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Simon
/
network-inference-pipeline
mirror of https://github.com/drostlab/network-inference-pipeline

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  1. schema: '2.0'
    2. 

  2. stages:
    3. 

  3.   inspect_tools@utilities:
    4. 

  4.     cmd:
    5. 

  5.     - mkdir -p results/tooling
    6. 

  6.     - singularity run --app manifest toolbox/bin/utilities.sif >results/tooling/utilities.manifest
    7. 

  7.     - singularity run --app specification toolbox/bin/utilities.sif 9ec8df2a1ad7633ed0893527ca1c8c4f56426ab868a0adccea366a9fbf799898
    8. 

  8.       >results/tooling/utilities.specification
    9. 

  9.     deps:
    10. 

  10.     - path: toolbox/bin/utilities.sif
    11. 

  11.       md5: bcc60b742c50c9b3c7ac466d653e2487
    12. 

  12.       size: 26841088
    13. 

  13.     outs:
    14. 

  14.     - path: results/tooling/utilities.manifest
    15. 

  15.       md5: ea94e4e836054dbf5b074d8fcc5c3fcc
    16. 

  16.       size: 691751
    17. 

  17.     - path: results/tooling/utilities.specification
    18. 

  18.       md5: b478b6629042ca3693e49bf237d67f5d
    19. 

  19.       size: 82
    20. 

  20.   acquire_data:
    21. 

  21.     cmd:
    22. 

  22.     - mkdir -p results
    23. 

  23.     - singularity exec toolbox/bin/utilities.sif wget -O results/raw-inputs.zip https://ndownloader.figshare.com/files/26052149
    24. 

  24.     deps:
    25. 

  25.     - path: https://ndownloader.figshare.com/files/26052149
    26. 

  26.       checksum: '"9ec0859fba86ca208118b92ebea977b2"'
    27. 

  27.       size: 51926003
    28. 

  28.     - path: results/tooling/utilities.specification
    29. 

  29.       md5: b478b6629042ca3693e49bf237d67f5d
    30. 

  30.       size: 82
    31. 

  31.     outs:
    32. 

  32.     - path: results/raw-inputs.zip
    33. 

  33.       md5: 9ec0859fba86ca208118b92ebea977b2
    34. 

  34.       size: 51926003
    35. 

  35.   extract_Yang_data:
    36. 

  36.     cmd: singularity exec toolbox/bin/utilities.sif sh src/extract_data.sh results/raw-inputs.zip
    37. 

  37.       "noise_GRN_share/bulk_Yang/*" results/raw/Yang
    38. 

  38.     deps:
    39. 

  39.     - path: results/raw-inputs.zip
    40. 

  40.       md5: 9ec0859fba86ca208118b92ebea977b2
    41. 

  41.       size: 51926003
    42. 

  42.     - path: results/tooling/utilities.specification
    43. 

  43.       md5: b478b6629042ca3693e49bf237d67f5d
    44. 

  44.       size: 82
    45. 

  45.     outs:
    46. 

  46.     - path: results/raw/Yang
    47. 

  47.       md5: 717f50b83204bd005e95a81af740ab8d.dir
    48. 

  48.       size: 21588641
    49. 

  49.       nfiles: 11
    50. 

  50.   clean_Yang_data:
    51. 

  51.     cmd: singularity exec toolbox/bin/utilities.sif sh src/clean_Yang.sh results/raw/Yang
    52. 

  52.       results/clean/Yang
    53. 

  53.     deps:
    54. 

  54.     - path: results/raw/Yang
    55. 

  55.       md5: 717f50b83204bd005e95a81af740ab8d.dir
    56. 

  56.       size: 21588641
    57. 

  57.       nfiles: 11
    58. 

  58.     - path: results/tooling/utilities.specification
    59. 

  59.       md5: b478b6629042ca3693e49bf237d67f5d
    60. 

  60.       size: 82
    61. 

  61.     - path: src/clean_Yang.sh
    62. 

  62.       md5: 03335834f78bcbf998a1a58261e50b61
    63. 

  63.       size: 485
    64. 

  64.     outs:
    65. 

  65.     - path: results/clean/Yang
    66. 

  66.       md5: 612f9167ca9ae3826517602309691430.dir
    67. 

  67.       size: 3572827
    68. 

  68.       nfiles: 7
    69. 

  69.   inspect_tools@Rmultitool:
    70. 

  70.     cmd:
    71. 

  71.     - mkdir -p results/tooling
    72. 

  72.     - singularity run --app manifest toolbox/bin/R-multitool.sif >results/tooling/R-multitool.manifest
    73. 

  73.     - singularity run --app specification toolbox/bin/R-multitool.sif adc703754189748fa75be2a4ec9f317f39409cfaf08eee163d7f8f59c6b511d1
    74. 

  74.       >results/tooling/R-multitool.specification
    75. 

  75.     deps:
    76. 

  76.     - path: toolbox/bin/R-multitool.sif
    77. 

  77.       md5: bc82f33c01b13bf11ad1c71f8698e701
    78. 

  78.       size: 770953216
    79. 

  79.     outs:
    80. 

  80.     - path: results/tooling/R-multitool.manifest
    81. 

  81.       md5: dc3df55d91790360a46e4788b246cf8a
    82. 

  82.       size: 31350
    83. 

  83.     - path: results/tooling/R-multitool.specification
    84. 

  84.       md5: bc675df8f8747327eb77a58fb0301770
    85. 

  85.       size: 503
    86. 

  86.   denoise_Yang_data:
    87. 

  87.     cmd: singularity exec toolbox/bin/R-multitool.sif sh src/denoise.sh results/clean/Yang
    88. 

  88.       counts_raw.csv results/denoised/Yang logs/denoised/Yang
    89. 

  89.     deps:
    90. 

  90.     - path: results/clean/Yang
    91. 

  91.       md5: 612f9167ca9ae3826517602309691430.dir
    92. 

  92.       size: 3572827
    93. 

  93.       nfiles: 7
    94. 

  94.     - path: results/tooling/R-multitool.specification
    95. 

  95.       md5: bc675df8f8747327eb77a58fb0301770
    96. 

  96.       size: 503
    97. 

  97.     - path: src/denoise.R
    98. 

  98.       md5: e225c6bb7e080f691f20fed4f7000711
    99. 

  99.       size: 899
    100. 

  100.     - path: src/denoise.sh
    101. 

  101.       md5: 2943d4aba67e432331a1c1c6925ac630
    102. 

  102.       size: 313
    103. 

  103.     outs:
    104. 

  104.     - path: results/denoised/Yang
    105. 

  105.       md5: 460fc635e0bc67e7f8e7a8868847ffd6.dir
    106. 

  106.       size: 13851757
    107. 

  107.       nfiles: 9
    108. 

  108.   slice_Yang_data:
    109. 

  109.     cmd: singularity exec toolbox/bin/utilities.sif sh src/slice.sh results/denoised/Yang
    110. 

  110.       results/sliced/Yang
    111. 

  111.     deps:
    112. 

  112.     - path: results/denoised/Yang
    113. 

  113.       md5: 460fc635e0bc67e7f8e7a8868847ffd6.dir
    114. 

  114.       size: 13851757
    115. 

  115.       nfiles: 9
    116. 

  116.     - path: results/tooling/utilities.specification
    117. 

  117.       md5: b478b6629042ca3693e49bf237d67f5d
    118. 

  118.       size: 82
    119. 

  119.     - path: src/slice.sh
    120. 

  120.       md5: b8c2aebb69164ab9c85b755ae42ba22e
    121. 

  121.       size: 409
    122. 

  122.     outs:
    123. 

  123.     - path: results/sliced/Yang
    124. 

  124.       md5: 064657575d70e478626ee2dec21d62f0.dir
    125. 

  125.       size: 864057
    126. 

  126.       nfiles: 20
    127. 

  127.   inspect_tools@NetworkInferenceJl:
    128. 

  128.     cmd:
    129. 

  129.     - mkdir -p results/tooling
    130. 

  130.     - singularity run --app manifest toolbox/bin/NetworkInference.jl.sif >results/tooling/NetworkInference.jl.manifest
    131. 

  131.     - singularity run --app specification toolbox/bin/NetworkInference.jl.sif 3e491ce8057710cc2f0cf020b178f6315889e1b19357716b5f0da301475f9098
    132. 

  132.       >results/tooling/NetworkInference.jl.specification
    133. 

  133.     deps:
    134. 

  134.     - path: toolbox/bin/NetworkInference.jl.sif
    135. 

  135.       md5: ae0aa7af639b3170a4fec7a3299a3e67
    136. 

  136.       size: 376860672
    137. 

  137.     outs:
    138. 

  138.     - path: results/tooling/NetworkInference.jl.manifest
    139. 

  139.       md5: 52899d0750870deebbdd60a3397e5e7d
    140. 

  140.       size: 11932
    141. 

  141.     - path: results/tooling/NetworkInference.jl.specification
    142. 

  142.       md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
    143. 

  143.       size: 373
    144. 

  144.   infer@Yang/NetworkInference.jl/PIDC:
    145. 

  145.     cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
    146. 

  146.       results/sliced/Yang results/networks/Yang/NetworkInference.jl/PIDC logs/networks/Yang/NetworkInference.jl/PIDC
    147. 

  147.       julia src/inference/NetworkInference.jl/infer_network.jl PIDC
    148. 

  148.     deps:
    149. 

  149.     - path: results/sliced/Yang
    150. 

  150.       md5: 064657575d70e478626ee2dec21d62f0.dir
    151. 

  151.       size: 864057
    152. 

  152.       nfiles: 20
    153. 

  153.     - path: results/tooling/NetworkInference.jl.specification
    154. 

  154.       md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
    155. 

  155.       size: 373
    156. 

  156.     - path: src/inference/NetworkInference.jl
    157. 

  157.       md5: c238c0ef87689cb377e3ced160111648.dir
    158. 

  158.       size: 371
    159. 

  159.       nfiles: 1
    160. 

  160.     - path: src/inference/infer_foreach_slice.sh
    161. 

  161.       md5: 417599e24e01a117745f41d89c23ef8f
    162. 

  162.       size: 1176
    163. 

  163.     outs:
    164. 

  164.     - path: results/networks/Yang/NetworkInference.jl/PIDC
    165. 

  165.       md5: d44ebf3bd6def39939c1c30e42fb92b7.dir
    166. 

  166.       size: 236779444
    167. 

  167.       nfiles: 20
    168. 

  168.   infer@Yang/NetworkInference.jl/CLR:
    169. 

  169.     cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
    170. 

  170.       results/sliced/Yang results/networks/Yang/NetworkInference.jl/CLR logs/networks/Yang/NetworkInference.jl/CLR
    171. 

  171.       julia src/inference/NetworkInference.jl/infer_network.jl CLR
    172. 

  172.     deps:
    173. 

  173.     - path: results/sliced/Yang
    174. 

  174.       md5: 064657575d70e478626ee2dec21d62f0.dir
    175. 

  175.       size: 864057
    176. 

  176.       nfiles: 20
    177. 

  177.     - path: results/tooling/NetworkInference.jl.specification
    178. 

  178.       md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
    179. 

  179.       size: 373
    180. 

  180.     - path: src/inference/NetworkInference.jl
    181. 

  181.       md5: c238c0ef87689cb377e3ced160111648.dir
    182. 

  182.       size: 371
    183. 

  183.       nfiles: 1
    184. 

  184.     - path: src/inference/infer_foreach_slice.sh
    185. 

  185.       md5: 417599e24e01a117745f41d89c23ef8f
    186. 

  186.       size: 1176
    187. 

  187.     outs:
    188. 

  188.     - path: results/networks/Yang/NetworkInference.jl/CLR
    189. 

  189.       md5: 430510c3e62be2d361b5e4f2d88827f2.dir
    190. 

  190.       size: 227389786
    191. 

  191.       nfiles: 20
    192. 

  192.   extract_Cuomo_data:
    193. 

  193.     cmd: singularity exec toolbox/bin/utilities.sif sh src/extract_data.sh results/raw-inputs.zip
    194. 

  194.       "noise_GRN_share/SC_Cuomo/*" results/raw/Cuomo
    195. 

  195.     deps:
    196. 

  196.     - path: results/raw-inputs.zip
    197. 

  197.       md5: 9ec0859fba86ca208118b92ebea977b2
    198. 

  198.       size: 51926003
    199. 

  199.     - path: results/tooling/utilities.specification
    200. 

  200.       md5: b478b6629042ca3693e49bf237d67f5d
    201. 

  201.       size: 82
    202. 

  202.     outs:
    203. 

  203.     - path: results/raw/Cuomo
    204. 

  204.       md5: f0143ff3cb97ab3c5c3b9530b3ea3931.dir
    205. 

  205.       size: 446579167
    206. 

  206.       nfiles: 11
    207. 

  207.   clean_Cuomo_data:
    208. 

  208.     cmd: singularity exec toolbox/bin/utilities.sif sh src/clean_Cuomo.sh results/raw/Cuomo
    209. 

  209.       results/clean/Cuomo
    210. 

  210.     deps:
    211. 

  211.     - path: results/raw/Cuomo
    212. 

  212.       md5: f0143ff3cb97ab3c5c3b9530b3ea3931.dir
    213. 

  213.       size: 446579167
    214. 

  214.       nfiles: 11
    215. 

  215.     - path: results/tooling/utilities.specification
    216. 

  216.       md5: b478b6629042ca3693e49bf237d67f5d
    217. 

  217.       size: 82
    218. 

  218.     - path: src/clean_Cuomo.sh
    219. 

  219.       md5: 5c6a3271d13cc48289d294ca64c35323
    220. 

  220.       size: 407
    221. 

  221.     outs:
    222. 

  222.     - path: results/clean/Cuomo
    223. 

  223.       md5: 0c27f5ad071ac55d3ea29f4e41ee33a4.dir
    224. 

  224.       size: 32982591
    225. 

  225.       nfiles: 4
    226. 

  226.   denoise_Cuomo_data:
    227. 

  227.     cmd: singularity exec toolbox/bin/R-multitool.sif sh src/denoise.sh results/clean/Cuomo
    228. 

  228.       counts_raw_day2.csv results/denoised/Cuomo logs/denoised/Cuomo
    229. 

  229.     deps:
    230. 

  230.     - path: results/clean/Cuomo
    231. 

  231.       md5: 0c27f5ad071ac55d3ea29f4e41ee33a4.dir
    232. 

  232.       size: 32982591
    233. 

  233.       nfiles: 4
    234. 

  234.     - path: results/tooling/R-multitool.specification
    235. 

  235.       md5: bc675df8f8747327eb77a58fb0301770
    236. 

  236.       size: 503
    237. 

  237.     - path: src/denoise.R
    238. 

  238.       md5: e225c6bb7e080f691f20fed4f7000711
    239. 

  239.       size: 899
    240. 

  240.     - path: src/denoise.sh
    241. 

  241.       md5: 2943d4aba67e432331a1c1c6925ac630
    242. 

  242.       size: 313
    243. 

  243.     outs:
    244. 

  244.     - path: results/denoised/Cuomo
    245. 

  245.       md5: df4978ec76edf2021462ac9c2f0b9b33.dir
    246. 

  246.       size: 191741510
    247. 

  247.       nfiles: 7
    248. 

  248.   slice_Cuomo_data:
    249. 

  249.     cmd: singularity exec toolbox/bin/utilities.sif sh src/slice.sh results/denoised/Cuomo
    250. 

  250.       results/sliced/Cuomo
    251. 

  251.     deps:
    252. 

  252.     - path: results/denoised/Cuomo
    253. 

  253.       md5: df4978ec76edf2021462ac9c2f0b9b33.dir
    254. 

  254.       size: 191741510
    255. 

  255.       nfiles: 7
    256. 

  256.     - path: results/tooling/utilities.specification
    257. 

  257.       md5: b478b6629042ca3693e49bf237d67f5d
    258. 

  258.       size: 82
    259. 

  259.     - path: src/slice.sh
    260. 

  260.       md5: b8c2aebb69164ab9c85b755ae42ba22e
    261. 

  261.       size: 409
    262. 

  262.     outs:
    263. 

  263.     - path: results/sliced/Cuomo
    264. 

  264.       md5: 14dbb0743d95091bd23bcb62c7d0aee6.dir
    265. 

  265.       size: 7478152
    266. 

  266.       nfiles: 12
    267. 

  267.   infer@Cuomo/NetworkInference.jl/PUC:
    268. 

  268.     cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
    269. 

  269.       results/sliced/Cuomo results/networks/Cuomo/NetworkInference.jl/PUC logs/networks/Cuomo/NetworkInference.jl/PUC
    270. 

  270.       julia src/inference/NetworkInference.jl/infer_network.jl PUC
    271. 

  271.     deps:
    272. 

  272.     - path: results/sliced/Cuomo
    273. 

  273.       md5: 14dbb0743d95091bd23bcb62c7d0aee6.dir
    274. 

  274.       size: 7478152
    275. 

  275.       nfiles: 12
    276. 

  276.     - path: results/tooling/NetworkInference.jl.specification
    277. 

  277.       md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
    278. 

  278.       size: 373
    279. 

  279.     - path: src/inference/NetworkInference.jl
    280. 

  280.       md5: c238c0ef87689cb377e3ced160111648.dir
    281. 

  281.       size: 371
    282. 

  282.       nfiles: 1
    283. 

  283.     - path: src/inference/infer_foreach_slice.sh
    284. 

  284.       md5: 417599e24e01a117745f41d89c23ef8f
    285. 

  285.       size: 1176
    286. 

  286.     outs:
    287. 

  287.     - path: results/networks/Cuomo/NetworkInference.jl/PUC
    288. 

  288.       md5: 383f7ee94db0b759d14a182e70358dbd.dir
    289. 

  289.       size: 16345552
    290. 

  290.       nfiles: 12
    291. 

  291.   fuse_Yang_data:
    292. 

  292.     cmd: singularity exec toolbox/bin/R-multitool.sif sh src/fuse_samples_foreach.sh
    293. 

  293.       results/denoised/Yang results/clean/Yang/samples.csv results/fused/Yang
    294. 

  294.     deps:
    295. 

  295.     - path: results/clean/Yang
    296. 

  296.       md5: 612f9167ca9ae3826517602309691430.dir
    297. 

  297.       size: 3572827
    298. 

  298.       nfiles: 7
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  299.     - path: results/denoised/Yang
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    301. 

  301.       size: 13851757
    302. 

  302.       nfiles: 9
    303. 

  303.     - path: results/tooling/R-multitool.specification
    304. 

  304.       md5: bc675df8f8747327eb77a58fb0301770
    305. 

  305.       size: 503
    306. 

  306.     - path: src/fuse_samples.R
    307. 

  307.       md5: 3351b6a733b256c9d0463044aef0f8a9
    308. 

  308.       size: 819
    309. 

  309.     - path: src/fuse_samples_foreach.sh
    310. 

  310.       md5: 5aee33d8918c59b2f746bc1c7723e0e8
    311. 

  311.       size: 305
    312. 

  312.     outs:
    313. 

  313.     - path: results/fused/Yang
    314. 

  314.       md5: 899074e95c3cc77759b8a19775890e4f.dir
    315. 

  315.       size: 9326957
    316. 

  316.       nfiles: 9
    317. 

  317.   infer@Cuomo/NetworkInference.jl/PIDC:
    318. 

  318.     cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
    319. 

  319.       results/sliced/Cuomo results/networks/Cuomo/NetworkInference.jl/PIDC logs/networks/Cuomo/NetworkInference.jl/PIDC
    320. 

  320.       julia src/inference/NetworkInference.jl/infer_network.jl PIDC
    321. 

  321.     deps:
    322. 

  322.     - path: results/sliced/Cuomo
    323. 

  323.       md5: 14dbb0743d95091bd23bcb62c7d0aee6.dir
    324. 

  324.       size: 7478152
    325. 

  325.       nfiles: 12
    326. 

  326.     - path: results/tooling/NetworkInference.jl.specification
    327. 

  327.       md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
    328. 

  328.       size: 373
    329. 

  329.     - path: src/inference/NetworkInference.jl
    330. 

  330.       md5: c238c0ef87689cb377e3ced160111648.dir
    331. 

  331.       size: 371
    332. 

  332.       nfiles: 1
    333. 

  333.     - path: src/inference/infer_foreach_slice.sh
    334. 

  334.       md5: 417599e24e01a117745f41d89c23ef8f
    335. 

  335.       size: 1176
    336. 

  336.     outs:
    337. 

  337.     - path: results/networks/Cuomo/NetworkInference.jl/PIDC
    338. 

  338.       md5: a4a4c79e0f10665a2dc2012d70bfabb2.dir
    339. 

  339.       size: 16525252
    340. 

  340.       nfiles: 12
    341. 

  341.   infer@Cuomo/NetworkInference.jl/MI:
    342. 

  342.     cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
    343. 

  343.       results/sliced/Cuomo results/networks/Cuomo/NetworkInference.jl/MI logs/networks/Cuomo/NetworkInference.jl/MI
    344. 

  344.       julia src/inference/NetworkInference.jl/infer_network.jl MI
    345. 

  345.     deps:
    346. 

  346.     - path: results/sliced/Cuomo
    347. 

  347.       md5: 14dbb0743d95091bd23bcb62c7d0aee6.dir
    348. 

  348.       size: 7478152
    349. 

  349.       nfiles: 12
    350. 

  350.     - path: results/tooling/NetworkInference.jl.specification
    351. 

  351.       md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
    352. 

  352.       size: 373
    353. 

  353.     - path: src/inference/NetworkInference.jl
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  354.       md5: c238c0ef87689cb377e3ced160111648.dir
    355. 

  355.       size: 371
    356. 

  356.       nfiles: 1
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  357.     - path: src/inference/infer_foreach_slice.sh
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  358.       md5: 417599e24e01a117745f41d89c23ef8f
    359. 

  359.       size: 1176
    360. 

  360.     outs:
    361. 

  361.     - path: results/networks/Cuomo/NetworkInference.jl/MI
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  362.       md5: 9052973b1c536239944542b1412b5598.dir
    363. 

  363.       size: 16852278
    364. 

  364.       nfiles: 12
    365. 

  365.   analyze@Cuomo/NetworkInference.jl/MI:
    366. 

  366.     cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
    367. 

  367.       results/networks/Cuomo/NetworkInference.jl/MI results/analysis/Cuomo/NetworkInference.jl/MI
    368. 

  368.       logs/analysis/Cuomo/NetworkInference.jl/MI Rscript src/analysis/analyze_for_network_variants.R
    369. 

  369.       src/analysis/data_variants.csv src/analysis/load_network_inference_jl_network.function.R
    370. 

  370.       png
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  371.     deps:
    372. 

  372.     - path: results/networks/Cuomo/NetworkInference.jl/MI
    373. 

  373.       md5: 9052973b1c536239944542b1412b5598.dir
    374. 

  374.       size: 16852278
    375. 

  375.       nfiles: 12
    376. 

  376.     - path: results/tooling/R-multitool.specification
    377. 

  377.       md5: bc675df8f8747327eb77a58fb0301770
    378. 

  378.       size: 503
    379. 

  379.     - path: src/analysis/analyze_for_network_variants.R
    380. 

  380.       md5: 51d10c7d0647b5a5eb857187b935ec07
    381. 

  381.       size: 6960
    382. 

  382.     - path: src/analysis/analyze_foreach_slice.sh
    383. 

  383.       md5: 2b1512007db296a19161a7d3663bf3b6
    384. 

  384.       size: 1334
    385. 

  385.     - path: src/analysis/data_variants.csv
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  386.       md5: 006662e316eb55017e1deb28132e1b6f
    387. 

  387.       size: 243
    388. 

  388.     - path: src/analysis/load_network_inference_jl_network.function.R
    389. 

  389.       md5: 680649f2a2d86d406e0e96713e296e98
    390. 

  390.       size: 492
    391. 

  391.     outs:
    392. 

  392.     - path: results/analysis/Cuomo/NetworkInference.jl/MI
    393. 

  393.       md5: 40f4d9ef2a77d8e871d4fed614ac226c.dir
    394. 

  394.       size: 82831001
    395. 

  395.       nfiles: 54
    396. 

  396.   infer@Yang/NetworkInference.jl/MI:
    397. 

  397.     cmd: singularity exec toolbox/bin/NetworkInference.jl.sif sh src/inference/infer_foreach_slice.sh
    398. 

  398.       results/sliced/Yang results/networks/Yang/NetworkInference.jl/MI logs/networks/Yang/NetworkInference.jl/MI
    399. 

  399.       julia src/inference/NetworkInference.jl/infer_network.jl MI
    400. 

  400.     deps:
    401. 

  401.     - path: results/sliced/Yang
    402. 

  402.       md5: 064657575d70e478626ee2dec21d62f0.dir
    403. 

  403.       size: 864057
    404. 

  404.       nfiles: 20
    405. 

  405.     - path: results/tooling/NetworkInference.jl.specification
    406. 

  406.       md5: 8506d8b02f87d46d2b3ed48d5cf1fa22
    407. 

  407.       size: 373
    408. 

  408.     - path: src/inference/NetworkInference.jl
    409. 

  409.       md5: c238c0ef87689cb377e3ced160111648.dir
    410. 

  410.       size: 371
    411. 

  411.       nfiles: 1
    412. 

  412.     - path: src/inference/infer_foreach_slice.sh
    413. 

  413.       md5: 417599e24e01a117745f41d89c23ef8f
    414. 

  414.       size: 1176
    415. 

  415.     outs:
    416. 

  416.     - path: results/networks/Yang/NetworkInference.jl/MI
    417. 

  417.       md5: 9697f8ebb89d825e0c3210f98d648fc2.dir
    418. 

  418.       size: 244914282
    419. 

  419.       nfiles: 20
    420. 

  420.   infer@Cuomo/GENIE3-R:
    421. 

  421.     cmd: singularity exec toolbox/bin/R-multitool.sif sh src/inference/infer_foreach_slice.sh
    422. 

  422.       results/sliced/Cuomo results/networks/Cuomo/GENIE3-R logs/networks/Cuomo/GENIE3-R
    423. 

  423.       Rscript src/inference/GENIE3-R/infer_network.R
    424. 

  424.     deps:
    425. 

  425.     - path: results/sliced/Cuomo
    426. 

  426.       md5: 14dbb0743d95091bd23bcb62c7d0aee6.dir
    427. 

  427.       size: 7478152
    428. 

  428.       nfiles: 12
    429. 

  429.     - path: results/tooling/R-multitool.specification
    430. 

  430.       md5: bc675df8f8747327eb77a58fb0301770
    431. 

  431.       size: 503
    432. 

  432.     - path: src/inference/GENIE3-R
    433. 

  433.       md5: a5df150e6e7d5e031ba6de4be3c27d86.dir
    434. 

  434.       size: 238
    435. 

  435.       nfiles: 1
    436. 

  436.     - path: src/inference/infer_foreach_slice.sh
    437. 

  437.       md5: 417599e24e01a117745f41d89c23ef8f
    438. 

  438.       size: 1176
    439. 

  439.     outs:
    440. 

  440.     - path: results/networks/Cuomo/GENIE3-R
    441. 

  441.       md5: fac15bf7c2889c4a7b559bd57cffeac7.dir
    442. 

  442.       size: 6477552
    443. 

  443.       nfiles: 12
    444. 

  444.   analyze@Cuomo/GENIE3-R:
    445. 

  445.     cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
    446. 

  446.       results/networks/Cuomo/GENIE3-R results/analysis/Cuomo/GENIE3-R logs/analysis/Cuomo/GENIE3-R
    447. 

  447.       Rscript src/analysis/analyze_for_network_variants.R src/analysis/data_variants.csv
    448. 

  448.       src/analysis/load_genie3r_network.function.R png
    449. 

  449.     deps:
    450. 

  450.     - path: results/networks/Cuomo/GENIE3-R
    451. 

  451.       md5: fac15bf7c2889c4a7b559bd57cffeac7.dir
    452. 

  452.       size: 6477552
    453. 

  453.       nfiles: 12
    454. 

  454.     - path: results/tooling/R-multitool.specification
    455. 

  455.       md5: bc675df8f8747327eb77a58fb0301770
    456. 

  456.       size: 503
    457. 

  457.     - path: src/analysis/analyze_for_network_variants.R
    458. 

  458.       md5: 51d10c7d0647b5a5eb857187b935ec07
    459. 

  459.       size: 6960
    460. 

  460.     - path: src/analysis/analyze_foreach_slice.sh
    461. 

  461.       md5: 2b1512007db296a19161a7d3663bf3b6
    462. 

  462.       size: 1334
    463. 

  463.     - path: src/analysis/data_variants.csv
    464. 

  464.       md5: 006662e316eb55017e1deb28132e1b6f
    465. 

  465.       size: 243
    466. 

  466.     - path: src/analysis/load_genie3r_network.function.R
    467. 

  467.       md5: 12202df92a0152f558c694b549de95f2
    468. 

  468.       size: 277
    469. 

  469.     outs:
    470. 

  470.     - path: results/analysis/Cuomo/GENIE3-R
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  471.       md5: b6a83af6ac6fc5df0d8e6f09b53738ee.dir
    472. 

  472.       size: 71745391
    473. 

  473.       nfiles: 54
    474. 

  474.   inspect_tools@arboreto:
    475. 

  475.     cmd:
    476. 

  476.     - mkdir -p results/tooling
    477. 

  477.     - singularity run --app manifest toolbox/bin/arboreto.sif >results/tooling/arboreto.manifest
    478. 

  478.     - singularity run --app specification toolbox/bin/arboreto.sif 540b9a053e4d862bfab972735d1d62af04485c186cf5735e98748ef5b5f8b27f
    479. 

  479.       >results/tooling/arboreto.specification
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  480.     deps:
    481. 

  481.     - path: toolbox/bin/arboreto.sif
    482. 

  482.       md5: b694f240a16512ff448830734d7d8267
    483. 

  483.       size: 1122693120
    484. 

  484.     outs:
    485. 

  485.     - path: results/tooling/arboreto.manifest
    486. 

  486.       md5: 4ebe1904f00a80abe10c5bd09f509d79
    487. 

  487.       size: 12757
    488. 

  488.     - path: results/tooling/arboreto.specification
    489. 

  489.       md5: 793af50d330ba258602678040a1f76c9
    490. 

  490.       size: 239
    491. 

  491.   analyze@Yang/NetworkInference.jl/CLR:
    492. 

  492.     cmd: singularity exec toolbox/bin/R-multitool.sif sh src/analysis/analyze_foreach_slice.sh
    493. 

  493.       results/networks/Yang/NetworkInference.jl/CLR results/analysis/Yang/NetworkInference.jl/CLR
    494. 

  494.       logs/analysis/Yang/NetworkInference.jl/CLR Rscript src/analysis/analyze_for_network_variants.R
    495. 

  495.       src/analysis/data_variants.csv src/analysis/load_network_inference_jl_network.function.R
    496. 

  496.       png
    497. 

  497.     deps:
    498. 

  498.     - path: results/networks/Yang/NetworkInference.jl/CLR
    499. 

  499.       md5: 430510c3e62be2d361b5e4f2d88827f2.dir
    500. 

  500.       size: 227389786
    501. 

  501.       nfiles: 20
    502. 

  502.     - path: results/tooling/R-multitool.specification
    503. 

  503.       md5: bc675df8f8747327eb77a58fb0301770
    504. 

  504.       size: 503
    505. 

  505.     - path: src/analysis/analyze_for_network_variants.R
    506. 

  506.       md5: 51d10c7d0647b5a5eb857187b935ec07
    507. 

  507.       size: 6960
    508. 

  508.     - path: src/analysis/analyze_foreach_slice.sh
    509. 

  509.       md5: 2b1512007db296a19161a7d3663bf3b6
    510. 

  510.       size: 1334
    511. 

  511.     - path: src/analysis/data_variants.csv
    512. 

  512.       md5: 006662e316eb55017e1deb28132e1b6f
    513. 

  513.       size: 243
    514. 

  514.     - path: src/analysis/load_network_inference_jl_network.function.R
    515. 

  515.       md5: 680649f2a2d86d406e0e96713e296e98
    516. 

  516.       size: 492
    517. 

  517.     outs:
    518. 

  518.     - path: results/analysis/Yang/NetworkInference.jl/CLR
    519. 

  519.       md5: 2eeaf1c368a78db981e7365c29ae463d.dir
    520. 

  520.       size: 209575109
    521. 

  521.       nfiles: 90
    522. 

  522.   infer@Yang/LEAP:
    523. 

  523.     cmd: singularity exec toolbox/bin/R-multitool.sif sh src/inference/infer_foreach_slice.sh
    524. 

  524.       results/sliced/Yang results/networks/Yang/LEAP logs/networks/Yang/LEAP Rscript
    525. 

  525.       src/inference/LEAP/infer_network.R
    526. 

  526.     deps:
    527. 

  527.     - path: results/sliced/Yang
    528. 

  528.       md5: 064657575d70e478626ee2dec21d62f0.dir
    529. 

  529.       size: 864057
    530. 

  530.       nfiles: 20
    531. 

  531.     - path: results/tooling/R-multitool.specification
    532. 

  532.       md5: bc675df8f8747327eb77a58fb0301770
    533. 

  533.       size: 503
    534. 

  534.     - path: src/inference/LEAP
    535. 

  535.       md5: 708b4f57275adfbe4a1202fcf7d76dec.dir
    536. 

  536.       size: 658
    537. 

  537.       nfiles: 1
    538. 

  538.     - path: src/inference/infer_foreach_slice.sh
    539. 

  539.       md5: 417599e24e01a117745f41d89c23ef8f
    540. 

  540.       size: 1176
    541. 

  541.     outs:
    542. 

  542.     - path: results/networks/Yang/LEAP
    543. 

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  962.       results/networks/Yang/NetworkInference.jl/PUC results/analysis/Yang/NetworkInference.jl/PUC
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  963.       logs/analysis/Yang/NetworkInference.jl/PUC Rscript src/analysis/analyze_for_network_variants.R
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  964.       src/analysis/data_variants.csv src/analysis/load_network_inference_jl_network.function.R
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  965.       png
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  966.     deps:
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  967.     - path: results/networks/Yang/NetworkInference.jl/PUC
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  977.     - path: src/analysis/analyze_foreach_slice.sh
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  980.     - path: src/analysis/data_variants.csv
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