sdk/cwl/tests/arvados-tests.yml

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 - job: dir-job.yml
   6   output:
   7     "outlist": {
   8         "size": 20,
   9         "location": "output.txt",
  10         "class": "File",
  11         "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
  12     }
  13   tool: keep-dir-test-input.cwl
  14   doc: Test directory in keep
  15
  16 - job: dir-job2.yml
  17   output:
  18     "outlist": {
  19         "size": 20,
  20         "location": "output.txt",
  21         "class": "File",
  22         "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
  23     }
  24   tool: keep-dir-test-input.cwl
  25   doc: Test directory in keep
  26
  27 - job: null
  28   output:
  29     "outlist": {
  30         "size": 20,
  31         "location": "output.txt",
  32         "class": "File",
  33         "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
  34     }
  35   tool: keep-dir-test-input2.cwl
  36   doc: Test default directory in keep
  37
  38 - job: null
  39   output:
  40     "outlist": {
  41         "size": 20,
  42         "location": "output.txt",
  43         "class": "File",
  44         "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592"
  45     }
  46   tool: keep-dir-test-input3.cwl
  47   doc: Test default directory in keep
  48
  49 - job: octo.yml
  50   output: {}
  51   tool: cat.cwl
  52   doc: Test hashes in filenames
  53
  54 - job: listing-job.yml
  55   output: {
  56     "out": {
  57         "class": "File",
  58         "location": "output.txt",
  59         "size": 5,
  60         "checksum": "sha1$724ba28f4a9a1b472057ff99511ed393a45552e1"
  61     }
  62   }
  63   tool: wf/listing_shallow.cwl
  64   doc: test shallow directory listing
  65
  66 - job: listing-job.yml
  67   output: {
  68     "out": {
  69         "class": "File",
  70         "location": "output.txt",
  71         "size": 5,
  72         "checksum": "sha1$724ba28f4a9a1b472057ff99511ed393a45552e1"
  73     }
  74   }
  75   tool: wf/listing_none.cwl
  76   doc: test no directory listing
  77
  78 - job: listing-job.yml
  79   output: {
  80     "out": {
  81         "class": "File",
  82         "location": "output.txt",
  83         "size": 5,
  84         "checksum": "sha1$724ba28f4a9a1b472057ff99511ed393a45552e1"
  85     }
  86   }
  87   tool: wf/listing_deep.cwl
  88   doc: test deep directory listing
  89
  90 - job: null
  91   output: {}
  92   tool: noreuse.cwl
  93   doc: "Test arv:ReuseRequirement"
  94
  95 - job: 12213-keepref-job.yml
  96   output: {
  97     "out": [
  98         {
  99             "checksum": "sha1$1c78028c0d69163391eef89316b44a57bde3fead",
 100             "location": "sample1_S01_R1_001.fastq.txt",
 101             "class": "File",
 102             "size": 32
 103         },
 104         {
 105             "checksum": "sha1$5f3b4df1b0f7fdced751fc6079778600ad9fdb45",
 106             "location": "sample2_S01_R1_001.fastq.txt",
 107             "class": "File",
 108             "size": 32
 109         }
 110     ]
 111   }
 112   tool: 12213-keepref-wf.cwl
 113   doc: "Test manipulating keep references with expression tools"
 114
 115 - job: null
 116   output:
 117     out: null
 118   tool: 12418-glob-empty-collection.cwl
 119   doc: "Test glob output on empty collection"
 120
 121 - job: null
 122   output:
 123     "out": {
 124         "location": "hello.out",
 125         "class": "File",
 126         "checksum": "sha1$ec5d3976351abab45a483a49ce714a8430cb203a",
 127         "size": 24
 128     }
 129   tool: 13976-keepref-wf.cwl
 130   doc: "Test issue 13976"
 131
 132 - job: null
 133   output:
 134     out: out
 135   tool: wf/runin-wf.cwl
 136   doc: "RunInSingleContainer cwl.input.json needs to be consistent with pathmapper manipulations"
 137
 138 - job: secondary/wf-job.yml
 139   output: {}
 140   tool: secondary/wf.cwl
 141   doc: "RunInSingleContainer applies secondaryFile discovery & manipulation before generating cwl.input.yml"
 142
 143 - job: null
 144   output:
 145     out: out
 146   tool: wf/runin-with-ttl-wf.cwl
 147   doc: "RunInSingleContainer respects outputTTL"
 148
 149 - job: secret_test_job.yml
 150   output: {
 151     "out": {
 152         "class": "File",
 153         "location": "hashed_example.txt",
 154         "size": 47,
 155         "checksum": "sha1$f45341c7f03b4dd10646c402908d1aea0d580f5d"
 156     }
 157   }
 158   tool: wf/secret_wf.cwl
 159   doc: "Test secret input parameters"
 160   tags: [ secrets ]
 161
 162 - job: null
 163   output:
 164     out: null
 165   tool: wf/runin-reqs-wf.cwl
 166   doc: "RunInSingleContainer handles dynamic resource requests on step"
 167
 168 - job: null
 169   output:
 170     out: null
 171   tool: wf/runin-reqs-wf2.cwl
 172   doc: "RunInSingleContainer handles dynamic resource requests on embedded subworkflow"
 173
 174 - job: null
 175   output:
 176     out: null
 177   tool: wf/runin-reqs-wf3.cwl
 178   should_fail: true
 179   doc: "RunInSingleContainer disallows dynamic resource request on subworkflow steps"
 180
 181 - job: null
 182   output:
 183     out: null
 184   tool: wf/runin-reqs-wf4.cwl
 185   doc: "RunInSingleContainer discovers static resource request in subworkflow steps"
 186
 187 - job: null
 188   output:
 189     out: null
 190   tool: wf/runin-reqs-wf5.cwl
 191   doc: "RunInSingleContainer has minimum 128 MiB RAM"
 192
 193 - job: secondaryFiles/inp3.yml
 194   output: {}
 195   tool: secondaryFiles/example1.cwl
 196   doc: Discover secondaryFiles at runtime if they are in keep
 197
 198 - job: null
 199   output: {}
 200   tool: secondaryFiles/example3.cwl
 201   doc: Discover secondaryFiles on default values
 202
 203 - job: null
 204   output:
 205     out: null
 206   tool: wf-defaults/wf1.cwl
 207   doc: "Can have separate default parameters including directory and file inside same directory"
 208
 209 - job: null
 210   output:
 211     out: null
 212   tool: wf-defaults/wf2.cwl
 213   doc: "Can have a parameter default value that is a directory literal with a file literal"
 214
 215 - job: null
 216   output:
 217     out: null
 218   tool: wf-defaults/wf3.cwl
 219   doc: "Do not accept a directory literal without a basename"
 220   should_fail: true
 221
 222 - job: null
 223   output:
 224     out: null
 225   tool: wf-defaults/wf4.cwl
 226   doc: default in embedded subworkflow missing 'id' field, v1.0
 227   should_fail: false
 228
 229 - job: null
 230   output:
 231     out: null
 232   tool: wf-defaults/wf8.cwl
 233   doc: default in embedded subworkflow missing 'id' field, v1.1
 234   should_fail: false
 235
 236 - job: null
 237   output:
 238     out: null
 239   tool: wf-defaults/wf5.cwl
 240   doc: default in embedded subworkflow
 241
 242 - job: null
 243   output:
 244     out: null
 245   tool: wf-defaults/wf6.cwl
 246   doc: default in RunInSingleContainer step
 247
 248 - job: null
 249   output:
 250     out: null
 251   tool: wf-defaults/wf7.cwl
 252   doc: workflow level default in RunInSingleContainer
 253
 254 - job: 13931-size-job.yml
 255   output:
 256     "out": {
 257         "checksum": "sha1$5bf6e5357bd42a6b1d2a3a040e16a91490064d26",
 258         "location": "size.txt",
 259         "class": "File",
 260         "size": 3
 261     }
 262   tool: 13931-size.cwl
 263   doc: Test that size is set for files in Keep
 264
 265 - job: 15241-writable-dir-job.json
 266   output: {
 267     "results": {
 268         "basename": "keep:6dd5fa20622d5a7a23c9147d0927da2a+180",
 269         "class": "Directory",
 270         "listing": [
 271             {
 272                 "basename": "d7514270f356df848477718d58308cc4+94",
 273                 "class": "Directory",
 274                 "listing": [
 275                     {
 276                         "basename": "a",
 277                         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 278                         "class": "File",
 279                         "location": "a",
 280                         "size": 0
 281                     },
 282                     {
 283                         "basename": "blurg.txt",
 284                         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 285                         "class": "File",
 286                         "location": "blurg.txt",
 287                         "size": 0
 288                     },
 289                     {
 290                         "basename": "c",
 291                         "class": "Directory",
 292                         "listing": [
 293                             {
 294                                 "basename": "d",
 295                                 "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 296                                 "class": "File",
 297                                 "location": "d",
 298                                 "size": 0
 299                             }
 300                         ],
 301                         "location": "c"
 302                     },
 303                     {
 304                         "basename": "b",
 305                         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 306                         "class": "File",
 307                         "location": "b",
 308                         "size": 0
 309                     }
 310                 ],
 311                 "location": "d7514270f356df848477718d58308cc4+94"
 312             }
 313         ],
 314         "location": "keep:6dd5fa20622d5a7a23c9147d0927da2a+180"
 315     }
 316   }
 317   tool: 15241-writable-dir.cwl
 318   doc: Test for writable collections
 319
 320 - job: badkeep.yml
 321   output: {}
 322   should_fail: true
 323   tool: 15295-bad-keep-ref.cwl
 324   doc: Test checking for invalid keepref
 325
 326 - job: listing-job.yml
 327   output: {
 328     "out": {
 329         "class": "File",
 330         "location": "output.txt",
 331         "size": 5,
 332         "checksum": "sha1$724ba28f4a9a1b472057ff99511ed393a45552e1"
 333     }
 334   }
 335   tool: 16169-no-listing-hint.cwl
 336   doc: "Test cwltool:LoadListingRequirement propagation"
 337
 338 - job: hello.yml
 339   output:
 340     "out": {
 341         "location": "hello.out",
 342         "class": "File",
 343         "checksum": "sha1$ec5d3976351abab45a483a49ce714a8430cb203a",
 344         "size": 24
 345     }
 346   tool: 16377-missing-default.cwl
 347   doc: "Test issue 16377 - missing default fails even when it should be overridden by valid input"
 348
 349 - job: hello.yml
 350   output:
 351     "out":
 352       "checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15"
 353       "class": "File"
 354       "location": "foo.txt"
 355       "size": 4
 356   tool: 17267-broken-schemas.cwl
 357   doc: "Test issue 17267 - inaccessible $schemas URL is not a fatal error"
 358
 359 - job: null
 360   output: {}
 361   tool: wf/trick_defaults2.cwl
 362   doc: "Test issue 17462 - secondary file objects on file defaults are not resolved"
 363
 364 - job: null
 365   output: {
 366     "stuff": {
 367         "location": "bar.txt",
 368         "basename": "bar.txt",
 369         "class": "File",
 370         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 371         "size": 0
 372     }
 373   }
 374   tool: 17521-dot-slash-glob.cwl
 375   doc: "Test issue 17521 - bug with leading './' capturing files in subdirectories"
 376
 377 - job: null
 378   output: {
 379     "stuff": {
 380         "basename": "foo",
 381         "class": "Directory",
 382         "listing": [
 383             {
 384                 "basename": "bar.txt",
 385                 "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 386                 "class": "File",
 387                 "location": "foo/bar.txt",
 388                 "size": 0
 389             }
 390         ],
 391         "location": "foo"
 392     }
 393   }
 394   tool: 10380-trailing-slash-dir.cwl
 395   doc: "Test issue 10380 - bug with trailing slash when capturing an output directory"
 396
 397 - job: null
 398   output: {
 399     "stuff": {
 400         "basename": "78f3957c41d044352303a3fa326dff1e+102",
 401         "class": "Directory",
 402         "listing": [
 403             {
 404                 "basename": "baz.txt",
 405                 "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 406                 "class": "File",
 407                 "location": "78f3957c41d044352303a3fa326dff1e+102/baz.txt",
 408                 "size": 0
 409             },
 410             {
 411                 "basename": "foo",
 412                 "class": "Directory",
 413                 "listing": [
 414                     {
 415                         "basename": "bar.txt",
 416                         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 417                         "class": "File",
 418                         "location": "78f3957c41d044352303a3fa326dff1e+102/foo/bar.txt",
 419                         "size": 0
 420                     }
 421                 ],
 422                 "location": "78f3957c41d044352303a3fa326dff1e+102/foo"
 423             }
 424         ],
 425         "location": "78f3957c41d044352303a3fa326dff1e+102"
 426     }
 427   }
 428   tool: 17801-runtime-outdir.cwl
 429   doc: "Test issue 17801 - bug using $(runtime.outdir) to capture the output directory"
 430
 431 - job: null
 432   output:
 433     "val": "keep:f225e6259bdd63bc7240599648dde9f1+97/hg19.fa"
 434   tool: 17858-pack-visit-crash.cwl
 435   doc: "Test issue 17858 - keep ref default inputs on ExpressionTool"
 436
 437 - job: 17879-ignore-sbg-fields-job.yml
 438   output:
 439     "outstr": "foo woble bar"
 440   tool: 17879-ignore-sbg-fields.cwl
 441   doc: "Test issue 17879 - ignores sbg fields"
 442
 443 - job: chipseq/chip-seq-single.json
 444   output: {}
 445   tool: chipseq/cwl-packed.json
 446   doc: "Test issue 18723 - correctly upload two directories with the same basename"
 447
 448 - job: null
 449   output: {}
 450   tool: 18994-basename/wf_ren.cwl
 451   doc: "Test issue 18994 - correctly stage file with modified basename"
 452
 453 - job: 19109-upload-secondary.yml
 454   output: {
 455     "out": {
 456         "basename": "file1.catted",
 457         "class": "File",
 458         "location": "file1.catted",
 459         "size": 20,
 460         "checksum": "sha1$c4cead17cebdd829f38c48e18a28f1da72339ef7"
 461     },
 462     "out2": {
 463         "basename": "file2.catted",
 464         "checksum": "sha1$6f71c5d1512519ede45bedfdd624e05fd8037b0d",
 465         "class": "File",
 466         "location": "file2.catted",
 467         "size": 12
 468     }
 469   }
 470   tool: 19109-upload-secondary.cwl
 471   doc: "Test issue 19109 - correctly discover & upload secondary files"
 472
 473 - job: 19678-name-id.yml
 474   output: {
 475     "processed_name": {
 476         "first": "foo",
 477         "last": "bar"
 478     }
 479   }
 480   tool: 19678-name-id.cwl
 481   doc: "Test issue 19678 - non-string type input parameter called 'name'"
 482
 483 - job: oom/fakeoom.yml
 484   output: {}
 485   tool: oom/19975-oom.cwl
 486   doc: "Test feature 19975 - retry on exit 137"
 487
 488 - job: oom/fakeoom.yml
 489   output: {}
 490   tool: oom/19975-oom-mispelled.cwl
 491   doc: "Test feature 19975 - retry on exit 137, old misspelled version"
 492
 493 - job: oom/fakeoom2.yml
 494   output: {}
 495   tool: oom/19975-oom.cwl
 496   doc: "Test feature 19975 - retry on memory error"
 497
 498 - job: oom/fakeoom3.yml
 499   output: {}
 500   tool: oom/19975-oom3.cwl
 501   doc: "Test feature 19975 - retry on custom error"
 502
 503 - job: null
 504   output:
 505     out: out
 506   tool: wf/runseparate-wf.cwl
 507   doc: "test arv:SeparateRunner"
 508
 509 - job: null
 510   output: {
 511     "val": {
 512         "basename": "testdir",
 513         "class": "Directory",
 514         "listing": [
 515             {
 516                 "basename": "a",
 517                 "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 518                 "class": "File",
 519                 "location": "testdir/a",
 520                 "size": 0
 521             },
 522             {
 523                 "basename": "b",
 524                 "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 525                 "class": "File",
 526                 "location": "testdir/b",
 527                 "size": 0
 528             },
 529             {
 530                 "basename": "c",
 531                 "class": "Directory",
 532                 "listing": [
 533                     {
 534                         "basename": "d",
 535                         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 536                         "class": "File",
 537                         "location": "testdir/c/d",
 538                         "size": 0
 539                     }
 540                 ],
 541                 "location": "testdir/c"
 542             }
 543         ],
 544         "location": "testdir"
 545     },
 546     "val2": [
 547         {
 548             "basename": "a",
 549             "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 550             "class": "File",
 551             "location": "a",
 552             "size": 0
 553         },
 554         {
 555             "basename": "b",
 556             "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 557             "class": "File",
 558             "location": "b",
 559             "size": 0
 560         }
 561     ]
 562   }
 563   tool: wf/output_dir_wf.cwl
 564   doc: "test same file appearing in output of both Directory and array"