368a722701800318",761   "language": "Python",762   "lines": 36,763   "truncated": false,764   "block": 12,765   "row": 6720766  },767  {768   "path": "tests/common.py",769   "sha256": "bc3bb4a395da187cfdd9aab407e60c67d07109aa7cefcd2efbee7f58c0410823",770   "language": "Python",771   "lines": 29,772   "truncated": false,773   "block": 12,774   "row": 5459775  },776  {777   "path": "tests/config/test_AE.py",778   "sha256": "63e4ed02091e0565e8cd2ff018254d68aa9e3a981e0495c5e2d520baa4ad98a4",779   "language": "Python",780   "lines": 56,781   "truncated": false,782   "block": 12,783   "row": 8588784  },785  {786   "path": "tests/config/test_AS.py",787   "sha256": "125caf7c18e6f7165550c040863746136f35dae1f075d819cad5c64abeefa397",788   "language": "Python",789   "lines": 56,790   "truncated": false,791   "block": 12,792   "row": 8949793  },794  {795   "path": "tests/config/test_MAE.py",796   "sha256": "242f7ee618f31f4fb5ddaefef1a584a549a14620223eb27e2a1cce6b1b234d54",797   "language": "Python",798   "lines": 21,799   "truncated": false,800   "block": 12,801   "row": 5581802  },803  {804   "path": "tests/config/test_RVC.py",805   "sha256": "43ba4522fcc8ca8c2dd07fd4cd6f3116bc5c31a8338b214193cbf5cf3d588dba",806   "language": "Python",807   "lines": 14,808   "truncated": false,809   "block": 12,810   "row": 5083811  },812  {813   "path": "tests/config/test_SampleAnnotation.py",814   "sha256": "7a727c0b60034066fe47aa2655ea2e5a3c15a65718dc3e1ec5d1985a64303cb8",815   "language": "Python",816   "lines": 49,817   "truncated": false,818   "block": 12,819   "row": 8858820  },821  {822   "path": "tests/config/test_config.py",823   "sha256": "976831f9bd5038562c9ad9125c640be7cd4054ef82d3c2cfdb905f8261a4e954",824   "language": "Python",825   "lines": 49,826   "truncated": false,827   "block": 12,828   "row": 8722829  },830  {831   "path": "tests/conftest.py",832   "sha256": "873388a3ac0931adb546ed604900671ac2b593ad6c92472aace7d8c79f23d7d1",833   "language": "Python",834   "lines": 32,835   "truncated": false,836   "block": 12,837   "row": 5909838  },839  {840   "path": "tests/full_test_run/full_kremer_test.sh",841   "sha256": "e88cad916b7b4f88317c37c31f6207e59bf7571c03c7ad56db8dffcfd23d3079",842   "language": "Shell",843   "lines": 66,844   "truncated": false,845   "block": 13,846   "row": 5374847  },848  {849   "path": "tests/full_test_run/kremer_test.R",850   "sha256": "b18897a575a84dd06b90ddb6b0331f4a2b38bc0f39577700b3561dd6851b9e25",851   "language": "R",852   "lines": 128,853   "truncated": false,854   "block": 13,855   "row": 2042856  },857  {858   "path": "tests/pipeline/test_AE.py",859   "sha256": "ade6ca86e7d54ab6b99b393efd36a432322d025fb7d3c520759adf0f15ba02d8",860   "language": "Python",861   "lines": 91,862   "truncated": false,863   "block": 12,864   "row": 12023865  },866  {867   "path": "tests/pipeline/test_AS.py",868   "sha256": "e688b5e9af6955f6e283cb05018d0b36f13661f47ec936a75321b7b8e17e6e69",869   "language": "Python",870   "lines": 64,871   "truncated": false,872   "block": 12,873   "row": 10314874  },875  {876   "path": "tests/pipeline/test_MAE.py",877   "sha256": "3ace7371749945b48097b6e62efa17b57df3600805532c60fe1a5762bbdbe5e7",878   "language": "Python",879   "lines": 44,880   "truncated": false,881   "block": 12,882   "row": 7944883  },884  {885   "path": "tests/pipeline/test_RVC.py",886   "sha256": "c57ec0483a034e6fd3c9c6f1e858f2395da8d4354885b33da6ee44666d128a40",887   "language": "Python",888   "lines": 43,889   "truncated": false,890   "block": 12,891   "row": 8762892  },893  {894   "path": "tests/pipeline/test_pipeline.py",895   "sha256": "fd09c43400cf902c8ff2c77538c4ab5a171bc3ada5fb328baa58d3ece4224714",896   "language": "Python",897   "lines": 44,898   "truncated": false,899   "block": 12,900   "row": 8126901  },902  {903   "path": "tests/test_cli.py",904   "sha256": "057d89badaf9a1fbaf08f7e518c3da6a63d10a910acdde656061a37008b5d603",905   "language": "Python",906   "lines": 22,907   "truncated": false,908   "block": 12,909   "row": 4880910  }911 ]912}