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$5f3b4df1b0f7fdced751fc6079778600ad9fdb45",
 106             "location": "sample2_S01_R1_001.fastq.txt",
 107             "class": "File",
 108             "size": 32
 109         }
 110     ]
 111   }
 112   tool: 12213-keepref-wf.cwl
 113   doc: "Test manipulating keep references with expression tools"
 114
 115 - job: null
 116   output:
 117     out: null
 118   tool: 12418-glob-empty-collection.cwl
 119   doc: "Test glob output on empty collection"
 120
 121 - job: null
 122   output:
 123     out: null
 124   tool: 13976-keepref-wf.cwl
 125   doc: "Test issue 13976"
 126
 127 - job: null
 128   output:
 129     out: out
 130   tool: wf/runin-wf.cwl
 131   doc: "RunInSingleContainer cwl.input.json needs to be consistent with pathmapper manipulations"
 132
 133 - job: secondary/wf-job.yml
 134   output: {}
 135   tool: secondary/wf.cwl
 136   doc: "RunInSingleContainer applies secondaryFile discovery & manipulation before generating cwl.input.yml"
 137
 138 - job: null
 139   output:
 140     out: out
 141   tool: wf/runin-with-ttl-wf.cwl
 142   doc: "RunInSingleContainer respects outputTTL"
 143
 144 - job: secret_test_job.yml
 145   output: {
 146     "out": {
 147         "class": "File",
 148         "location": "hashed_example.txt",
 149         "size": 47,
 150         "checksum": "sha1$f45341c7f03b4dd10646c402908d1aea0d580f5d"
 151     }
 152   }
 153   tool: wf/secret_wf.cwl
 154   doc: "Test secret input parameters"
 155   tags: [ secrets ]
 156
 157 - job: null
 158   output:
 159     out: null
 160   tool: wf/runin-reqs-wf.cwl
 161   doc: "RunInSingleContainer handles dynamic resource requests on step"
 162
 163 - job: null
 164   output:
 165     out: null
 166   tool: wf/runin-reqs-wf2.cwl
 167   doc: "RunInSingleContainer handles dynamic resource requests on embedded subworkflow"
 168
 169 - job: null
 170   output:
 171     out: null
 172   tool: wf/runin-reqs-wf3.cwl
 173   should_fail: true
 174   doc: "RunInSingleContainer disallows dynamic resource request on subworkflow steps"
 175
 176 - job: null
 177   output:
 178     out: null
 179   tool: wf/runin-reqs-wf4.cwl
 180   doc: "RunInSingleContainer discovers static resource request in subworkflow steps"
 181
 182 - job: null
 183   output:
 184     out: null
 185   tool: wf/runin-reqs-wf5.cwl
 186   doc: "RunInSingleContainer has minimum 128 MiB RAM"
 187
 188 - job: secondaryFiles/inp3.yml
 189   output: {}
 190   tool: secondaryFiles/example1.cwl
 191   doc: Discover secondaryFiles at runtime if they are in keep
 192
 193 - job: null
 194   output: {}
 195   tool: secondaryFiles/example3.cwl
 196   doc: Discover secondaryFiles on default values
 197
 198 - job: null
 199   output:
 200     out: null
 201   tool: wf-defaults/wf1.cwl
 202   doc: "Can have separate default parameters including directory and file inside same directory"
 203
 204 - job: null
 205   output:
 206     out: null
 207   tool: wf-defaults/wf2.cwl
 208   doc: "Can have a parameter default value that is a directory literal with a file literal"
 209
 210 - job: null
 211   output:
 212     out: null
 213   tool: wf-defaults/wf3.cwl
 214   doc: "Do not accept a directory literal without a basename"
 215   should_fail: true
 216
 217 - job: null
 218   output:
 219     out: null
 220   tool: wf-defaults/wf4.cwl
 221   doc: default in embedded subworkflow missing 'id' field
 222   should_fail: true
 223
 224 - job: null
 225   output:
 226     out: null
 227   tool: wf-defaults/wf5.cwl
 228   doc: default in embedded subworkflow
 229
 230 - job: null
 231   output:
 232     out: null
 233   tool: wf-defaults/wf6.cwl
 234   doc: default in RunInSingleContainer step
 235
 236 - job: null
 237   output:
 238     out: null
 239   tool: wf-defaults/wf7.cwl
 240   doc: workflow level default in RunInSingleContainer
 241
 242 - job: 13931-size-job.yml
 243   output:
 244     "out": {
 245         "checksum": "sha1$5bf6e5357bd42a6b1d2a3a040e16a91490064d26",
 246         "location": "size.txt",
 247         "class": "File",
 248         "size": 3
 249     }
 250   tool: 13931-size.cwl
 251   doc: Test that size is set for files in Keep
 252
 253 - job: 15241-writable-dir-job.json
 254   output: {
 255     "results": {
 256         "basename": "keep:6dd5fa20622d5a7a23c9147d0927da2a+180",
 257         "class": "Directory",
 258         "listing": [
 259             {
 260                 "basename": "d7514270f356df848477718d58308cc4+94",
 261                 "class": "Directory",
 262                 "listing": [
 263                     {
 264                         "basename": "a",
 265                         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 266                         "class": "File",
 267                         "location": "a",
 268                         "size": 0
 269                     },
 270                     {
 271                         "basename": "blurg.txt",
 272                         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 273                         "class": "File",
 274                         "location": "blurg.txt",
 275                         "size": 0
 276                     },
 277                     {
 278                         "basename": "c",
 279                         "class": "Directory",
 280                         "listing": [
 281                             {
 282                                 "basename": "d",
 283                                 "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 284                                 "class": "File",
 285                                 "location": "d",
 286                                 "size": 0
 287                             }
 288                         ],
 289                         "location": "c"
 290                     },
 291                     {
 292                         "basename": "b",
 293                         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
 294                         "class": "File",
 295                         "location": "b",
 296                         "size": 0
 297                     }
 298                 ],
 299                 "location": "d7514270f356df848477718d58308cc4+94"
 300             }
 301         ],
 302         "location": "keep:6dd5fa20622d5a7a23c9147d0927da2a+180"
 303     }
 304   }
 305   tool: 15241-writable-dir.cwl
 306   doc: Test for writable collections
 307
 308 - job: badkeep.yml
 309   output: {}
 310   should_fail: true
 311   tool: 15295-bad-keep-ref.cwl
 312   doc: Test checking for invalid keepref
 313
 314 - job: listing-job.yml
 315   output: {
 316     "out": {
 317         "class": "File",
 318         "location": "output.txt",
 319         "size": 5,
 320         "checksum": "sha1$724ba28f4a9a1b472057ff99511ed393a45552e1"
 321     }
 322   }
 323   tool: 16169-no-listing-hint.cwl
 324   doc: "Test cwltool:LoadListingRequirement propagation"