common-workflow-lab/wdl-cwl-translator

Issues

• workflow level non-bound WDL declarations

  #147 opened 8 months ago by mr-c
  0

• 'Apply' object has no attribute 'expr'

  #200 opened 8 months ago by admi2u
  11

• Work through the WDL Conformance Tests from DataBiosphere

  #246 opened 8 months ago by mr-c
  0

• WDL Expressions in workflow input definitions

  #240 opened 8 months ago by mr-c
  0

• Fix dependencies in setup.py and requirements.txt

  #111 opened 8 months ago by kinow
  1

• Try to centralize strings parsing in get_expr_string

  #185 opened 3 years ago by kinow
  1

• Some WDL Maps are not handled

  #77 opened 3 years ago by dinithiW
  8

• Simplify translate_wdl_placeholder

  #114 opened 3 years ago by kinow
  0

• translate WDL's sub() as replaceAll() equivalent not replace()

  #128 opened 3 years ago by kinow
  4

• static mandatory string component should go outside CWL Parameter References

  #127 opened 3 years ago by mr-c
  1

• implement read_lines

  #175 opened 3 years ago by mr-c
  0

• handle advanced quoting in expressions in the WDL command block

  #131 opened 3 years ago by mr-c
  0

• WDL If-then-else expressions are not handled

  #74 opened 3 years ago by dinithiW
  7

• basic WDL scatter functionality

  #146 opened 3 years ago by mr-c
  2

• advanced scatter: more than one in the same workflow, nested scatters, etc..

  #183 opened 3 years ago by mr-c
  0

• Be able to convert a single real-world WDL pipeline

  #85 opened 3 years ago by mr-c
  6

• read_*(stdout())

  #178 opened 3 years ago by mr-c
  0

• JOSS Paper

  #180 opened 3 years ago by kinow
  1

• implement range()

  #176 opened 3 years ago by mr-c
  0

• WDL workflow output definitions with functions

  #159 opened 3 years ago by mr-c
  1

• synthesize follow on step if there are dependencies between outputs of the same task

  #169 opened 3 years ago by mr-c
  0

• create one new CWL file for each Task / Workflow

  #84 opened 3 years ago by mr-c
  0

• align_and_count.cwl fails validation

  #153 opened 3 years ago by mr-c
  1

• split `get_cwl_task_outputs` into separate functions for the separate uses

  #157 opened 3 years ago by mr-c
  1

• nested WDL struts

  #158 opened 3 years ago by mr-c
  0

• WDL `runtime.disks` with suffixes, WDL expressions

  #105 opened 3 years ago by mr-c
  1

• WDL's `size()` function

  #103 opened 3 years ago by mr-c
  0

• implement WDL's `ceil()` function

  #104 opened 3 years ago by mr-c
  0

• Workflow imports are not handled

  #71 opened 3 years ago by dinithiW
  1

• WDL structs are not handled

  #72 opened 3 years ago by dinithiW
  3

• a complex expression involving size if-then-else and numeric comparisions

  #148 opened 3 years ago by mr-c
  0

• find a way to use available_inputs from the miniwdl object to handle workflow inputs

  #142 opened 3 years ago by ntachukwu
  1

• WDL Workflow task calls are not handled

  #73 opened 3 years ago by dinithiW
  2

• Collaboration with miniwdl

  #144 opened 3 years ago by melibleq
  2

• Make use of the "pos" attribute on MiniWDL objects for better error messages

  #129 opened 3 years ago by mr-c
  0

• WDL `command` section: Consider a more object-oriented approach for WDL function

  #91 opened 3 years ago by mr-c
  14

• Support multiple tasks in the same WDL pipeline

  #99 opened 3 years ago by kinow
  2

• support multiple Task definitions in one file via CWL's $graph

  #67 opened 3 years ago by mr-c
  0

• Make sure no runtime errors if we have more than one `$(` in the WDL command

  #130 opened 3 years ago by kinow
  3

• add inputs( ) function to OOP implementation

  #113 opened 3 years ago by ntachukwu
  0

• Design classes and relationships for the OO approach

  #109 opened 3 years ago by kinow
  0

• Update readme with instructions for running tests

  #108 opened 3 years ago by kinow
  7

• support WDL's `runtime.disks` using fixed numeric values

  #95 opened 3 years ago by mr-c
  13

• WDL runtime requirement cpu not being parsed correctly

  #98 opened 3 years ago by kinow
  0

• Support an empty WDL Task `output` section

  #89 opened 3 years ago by mr-c
  0

• WDL read_string

  #81 opened 3 years ago by mr-c
  3

• re-do optional inputs default values

  #80 opened 3 years ago by mr-c
  0

• CWL expressions/parameter references: use dot notation instead of bracket notation when possible

  #86 opened 3 years ago by mr-c
  1

• stdout() is not handled

  #75 opened 3 years ago by dinithiW
  2

• Confirm all Tasks in the WARP pipelines convert without error

  #68 opened 3 years ago by mr-c
  0