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
rootmanifests1cgithub.com__ngseq__virapipe.json
github.com__ngseq__virapipe.json336 linesDownload Raw Back to 1c
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/ngseq/virapipe",4 "url": "https://github.com/NGSeq/ViraPipe",5 "host": "github.com",6 "commit": "a95014d827f80067e8cd1c14ed81640e0377355c",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "c13791d49d1626c30025a73d79b3dd39cdfc9f0a5e43dd1c46c25f12959b2b6c",14   "language": "License",15   "lines": 21,16   "truncated": false,17   "block": 6,18   "row": 183919  },20  {21   "path": "README.md",22   "sha256": "12af78b426e37a930426c9bc47912c8751d6d8e919b32a1b92f2019a79b00960",23   "language": "Text",24   "lines": 106,25   "truncated": false,26   "block": 8,27   "row": 1037328  },29  {30   "path": "scripts/blast_search.sh",31   "sha256": "0a73cb9932c0b100884593f373ece55b27834f28b7014475edb0edfa6c8bb090",32   "language": "Shell",33   "lines": 28,34   "truncated": false,35   "block": 8,36   "row": 855937  },38  {39   "path": "scripts/filter.py",40   "sha256": "0dc6ed7362291617b665dd609188c00bd1bb1922809d9f29ac892b85966952c5",41   "language": "Python",42   "lines": 22,43   "truncated": false,44   "block": 6,45   "row": 2322946  },47  {48   "path": "scripts/sequential.sh",49   "sha256": "19dee7dddfab00557c5e5f4061d242193d54c6d41fd5430a62fba69394010f40",50   "language": "Shell",51   "lines": 33,52   "truncated": false,53   "block": 8,54   "row": 855155  },56  {57   "path": "scripts/virapipe.sh",58   "sha256": "e7550795f8ae0ec0a2ace6b5c82e1d9ea1e53ec9f8a2c49df74a1da3b4142c3c",59   "language": "Shell",60   "lines": 63,61   "truncated": false,62   "block": 8,63   "row": 925264  },65  {66   "path": "src/main/java/org/ngseq/metagenomics/AlignInterleaved.java",67   "sha256": "53b55d5875b9088f5d98c7c3236cc1ca16a75a3f0627421c1415e9bd234d44a2",68   "language": "Java",69   "lines": 152,70   "truncated": false,71   "block": 5,72   "row": 1288573  },74  {75   "path": "src/main/java/org/ngseq/metagenomics/AlignInterleavedMulti.java",76   "sha256": "08522df6e2ce8bb4704b1708d86279d03e4a32bee9643fec7fdb06224e71f1c3",77   "language": "Java",78   "lines": 164,79   "truncated": false,80   "block": 5,81   "row": 1289982  },83  {84   "path": "src/main/java/org/ngseq/metagenomics/AlignNFilter.java",85   "sha256": "af72907c78cba7bfefeb2776820c229e55303727e7e7819aab96f5c332a633bd",86   "language": "Java",87   "lines": 243,88   "truncated": false,89   "block": 5,90   "row": 1314891  },92  {93   "path": "src/main/java/org/ngseq/metagenomics/Assemble.java",94   "sha256": "16a00d13d74314d464c83b9582d3adaed0c387e599efab8499442f1753a0a1ac",95   "language": "Java",96   "lines": 201,97   "truncated": false,98   "block": 5,99   "row": 13007100  },101  {102   "path": "src/main/java/org/ngseq/metagenomics/BlastN.java",103   "sha256": "fb2ccaf70efb1f4de332c6484099c7a5f73ffcc0b0634c8d459c2c4d42237e91",104   "language": "Java",105   "lines": 158,106   "truncated": false,107   "block": 5,108   "row": 13000109  },110  {111   "path": "src/main/java/org/ngseq/metagenomics/BlastNFilter.java",112   "sha256": "0d3e9a7198f3ea20843797efad8b75ed921d3354925847f6df74b8f2ee12f868",113   "language": "Java",114   "lines": 197,115   "truncated": false,116   "block": 5,117   "row": 13134118  },119  {120   "path": "src/main/java/org/ngseq/metagenomics/BlastRecord.java",121   "sha256": "cbdba98b2650577f59bbe23d06bc9f92cfcce6b38bc306370348302ff728e882",122   "language": "Java",123   "lines": 123,124   "truncated": false,125   "block": 5,126   "row": 12117127  },128  {129   "path": "src/main/java/org/ngseq/metagenomics/Decompress.java",130   "sha256": "693f19cdafe1cef0059f89ed0c3a06e58c1d309549890559994a48ee12bc8fd2",131   "language": "Java",132   "lines": 242,133   "truncated": false,134   "block": 5,135   "row": 13061136  },137  {138   "path": "src/main/java/org/ngseq/metagenomics/DecompressInterleave.java",139   "sha256": "527afc2173216805102280fc80a9af21e6d17012875324f226020c03a36e69bb",140   "language": "Java",141   "lines": 262,142   "truncated": false,143   "block": 5,144   "row": 13125145  },146  {147   "path": "src/main/java/org/ngseq/metagenomics/FastaFilter.java",148   "sha256": "ea328da029835374e6ede06823c22de6d275118a2b17b07b0724978048168c51",149   "language": "Java",150   "lines": 70,151   "truncated": false,152   "block": 5,153   "row": 12415154  },155  {156   "path": "src/main/java/org/ngseq/metagenomics/FastqFilter.java",157   "sha256": "89fa98d12133aff88ccd710cd0a7dc2ccec73957cefafeea4bc192cb02e1951e",158   "language": "Java",159   "lines": 198,160   "truncated": false,161   "block": 5,162   "row": 13032163  },164  {165   "path": "src/main/java/org/ngseq/metagenomics/FastqGroupper.java",166   "sha256": "af915dd1da75b1c446bec9300ff33d910d9d3025cdd990a60e45dc6fc2ec9dea",167   "language": "Java",168   "lines": 135,169   "truncated": false,170   "block": 5,171   "row": 12670172  },173  {174   "path": "src/main/java/org/ngseq/metagenomics/HDFSWriter.java",175   "sha256": "d4d580a054fe6a3d1182f889ef63219a0453f8cf1b579e49a1f2d5aa20d7372f",176   "language": "Java",177   "lines": 317,178   "truncated": false,179   "block": 5,180   "row": 13263181  },182  {183   "path": "src/main/java/org/ngseq/metagenomics/HMMSearch.java",184   "sha256": "300c8fd81d3913927bd4e281458b3312bc749867ce2df3887ce0f0de0f988be5",185   "language": "Java",186   "lines": 171,187   "truncated": false,188   "block": 5,189   "row": 12861190  },191  {192   "path": "src/main/java/org/ngseq/metagenomics/Interleave.java",193   "sha256": "46c9a400f68352313e0e13b8573e91906f32069ad0bd78e3b5199fa5b4045f32",194   "language": "Java",195   "lines": 249,196   "truncated": false,197   "block": 5,198   "row": 13013199  },200  {201   "path": "src/main/java/org/ngseq/metagenomics/InterleaveMulti.java",202   "sha256": "2ca35dbb1eeb81e2cbf717e63288cad566dbc5e390b481bbad9bf97e426e9efc",203   "language": "Java",204   "lines": 232,205   "truncated": false,206   "block": 5,207   "row": 13018208  },209  {210   "path": "src/main/java/org/ngseq/metagenomics/MergeFastq.java",211   "sha256": "85e1a4e51a221f668dba17e2ac4c09d22894c2450a2434c55b023042559f7ccd",212   "language": "Java",213   "lines": 36,214   "truncated": false,215   "block": 5,216   "row": 11710217  },218  {219   "path": "src/main/java/org/ngseq/metagenomics/MyAlignment.java",220   "sha256": "61af135196a40e8374886f8dd752848e9001fd914b612377bdd23abeb7e3254e",221   "language": "Java",222   "lines": 111,223   "truncated": false,224   "block": 5,225   "row": 12217226  },227  {228   "path": "src/main/java/org/ngseq/metagenomics/MyRead.java",229   "sha256": "e4fcbceb5bedec2339efd22d183c5e3c495f1dcae2b119cae9ccecc2ec427ed8",230   "language": "Java",231   "lines": 166,232   "truncated": false,233   "block": 5,234   "row": 12317235  },236  {237   "path": "src/main/java/org/ngseq/metagenomics/NormalizeRDD.java",238   "sha256": "93b0b6b8caf045cd6f47cfceb1c9888628dc5b5e6fc6f5545d65ed996a03f3ad",239   "language": "Java",240   "lines": 130,241   "truncated": false,242   "block": 5,243   "row": 12791244  },245  {246   "path": "src/main/java/org/ngseq/metagenomics/RenameContigsUniq.java",247   "sha256": "8e53a086b28424f3e46120d35b8a64f320afbf9be08dc4c07894523d10ee3203",248   "language": "Java",249   "lines": 71,250   "truncated": false,251   "block": 5,252   "row": 12233253  },254  {255   "path": "src/main/java/org/ngseq/metagenomics/RepartitionFastq.java",256   "sha256": "70f92eae10ffb026a54e0388d9050c3f7182930d13aedf2d1804238d1f8d375c",257   "language": "Java",258   "lines": 38,259   "truncated": false,260   "block": 5,261   "row": 11756262  },263  {264   "path": "src/main/java/org/ngseq/metagenomics/SQLQueryBAM.java",265   "sha256": "e345e69edb3f88915b3165b2ad9648c2bbbf1f02cc39c9bb2b989fb8cc7f9b7a",266   "language": "Java",267   "lines": 89,268   "truncated": false,269   "block": 5,270   "row": 12347271  },272  {273   "path": "src/main/java/org/ngseq/metagenomics/SQLQueryBlast.java",274   "sha256": "08604e031fff1007670e9204b672a0cf556fc95060a942cb9877c2ff4b83da44",275   "language": "Java",276   "lines": 155,277   "truncated": false,278   "block": 5,279   "row": 12831280  },281  {282   "path": "src/main/java/org/ngseq/metagenomics/SQLQueryFastq.java",283   "sha256": "87cfed7b619ef6cc773515d3bf3ac6ea72c238e60f31001710ce0a383087df06",284   "language": "Java",285   "lines": 127,286   "truncated": false,287   "block": 5,288   "row": 12691289  },290  {291   "path": "src/main/java/org/ngseq/metagenomics/SamToFastq.java",292   "sha256": "c9e5b074f5ae97d1511d45668a64dea00154076bbe19f2a602253320eaa88026",293   "language": "Java",294   "lines": 70,295   "truncated": false,296   "block": 5,297   "row": 12101298  },299  {300   "path": "src/main/java/org/ngseq/metagenomics/SplitFasta.java",301   "sha256": "01bad9c69d3fac8898e50866e1ff5ae4016308b7a323038f9e52f5ac124accf0",302   "language": "Java",303   "lines": 49,304   "truncated": false,305   "block": 5,306   "row": 11930307  },308  {309   "path": "src/main/scala/org/ngseq/metagenomics/Codondict.scala",310   "sha256": "dc3cf367fcccfdd846f18d9a2cc3ecb34b5c894dfdf2513239cbe4c83067286e",311   "language": "Scala",312   "lines": 58,313   "truncated": false,314   "block": 8,315   "row": 6398316  },317  {318   "path": "src/main/scala/org/ngseq/metagenomics/ORF.scala",319   "sha256": "16ff87a80491d57c91928b765baaacba6d4ebd9db0ca43b33e2081df51dcd8a5",320   "language": "Scala",321   "lines": 166,322   "truncated": false,323   "block": 8,324   "row": 6403325  },326  {327   "path": "src/main/scala/org/ngseq/metagenomics/Protein_RDD.scala",328   "sha256": "441f820f7e412046f98b8bc11a09a7a4cf246c772c53333b4fc1156d6409e1f1",329   "language": "Scala",330   "lines": 73,331   "truncated": false,332   "block": 8,333   "row": 6401334  }335 ]336}