Team Ai
Datasetpublic

OpenScientificCodeRegistry/Database

Open Scientific Code Registry (OSCR): the authors' scripts The code published by the authors of open-access neuroscience papers, as found and verified by Open Scientific Code Registry (OSCR). Each file is here exactly as it is at the source, at the verified commit, under the license of its repository. 421,275 unique files (3,782 MB of text) from 8,849 repositories, in 24 Parquet block(s). Only files whose repository's license allows redistribution, confirmed by the repository's… See the full description on the dataset page: https://huggingface.co/datasets/OpenScientificCodeRegistry/Database.

sourceHugging Faceotherupdated 2d agoView on Hugging Face
0likes5.6kdownloads
github.com__chapmanb__bcbio-nextgen.json2784 linesDownload Raw Back to 3d
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/chapmanb/bcbio-nextgen",4 "url": "https://github.com/chapmanb/bcbio-nextgen",5 "host": "github.com",6 "commit": "594339fd1a9694c8f8ed61084e2bd5740cfd59b0",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE.txt",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE.txt",13   "sha256": "7c99126526bfe84cce744d8bc3d7d06f2908de61027275561d2464e41773be0e",14   "language": "License",15   "lines": 20,16   "truncated": false,17   "block": 6,18   "row": 173419  },20  {21   "path": "README.md",22   "sha256": "5115f999753eb14588facf9505190fdb7dda7922500b5a37cec7c5391add50af",23   "language": "Text",24   "lines": 84,25   "truncated": false,26   "block": 8,27   "row": 1057528  },29  {30   "path": "bcbio/__init__.py",31   "sha256": "e3c291c2461e005adc6cea56d334f8d31b97ed8c0ca472f8b836502d539d3d71",32   "language": "Python",33   "lines": 2,34   "truncated": false,35   "block": 6,36   "row": 2036937  },38  {39   "path": "bcbio/bam/__init__.py",40   "sha256": "3283f5adddfd9c526917598f964520654780d7e58cd24fc4068e0d4e50dd88f3",41   "language": "Python",42   "lines": 635,43   "truncated": false,44   "block": 7,45   "row": 1019846  },47  {48   "path": "bcbio/bam/callable.py",49   "sha256": "a6f3c7857c0a7309fbb37182d0713ce8e0f15ee76eb70972247e30eca57e04df",50   "language": "Python",51   "lines": 374,52   "truncated": false,53   "block": 7,54   "row": 826455  },56  {57   "path": "bcbio/bam/counts.py",58   "sha256": "c5082c308f50003d1a568ab2a55ccd8451c454bbc30eee17648e8143eb6414fa",59   "language": "Python",60   "lines": 66,61   "truncated": false,62   "block": 6,63   "row": 3285764  },65  {66   "path": "bcbio/bam/coverage.py",67   "sha256": "3aaedf05efebc5ee2ed4163abc1dfa2e98d777c7c31871d114318599b91f7ef7",68   "language": "Python",69   "lines": 148,70   "truncated": false,71   "block": 6,72   "row": 4387573  },74  {75   "path": "bcbio/bam/cram.py",76   "sha256": "070b95493fe8cdf3d883c04546f65327a056c376c6166cc967454dee30b32516",77   "language": "Python",78   "lines": 67,79   "truncated": false,80   "block": 6,81   "row": 3420082  },83  {84   "path": "bcbio/bam/fasta.py",85   "sha256": "21f806f16fd08436349abda80e7e486948558463cf7b61537eb84da9f5f18f54",86   "language": "Python",87   "lines": 42,88   "truncated": false,89   "block": 6,90   "row": 2843991  },92  {93   "path": "bcbio/bam/fastq.py",94   "sha256": "d7117992b0bd7aeb5c4fd2af230018ed23edcbe2e208ef61933ce60654fac1b2",95   "language": "Python",96   "lines": 317,97   "truncated": false,98   "block": 7,99   "row": 4970100  },101  {102   "path": "bcbio/bam/readstats.py",103   "sha256": "6b99dfe2e4b6899ccc27957311c8904ee20d31f760c09f93e4d44b3134e26a8e",104   "language": "Python",105   "lines": 121,106   "truncated": false,107   "block": 6,108   "row": 41504109  },110  {111   "path": "bcbio/bam/ref.py",112   "sha256": "7d8a5ce8d91be8bbeab1d4f149b0e5257e0f1fd3062d30bc22996db7e73ab34e",113   "language": "Python",114   "lines": 26,115   "truncated": false,116   "block": 6,117   "row": 25287118  },119  {120   "path": "bcbio/bam/skewer.py",121   "sha256": "c21cee4e170a8bc550a12e126bd7895adcc46e89d9b15f998e3d2e7620e8b5d8",122   "language": "Python",123   "lines": 82,124   "truncated": false,125   "block": 6,126   "row": 36385127  },128  {129   "path": "bcbio/bam/trim.py",130   "sha256": "e8a6ea7162064f070cc9d5736e093760eceba292f4b65be7cb7eb2b61b15585f",131   "language": "Python",132   "lines": 267,133   "truncated": false,134   "block": 7,135   "row": 5393136  },137  {138   "path": "bcbio/bed/__init__.py",139   "sha256": "43c1587ebe568d02b36b306b1137a3b3f79442902aaa6688f134b7e428f7e957",140   "language": "Python",141   "lines": 70,142   "truncated": false,143   "block": 6,144   "row": 32101145  },146  {147   "path": "bcbio/broad/__init__.py",148   "sha256": "1d4f3137a3c6ebaac81ff5ccb304145535651f2ba87fb1fcdce6b10b336a3e96",149   "language": "Python",150   "lines": 598,151   "truncated": false,152   "block": 7,153   "row": 10053154  },155  {156   "path": "bcbio/broad/metrics.py",157   "sha256": "66054963ddb9e8b4fae4fb0fe21ee119899c665f9ca6106255761b018614af74",158   "language": "Python",159   "lines": 502,160   "truncated": false,161   "block": 7,162   "row": 9133163  },164  {165   "path": "bcbio/broad/picardrun.py",166   "sha256": "13f0852e9e2daf12975a2d55584e32221c80e77cb2bd7e5b24ac5211b219b4ab",167   "language": "Python",168   "lines": 310,169   "truncated": false,170   "block": 7,171   "row": 5812172  },173  {174   "path": "bcbio/chipseq/__init__.py",175   "sha256": "7e1ec4e9b4300075cfc324f80cdfc9d19140b48f7b837de24d315477a84947e6",176   "language": "Python",177   "lines": 212,178   "truncated": false,179   "block": 7,180   "row": 2212181  },182  {183   "path": "bcbio/chipseq/antibodies.py",184   "sha256": "147a0c97abeb999f50454a04db88ac930f6206aa37b57ab396f5f72e473d0d92",185   "language": "Python",186   "lines": 45,187   "truncated": false,188   "block": 6,189   "row": 28278190  },191  {192   "path": "bcbio/chipseq/atac.py",193   "sha256": "d9f8d025f70a22fa9747d70b31b555bd69782239f38461721b9b2fb525d8772a",194   "language": "Python",195   "lines": 301,196   "truncated": false,197   "block": 7,198   "row": 4537199  },200  {201   "path": "bcbio/chipseq/macs2.py",202   "sha256": "530d5e72c17d5a6ab84770afe3e0912ef22406fcd33ed5421fef63cee9a6bf21",203   "language": "Python",204   "lines": 111,205   "truncated": false,206   "block": 6,207   "row": 41047208  },209  {210   "path": "bcbio/chipseq/peaks.py",211   "sha256": "8f354dd75b8d22c83fc60c26d8187e298c91da53e7886731c0670c16c2998bd8",212   "language": "Python",213   "lines": 376,214   "truncated": false,215   "block": 7,216   "row": 7109217  },218  {219   "path": "bcbio/cwl/__init__.py",220   "sha256": "b8a43670036aab2daaf74bb217f1230f01f91cd0a041a26d8b8a12ce56283684",221   "language": "Python",222   "lines": 2,223   "truncated": false,224   "block": 6,225   "row": 20542226  },227  {228   "path": "bcbio/cwl/create.py",229   "sha256": "1afa6c035477751ace775ca14093946cb96a351a8b99074dbe920a7ed577fa99",230   "language": "Python",231   "lines": 903,232   "truncated": false,233   "block": 7,234   "row": 11657235  },236  {237   "path": "bcbio/cwl/cwlutils.py",238   "sha256": "ce649cbbdb49d008e48b87a087d43d3ba013c53b650b9010ab25b6266191f02c",239   "language": "Python",240   "lines": 266,241   "truncated": false,242   "block": 7,243   "row": 3516244  },245  {246   "path": "bcbio/cwl/defs.py",247   "sha256": "95fc04ee733f31fefa3f3ded41e181d16e91feba94510d95575a6b306cae4be6",248   "language": "Python",249   "lines": 683,250   "truncated": false,251   "block": 7,252   "row": 11592253  },254  {255   "path": "bcbio/cwl/hpc.py",256   "sha256": "4bccc1b9fb392c8a3732713f84b5c19e1ae0f4a5f85a37c308923805d63a0422",257   "language": "Python",258   "lines": 550,259   "truncated": false,260   "block": 7,261   "row": 7644262  },263  {264   "path": "bcbio/cwl/inspect.py",265   "sha256": "0cc59eb397c92219b26fd8c1844cf2bd3e5cbedfdbf8a85e68a01f89ec11a8f6",266   "language": "Python",267   "lines": 101,268   "truncated": false,269   "block": 6,270   "row": 37621271  },272  {273   "path": "bcbio/cwl/main.py",274   "sha256": "44b49d1f8d1593f2aa2d14b170162613d6a05fc225f19098aeaf07bba0fb2340",275   "language": "Python",276   "lines": 12,277   "truncated": false,278   "block": 6,279   "row": 23192280  },281  {282   "path": "bcbio/cwl/tool.py",283   "sha256": "920f2fe948c65955b03743293c8d4dfe667feb9339c73cbe8d526ca2f2ae9d96",284   "language": "Python",285   "lines": 369,286   "truncated": false,287   "block": 7,288   "row": 6931289  },290  {291   "path": "bcbio/cwl/workflow.py",292   "sha256": "d9ed305dd568cf6e0acfa0225cdb6589400b20259e307cbf1876758ed52e3fad",293   "language": "Python",294   "lines": 495,295   "truncated": false,296   "block": 7,297   "row": 8908298  },299  {300   "path": "bcbio/distributed/__init__.py",301   "sha256": "369468ecf6a366fbb91d9ff8a1e97547a0eb4912cebcd2fd20a7a267c1f55ffd",302   "language": "Python",303   "lines": 2,304   "truncated": false,305   "block": 6,306   "row": 20545307  },308  {309   "path": "bcbio/distributed/clargs.py",310   "sha256": "00261edf424d867b76abf9cfee2a63f945df40d88f373fb6aa725941868624b9",311   "language": "Python",312   "lines": 29,313   "truncated": false,314   "block": 6,315   "row": 27191316  },317  {318   "path": "bcbio/distributed/clusterk.py",319   "sha256": "fd42299d6c905023931aa3cdcfe0c51871ebceef9f37de30bd3eb59e211ca59c",320   "language": "Python",321   "lines": 34,322   "truncated": false,323   "block": 6,324   "row": 27233325  },326  {327   "path": "bcbio/distributed/ipython.py",328   "sha256": "ba14f518b249a17e5df39b688bf88814bce73423c3bef751e7ce6d8fff73b0f3",329   "language": "Python",330   "lines": 141,331   "truncated": false,332   "block": 6,333   "row": 42790334  },335  {336   "path": "bcbio/distributed/ipythontasks.py",337   "sha256": "0264e02318aa608a06ed664c47e9e385513bd22eac4c9bd052e19364bbacd88f",338   "language": "Python",339   "lines": 617,340   "truncated": false,341   "block": 7,342   "row": 8550343  },344  {345   "path": "bcbio/distributed/multi.py",346   "sha256": "8d59dc97d23f6e8058c78381e2fdfc2db82e8255cf63523242b3033035756977",347   "language": "Python",348   "lines": 89,349   "truncated": false,350   "block": 6,351   "row": 38124352  },353  {354   "path": "bcbio/distributed/multitasks.py",355   "sha256": "271fd3d9876cb6eca11b5ba6fb15103cd692383d7582c1579574774b2642a6ce",356   "language": "Python",357   "lines": 482,358   "truncated": false,359   "block": 7,360   "row": 4560361  },362  {363   "path": "bcbio/distributed/objectstore.py",364   "sha256": "b01ade7e4a75444eab430b5acfd035d099126097ffdfb39e29c9346ac89d91d9",365   "language": "Python",366   "lines": 712,367   "truncated": false,368   "block": 7,369   "row": 9497370  },371  {372   "path": "bcbio/distributed/prun.py",373   "sha256": "9b0d9620251c66de1147f8700be82e78c68d13f188ec90885d909386d37e53d0",374   "language": "Python",375   "lines": 69,376   "truncated": false,377   "block": 6,378   "row": 35570379  },380  {381   "path": "bcbio/distributed/resources.py",382   "sha256": "feacdbb8d810049d895ced32baea9e01285fb0503d7fdc2828ee39b1427545e7",383   "language": "Python",384   "lines": 234,385   "truncated": false,386   "block": 7,387   "row": 2579388  },389  {390   "path": "bcbio/distributed/runfn.py",391   "sha256": "cf021d2084de885b7aecfe7f5fc7074b09ac21dc840859c0c4af8c93f505f78c",392   "language": "Python",393   "lines": 649,394   "truncated": false,395   "block": 7,396   "row": 10216397  },398  {399   "path": "bcbio/distributed/split.py",400   "sha256": "b16035d35a9ab0520bfa9aa47f66630309f8bcc0508522c7116c80e8f7d28add",401   "language": "Python",402   "lines": 143,403   "truncated": false,404   "block": 6,405   "row": 43888406  },407  {408   "path": "bcbio/distributed/transaction.py",409   "sha256": "8912b9c9976f5f5353fae44ddb5f4e9b295df670d3d51eeebe8c948664c6842c",410   "language": "Python",411   "lines": 159,412   "truncated": false,413   "block": 6,414   "row": 41825415  },416  {417   "path": "bcbio/dragen/dragen.py",418   "sha256": "ed3667572951a25942f8cd2d94664efb49828f7522d06a4e35bdf17aac46e17a",419   "language": "Python",420   "lines": 86,421   "truncated": false,422   "block": 6,423   "row": 37700424  },425  {426   "path": "bcbio/galaxy/__init__.py",427   "sha256": "f758cbe85bcd4b79197060c229afc94861b3772bdfabdc14ce41a7937891bb95",428   "language": "Python",429   "lines": 2,430   "truncated": false,431   "block": 6,432   "row": 20442433  },434  {435   "path": "bcbio/galaxy/api.py",436   "sha256": "a90c7ca6df3e749379e13ffdabc4e87ac13e394bc29925e54a1539746c653e92",437   "language": "Python",438   "lines": 82,439   "truncated": false,440   "block": 6,441   "row": 35345442  },443  {444   "path": "bcbio/galaxy/loc.py",445   "sha256": "0d887f2670b5394b4476758759d81fa7cd85dbcb93955359c3b16e21e8ae65da",446   "language": "Python",447   "lines": 88,448   "truncated": false,449   "block": 6,450   "row": 36401451  },452  {453   "path": "bcbio/galaxy/nglims.py",454   "sha256": "69dbb2408a6cea557f9af98787fa4b8bd2ad3c9e9afaa4e246e190e2e98b3b7f",455   "language": "Python",456   "lines": 189,457   "truncated": false,458   "block": 7,459   "row": 750460  },461  {462   "path": "bcbio/graph/__init__.py",463   "sha256": "838aa7abd6c0345fdf663851f9521dea063f524460085aaecfcfcc94df320aef",464   "language": "Python",465   "lines": 3,466   "truncated": false,467   "block": 6,468   "row": 20630469  },470  {471   "path": "bcbio/graph/collectl.py",472   "sha256": "40056c1d553050867e81df55934705586330422fd8b926e90bff0d2fb45e25dc",473   "language": "Python",474   "lines": 312,475   "truncated": false,476   "block": 7,477   "row": 4479478  },479  {480   "path": "bcbio/graph/graph.py",481   "sha256": "a96dc776ed5479b3db34e481b287f076663c1e863b8ce6146d53b48570ddfb1a",482   "language": "Python",483   "lines": 455,484   "truncated": false,485   "block": 7,486   "row": 6615487  },488  {489   "path": "bcbio/heterogeneity/__init__.py",490   "sha256": "915665a16b36804f2c3765f44839d33c81a8b1442329238facf88c6eaa135411",491   "language": "Python",492   "lines": 146,493   "truncated": false,494   "block": 6,495   "row": 43060496  },497  {498   "path": "bcbio/heterogeneity/bubbletree.py",499   "sha256": "7e8c78dd794bc80898e9445601d853c58b782cfacbc1422a58739e4537246791",500   "language": "Python",501   "lines": 501,502   "truncated": false,503   "block": 7,504   "row": 9153505  },506  {507   "path": "bcbio/heterogeneity/chromhacks.py",508   "sha256": "9471dba77abf70e5552e30820351dcbbf84bd96248d1e45ef404dbe29ea57607",509   "language": "Python",510   "lines": 95,511   "truncated": false,512   "block": 6,513   "row": 35855514  },515  {516   "path": "bcbio/heterogeneity/loh.py",517   "sha256": "da9ff30e9db9cd3207ec6cbf49ce1293fc3e43e8656f95123c82b2f1d4b4356c",518   "language": "Python",519   "lines": 434,520   "truncated": false,521   "block": 7,522   "row": 6921523  },524  {525   "path": "bcbio/heterogeneity/phylowgs.py",526   "sha256": "b59eeefb7b14d595b2f814f5534be51bc1a401b18a3403686fabbf04cd234e5e",527   "language": "Python",528   "lines": 265,529   "truncated": false,530   "block": 7,531   "row": 4682532  },533  {534   "path": "bcbio/heterogeneity/theta.py",535   "sha256": "475cf9c7dd519ff5fa0ff4aa63320f7ea6968caf50c99b0b86d5fdb76473012e",536   "language": "Python",537   "lines": 221,538   "truncated": false,539   "block": 7,540   "row": 3036541  },542  {543   "path": "bcbio/hla/__init__.py",544   "sha256": "36064f042601c6f0c7b17a39848987dc08921f8596877d5b19c5044ba2cbdf54",545   "language": "Python",546   "lines": 32,547   "truncated": false,548   "block": 6,549   "row": 25499550  },551  {552   "path": "bcbio/hla/bwakit.py",553   "sha256": "f23077829e094b351521db0dadba747b05342e1a4f057fd4151db0816b69888a",554   "language": "Python",555   "lines": 89,556   "truncated": false,557   "block": 6,558   "row": 38867559  },560  {561   "path": "bcbio/hla/groups.py",562   "sha256": "3f77e2a46840e122938a36c59b9f207e6f6df065420a9331763798ba62d5c13d",563   "language": "Python",564   "lines": 564,565   "truncated": false,566   "block": 7,567   "row": 6525568  },569  {570   "path": "bcbio/hla/optitype.py",571   "sha256": "fa5cfb0b14b300c46920d1ff6903c7b84b4602dbcc9007c4c00266eba183ca4c",572   "language": "Python",573   "lines": 148,574   "truncated": false,575   "block": 6,576   "row": 44362577  },578  {579   "path": "bcbio/hmmer/__init__.py",580   "sha256": "bc24cad951b3ae20851b6bc9a1089e9a3696bedad47009db6f35f4cd164075c2",581   "language": "Python",582   "lines": 2,583   "truncated": false,584   "block": 6,585   "row": 20319586  },587  {588   "path": "bcbio/hmmer/search.py",589   "sha256": "9e44d06b9d0d66f4c0e58ac9f59c6f1cdbc0076e007f69c3fa598d9bba36adbd",590   "language": "Python",591   "lines": 96,592   "truncated": false,593   "block": 6,594   "row": 38003595  },596  {597   "path": "bcbio/illumina/__init__.py",598   "sha256": "1869e57d400b3a6e053942822ad120a5768729e761f0a0325baf1bf019ec50f4",599   "language": "Python",600   "lines": 2,601   "truncated": false,602   "block": 6,603   "row": 20498604  },605  {606   "path": "bcbio/illumina/demultiplex.py",607   "sha256": "4cedb6e38815e91606ac1c8748c49014f62146b50102c83ff5c77f163226e8b5",608   "language": "Python",609   "lines": 51,610   "truncated": false,611   "block": 6,612   "row": 33357613  },614  {615   "path": "bcbio/illumina/flowcell.py",616   "sha256": "da76dc5c4ef0b83ad92e1ab4a73097082829995e4aa1b29a26064cc8ab971bde",617   "language": "Python",618   "lines": 81,619   "truncated": false,620   "block": 6,621   "row": 35867622  },623  {624   "path": "bcbio/illumina/machine.py",625   "sha256": "9ae9783a2f1100155033f1e7f4b832b567ccadd8695b5716ebe9df3a1e009038",626   "language": "Python",627   "lines": 176,628   "truncated": false,629   "block": 6,630   "row": 45327631  },632  {633   "path": "bcbio/illumina/samplesheet.py",634   "sha256": "07db50c670300933d1d8e61020a18a1f03bf777ae4d05127aa178443c459f333",635   "language": "Python",636   "lines": 133,637   "truncated": false,638   "block": 6,639   "row": 41443640  },641  {642   "path": "bcbio/illumina/transfer.py",643   "sha256": "e6aa22cae187b9d6db65be0ba90a1db2bb92afa8521c253293fb97b78df00bab",644   "language": "Python",645   "lines": 46,646   "truncated": false,647   "block": 6,648   "row": 31990649  },650  {651   "path": "bcbio/install.py",652   "sha256": "7f3a116600d09b1d4ed6701760ec032ef9e1fb8c684be9ba706c736dcc69f7c4",653   "language": "Python",654   "lines": 824,655   "truncated": false,656   "block": 7,657   "row": 11407658  },659  {660   "path": "bcbio/log/__init__.py",661   "sha256": "9ccea321466c278a87f391fe71a80ff5816499d19a2be7b090edab45ee26261a",662   "language": "Python",663   "lines": 165,664   "truncated": false,665   "block": 6,666   "row": 44827667  },668  {669   "path": "bcbio/log/logbook_zmqpush.py",670   "sha256": "c9c8368ebd766a7b38661652d718c9022ccf451f00a5a2998e0313bf23adbdd3",671   "language": "Python",672   "lines": 134,673   "truncated": false,674   "block": 6,675   "row": 39424676  },677  {678   "path": "bcbio/ngsalign/__init__.py",679   "sha256": "ab48817bd41875fced68eece9dfd8ee82d4d988d7f632e4f7eca6baf36b0e30a",680   "language": "Python",681   "lines": 2,682   "truncated": false,683   "block": 6,684   "row": 20517685  },686  {687   "path": "bcbio/ngsalign/alignprep.py",688   "sha256": "5ac18a1dd8b116aa676618a3b4bf172804df5585d2c68ecd6df8c284b1efcd35",689   "language": "Python",690   "lines": 726,691   "truncated": false,692   "block": 7,693   "row": 11046694  },695  {696   "path": "bcbio/ngsalign/bbmap.py",697   "sha256": "82b46a285f79928e260360b4ccad3d813d5c2959cb5dd71592cf6b52518c672a",698   "language": "Python",699   "lines": 39,700   "truncated": false,701   "block": 6,702   "row": 31413703  },704  {705   "path": "bcbio/ngsalign/bismark.py",706   "sha256": "1fef7324dac8fca2f0ec0c5db4eabc0eb0719439202a065064bb5ae3dd6e3088",707   "language": "Python",708   "lines": 157,709   "truncated": false,710   "block": 6,711   "row": 45363712  },713  {714   "path": "bcbio/ngsalign/bowtie.py",715   "sha256": "cf5ea5a4beb386b636f64b3a9fafa72cd07c07e9c54361c157ba2170f5fa171b",716   "language": "Python",717   "lines": 74,718   "truncated": false,719   "block": 6,720   "row": 36248721  },722  {723   "path": "bcbio/ngsalign/bowtie2.py",724   "sha256": "588b93414b3979833778ce17a92cb6fa9858cc58d0f9004b3e4b4d37b7b0e370",725   "language": "Python",726   "lines": 152,727   "truncated": false,728   "block": 6,729   "row": 44886730  },731  {732   "path": "bcbio/ngsalign/bsmap.py",733   "sha256": "12943bf126db36f0db40b580dae4766b5effd2706904f84de0af96793a96c05d",734   "language": "Python",735   "lines": 52,736   "truncated": false,737   "block": 6,738   "row": 32364739  },740  {741   "path": "bcbio/ngsalign/bwa.py",742   "sha256": "978b6eaeec5a0408332748816f09bb16a5c5e3d10accc76ecfc759a69788693c",743   "language": "Python",744   "lines": 359,745   "truncated": false,746   "block": 7,747   "row": 7684748  },749  {750   "path": "bcbio/ngsalign/hisat2.py",751   "sha256": "9f495ee4b1d394dbd5ec7b6826a46cbc06bf5ae7402a141d391e4fbe2b364a1b",752   "language": "Python",753   "lines": 146,754   "truncated": false,755   "block": 6,756   "row": 43517757  },758  {759   "path": "bcbio/ngsalign/minimap2.py",760   "sha256": "f567f887aa53a295535942381b0ec1fcdb783602bb555a447791775a334089a4",761   "language": "Python",762   "lines": 51,763   "truncated": false,764   "block": 6,765   "row": 33534766  },767  {768   "path": "bcbio/ngsalign/mosaik.py",769   "sha256": "b190f2417926db5dd0924458c9ea60479d4a65d93fa788617f7e0e0891c1ff05",770   "language": "Python",771   "lines": 92,772   "truncated": false,773   "block": 6,774   "row": 38917775  },776  {777   "path": "bcbio/ngsalign/novoalign.py",778   "sha256": "4eed3c983319c4bf7c0ac3b13d8b1a0cb129fe8fceeb9f05d035c35724bdbb1a",779   "language": "Python",780   "lines": 148,781   "truncated": false,782   "block": 6,783   "row": 43852784  },785  {786   "path": "bcbio/ngsalign/postalign.py",787   "sha256": "07d2d0159fedec8bd7707b9a41609129b620ce01c984c4d41ff36f3deec0488a",788   "language": "Python",789   "lines": 337,790   "truncated": false,791   "block": 7,792   "row": 7223793  },794  {795   "path": "bcbio/ngsalign/rtg.py",796   "sha256": "5f93eaeff891e3f4d813de5729e00953a20b489d25c12e97d91080bef9ab02db",797   "language": "Python",798   "lines": 100,799   "truncated": false,800   "block": 6,801   "row": 37733802  },803  {804   "path": "bcbio/ngsalign/snap.py",805   "sha256": "e2dae021180ec302608c0819ece5c92c1b5090ce9a88478c1e3fc896731659d3",806   "language": "Python",807   "lines": 86,808   "truncated": false,809   "block": 6,810   "row": 39425811  },812  {813   "path": "bcbio/ngsalign/star.py",814   "sha256": "05d7a87eb4d0d1932164193fd557b9bbe657318095a65d10d07b6924fc4fab8a",815   "language": "Python",816   "lines": 333,817   "truncated": false,818   "block": 7,819   "row": 6321820  },821  {822   "path": "bcbio/ngsalign/tophat.py",823   "sha256": "73cc8d35e7480c66d1d5cd611bbdf812026e5055f662e1b49677ede77fc5a7b7",824   "language": "Python",825   "lines": 370,826   "truncated": false,827   "block": 7,828   "row": 6095829  },830  {831   "path": "bcbio/picard/__init__.py",832   "sha256": "535f7cb57e95452005682d26068173d80a8181d64d83ab0d3c7c5281309658b1",833   "language": "Python",834   "lines": 2,835   "truncated": false,836   "block": 6,837   "row": 20735838  },839  {840   "path": "bcbio/picard/metrics.py",841   "sha256": "c783d9c69d54b773a2ba7789dfb9ffee5eef7fa65299d33eb958d1a562aae0eb",842   "language": "Python",843   "lines": 2,844   "truncated": false,845   "block": 6,846   "row": 20659847  },848  {849   "path": "bcbio/picard/utils.py",850   "sha256": "337a847cd333073314f2fe0940311bf75e9ec3fe2236b724bb9e17db3f52b3c1",851   "language": "Python",852   "lines": 2,853   "truncated": false,854   "block": 6,855   "row": 20481856  },857  {858   "path": "bcbio/pipeline/__init__.py",859   "sha256": "fc9cff6e8388cce85a2583d0b227d16675923be334ab5ddc0fbb5bfbfe95bc06",860   "language": "Python",861   "lines": 14,862   "truncated": false,863   "block": 6,864   "row": 23331865  },866  {867   "path": "bcbio/pipeline/alignment.py",868   "sha256": "d8f05a2227957be36813ab5e442930b286d5382f69184fc23b2f4948e3f83208",869   "language": "Python",870   "lines": 173,871   "truncated": false,872   "block": 7,873   "row": 606874  },875  {876   "path": "bcbio/pipeline/archive.py",877   "sha256": "e528ba1d9b9ec8e45d7bae6f7c923ed27218974f2d531cfb9aaf53c23d9c3595",878   "language": "Python",879   "lines": 31,880   "truncated": false,881   "block": 6,882   "row": 25534883  },884  {885   "path": "bcbio/pipeline/cleanbam.py",886   "sha256": "283aae8b5bdfecdcdaa1169f557de9a31c833aec30544209d4b4f16114aad0db",887   "language": "Python",888   "lines": 161,889   "truncated": false,890   "block": 7,891   "row": 1128892  },893  {894   "path": "bcbio/pipeline/config_utils.py",895   "sha256": "0a08eb08301440767d62948c7c34e61c8e797e92b6a7d12b9e053407cd1f5658",896   "language": "Python",897   "lines": 492,898   "truncated": false,899   "block": 7,900   "row": 8457901  },902  {903   "path": "bcbio/pipeline/datadict.py",904   "sha256": "fb8d28b457471aeea009a8383bfbd289a274aeba463d777b6a439b9582f97c76",905   "language": "Python",906   "lines": 434,907   "truncated": false,908   "block": 7,909   "row": 8661910  },911  {912   "path": "bcbio/pipeline/disambiguate/__init__.py",913   "sha256": "11d8605dc2cfa0da1c6a82e8be4bc9a436c057592c111703e8a25b892bb94470",914   "language": "Python",915   "lines": 167,916   "truncated": false,917   "block": 7,918   "row": 162919  },920  {921   "path": "bcbio/pipeline/disambiguate/run.py",922   "sha256": "28f4fd95a65a6552b7eba20ab4240f3e314e799809e598cb70ec8bdb94c6ae5a",923   "language": "Python",924   "lines": 352,925   "truncated": false,926   "block": 7,927   "row": 7479928  },929  {930   "path": "bcbio/pipeline/fastq.py",931   "sha256": "1d25bcd607edd20d0466bfdf8589e771fe632d0fb0af7b1e1f749ad89bee20ff",932   "language": "Python",933   "lines": 140,934   "truncated": false,935   "block": 6,936   "row": 43127937  },938  {939   "path": "bcbio/pipeline/genome.py",940   "sha256": "326896f2d1644293e7a5e3cce43549dd063ad4d574a779a0ef45c6a6d38fdbb9",941   "language": "Python",942   "lines": 285,943   "truncated": false,944   "block": 7,945   "row": 5705946  },947  {948   "path": "bcbio/pipeline/main.py",949   "sha256": "5e7c128606103297ec91f3b1b87c71fb2f1f727e8e97f28639d96ceb8bb8296f",950   "language": "Python",951   "lines": 533,952   "truncated": false,953   "block": 7,954   "row": 10325955  },956  {957   "path": "bcbio/pipeline/merge.py",958   "sha256": "2faab2475f146f4fa8133521ea6f825351ea0114ec4967d3c99059a49a8095e2",959   "language": "Python",960   "lines": 131,961   "truncated": false,962   "block": 6,963   "row": 43823964  },965  {966   "path": "bcbio/pipeline/qcsummary.py",967   "sha256": "ec974f5b9105a0bb834264f2210837ef8955ee76fdee6b36eeead3ef1b5ee70f",968   "language": "Python",969   "lines": 411,970   "truncated": false,971   "block": 7,972   "row": 7691973  },974  {975   "path": "bcbio/pipeline/region.py",976   "sha256": "1a2a310353c101ad2a7c487c90351a5de35c77cc83231a5db50f2d1a545e9ca0",977   "language": "Python",978   "lines": 189,979   "truncated": false,980   "block": 7,981   "row": 619982  },983  {984   "path": "bcbio/pipeline/rnaseq.py",985   "sha256": "12edb3bb19cf855878346fe262f447bd1b01637996c377efcc55b5de335acb8d",986   "language": "Python",987   "lines": 608,988   "truncated": false,989   "block": 7,990   "row": 10382991  },992  {993   "path": "bcbio/pipeline/run_info.py",994   "sha256": "08deb4269dc9192c31593f6713680f15c65231337d27588782695e6647dcf1c4",995   "language": "Python",996   "lines": 1165,997   "truncated": false,998   "block": 8,999   "row": 4351000  },1001  {1002   "path": "bcbio/pipeline/sample.py",1003   "sha256": "a258deef477bebc6a9ace5ecb11aa4869ce46596e63f2b7dc530cd89440bd429",1004   "language": "Python",1005   "lines": 427,1006   "truncated": false,1007   "block": 7,1008   "row": 85011009  },1010  {1011   "path": "bcbio/pipeline/shared.py",1012   "sha256": "17d54209934693e84c23247f3a935e382d26956546578f0b1d2b5d3448a8d0ac",1013   "language": "Python",1014   "lines": 302,1015   "truncated": false,1016   "block": 7,1017   "row": 51851018  },1019  {1020   "path": "bcbio/pipeline/sra.py",1021   "sha256": "63ab42e3421fd88fe390df70bee3a41837de2e4508d8cab207ed80d4dcf544dd",1022   "language": "Python",1023   "lines": 135,1024   "truncated": false,1025   "block": 6,1026   "row": 417631027  },1028  {1029   "path": "bcbio/pipeline/tools.py",1030   "sha256": "c659ca5f3704e17314dac81c718e6d8c3730b0bc01c072dcb9b927c71dc01a73",1031   "language": "Python",1032   "lines": 37,1033   "truncated": false,1034   "block": 6,1035   "row": 288661036  },1037  {1038   "path": "bcbio/pipeline/variation.py",1039   "sha256": "ba7119a057c475999c8ffc48a0123f1b169f3377ca5380d2b486e0d182d9e0ad",1040   "language": "Python",1041   "lines": 171,1042   "truncated": false,1043   "block": 7,1044   "row": 2841045  },1046  {1047   "path": "bcbio/provenance/__init__.py",1048   "sha256": "262ad7d5e093ed5459d00295243670aa9d4c268ca2beb3a76477e6c5631c256e",1049   "language": "Python",1050   "lines": 2,1051   "truncated": false,1052   "block": 6,1053   "row": 206091054  },1055  {1056   "path": "bcbio/provenance/data.py",1057   "sha256": "63ffa23c096c3c6242a7a689bce6d28090bcba7316f8f4300d6d561f3cc13f65",1058   "language": "Python",1059   "lines": 39,1060   "truncated": false,1061   "block": 6,1062   "row": 297431063  },1064  {1065   "path": "bcbio/provenance/diagnostics.py",1066   "sha256": "cb53f6da912f19b20745bc0df948a3a7e781dd1360a211ffb1768ab38b29d665",1067   "language": "Python",1068   "lines": 77,1069   "truncated": false,1070   "block": 6,1071   "row": 338151072  },1073  {1074   "path": "bcbio/provenance/do.py",1075   "sha256": "0bb102bc6e98b62c27a0703c86e2a55862a3336965ceb162f6895abbdfc91ae5",1076   "language": "Python",1077   "lines": 157,1078   "truncated": false,1079   "block": 6,1080   "row": 423511081  },1082  {1083   "path": "bcbio/provenance/profile.py",1084   "sha256": "ac73308eb6d0a59e751f2ae02785b884ae71fa2c95dcaee980046c55f50980f4",1085   "language": "Python",1086   "lines": 12,1087   "truncated": false,1088   "block": 6,1089   "row": 218141090  },1091  {1092   "path": "bcbio/provenance/programs.py",1093   "sha256": "962033358b1bdad78ca6c9d9d42b0c04e4657fd2be2f31433070f0fbd2d0dba0",1094   "language": "Python",1095   "lines": 289,1096   "truncated": false,1097   "block": 7,1098   "row": 44771099  },1100  {1101   "path": "bcbio/provenance/system.py",1102   "sha256": "195663a9b1441ea1b21101aa85c1e732e37064e18d4a65cfff3af3c73bbebf58",1103   "language": "Python",1104   "lines": 224,1105   "truncated": false,1106   "block": 7,1107   "row": 31301108  },1109  {1110   "path": "bcbio/provenance/versioncheck.py",1111   "sha256": "547c1999b04418afc8167ad71ab4df496b78d968ab4d2a14e4eade689ccffb8c",1112   "language": "Python",1113   "lines": 97,1114   "truncated": false,1115   "block": 6,1116   "row": 389871117  },1118  {1119   "path": "bcbio/qc/__init__.py",1120   "sha256": "55f03e645d7846ca616f72862b0d9ce25210cee8e0a792f24e94db986782f9e8",1121   "language": "Python",1122   "lines": 2,1123   "truncated": false,1124   "block": 6,1125   "row": 203451126  },1127  {1128   "path": "bcbio/qc/atac.py",1129   "sha256": "3cd9217037ccd7c9edf4d5f410a703f9cff170d251d80ba3fe94c09f131f83ad",1130   "language": "Python",1131   "lines": 6,1132   "truncated": false,1133   "block": 6,1134   "row": 208681135  },1136  {1137   "path": "bcbio/qc/atropos.py",1138   "sha256": "d44383e1b2177b590846d519f9f705da8daa8f83bb8d0c47894fc51df09b03d3",1139   "language": "Python",1140   "lines": 21,1141   "truncated": false,1142   "block": 6,1143   "row": 248691144  },1145  {1146   "path": "bcbio/qc/chipseq.py",1147   "sha256": "426e9a51d0b4d0f8e4edeacaac8a68e46e02203092751d7906f3f3c843f6d25a",1148   "language": "Python",1149   "lines": 84,1150   "truncated": false,1151   "block": 6,1152   "row": 356231153  },1154  {1155   "path": "bcbio/qc/contamination.py",1156   "sha256": "62282338aa8965d242849e073de752a0fb2eb8da0e1e4bfad2ed9b5416f52371",1157   "language": "Python",1158   "lines": 113,1159   "truncated": false,1160   "block": 6,1161   "row": 426211162  },1163  {1164   "path": "bcbio/qc/coverage.py",1165   "sha256": "ed350bc5f0975222aef076e3294f26ce66964f289aba98eae422b073907fd519",1166   "language": "Python",1167   "lines": 118,1168   "truncated": false,1169   "block": 6,1170   "row": 424641171  },1172  {1173   "path": "bcbio/qc/damage.py",1174   "sha256": "9c79f4e5646685eef72241bf0c632bdebc1f14cf12fe97890658565db0245726",1175   "language": "Python",1176   "lines": 27,1177   "truncated": false,1178   "block": 6,1179   "row": 265341180  },1181  {1182   "path": "bcbio/qc/fastqc.py",1183   "sha256": "99728c63b6ad4d59845434b7499dfd85d2f31795a62798631b7cb04b30ff1641",1184   "language": "Python",1185   "lines": 135,1186   "truncated": false,1187   "block": 6,1188   "row": 434601189  },1190  {1191   "path": "bcbio/qc/kraken.py",1192   "sha256": "5b933a8667c235a1206962b0e18d815a86d2fd51ef462a6a2e089cbf9cce9daf",1193   "language": "Python",1194   "lines": 95,1195   "truncated": false,1196   "block": 6,1197   "row": 392751198  },1199  {1200   "path": "bcbio/qc/multiqc.py",

Showing the first 1,200 of 2784 lines. Download the file for the rest.