mapSubject error needs fixing

Hello All,

I have a CWL script which uses edit inplace for editing the results in the working directory, but the CWL.

Expected Behavior

It should run and give me the output

Actual Behavior

it complains,

Duplicate keys will become an error in future releases, and are errors by default when using the new API.

warnings.warn(DuplicateKeyFutureWarning(*args)) Tool definition failed validation: (“mapSubject ‘%s’ value ‘%s’ is not a dictand does not have a mapPredicate”, ‘-class’, None)

Workflow Code

cwlVersion: v1.0
class: CommandLineTool
doc: Sp

baseCommand: [python,-m,spladder.spladder]

hints:
  cwltool:InplaceUpdateRequirement:
    inplaceUpdate: true
requirements:
  EnvVarRequirement:
     envDef:
       PYTHONPATH: /cluster/home/usr/spladder/python
  -class: InlineJavascriptRequirement
  -class: InitialWorkDirRequirement
  listing: 
   - entry: $(inputs.spladder_dir)
     writable: true


inputs:
 spladder_gtf: 
  type: File
  inputBinding:
   position: 3
   prefix: -a
 spladder_bams: 
  type: File[]
  inputBinding:
   position: 1
   prefix: -b
   itemSeparator: ","
  secondaryFiles: .bai
 spladder_dir:
  type: Directory
  inputBinding:
   position: 2
   prefix: -o
 spladder_phase2:
  type: string
  inputBinding:
   position: 4
   prefix: -T
 spladder_merge_graphs:
  type: string
  inputBinding:
    position: 5
    prefix: -M
 spladder_qmode:
  type: string
  inputBinding:
    position: 7
    prefix: --qmode
 spladder_quantify_graph:
  type: string
  inputBinding:
    position: 6
    prefix: --quantify_graph


outputs:
 spladder_out:
  type: Directory
  outputBinding:
   glob: $(inputs.spladder_dir.basename)

$namespaces:
  cwltool: http://commonwl.org/cwltool#

Full Traceback

found duplicate key "-class" with value "InitialWorkDirRequirement" (original value: "InlineJavascriptRequirement")
  in "file:///cluster/home/aalva/Projects/PHRT-Immuno/scripts/cwl/spladder_part3.cwl", line 15, column 3

To suppress this check see:
    http://yaml.readthedocs.io/en/latest/api.html#duplicate-keys

Duplicate keys will become an error in future releases, and are errors
by default when using the new API.

  warnings.warn(DuplicateKeyFutureWarning(*args))
Tool definition failed validation:
("mapSubject '%s' value '%s' is not a dictand does not have a mapPredicate", '-class', None)
Traceback (most recent call last):
  File "/cluster/home/aalva/software/anaconda/envs/py2/lib/python2.7/site-packages/cwltool/main.py", line 657, in main
    do_validate=loadingContext.do_validate)
  File "/cluster/home/aalva/software/anaconda/envs/py2/lib/python2.7/site-packages/cwltool/load_tool.py", line 284, in validate_document
    workflowobj, fileuri, checklinks=do_validate)
  File "/cluster/home/aalva/software/anaconda/envs/py2/lib/python2.7/site-packages/schema_salad/ref_resolver.py", line 861, in resolve_all
    self._resolve_idmap(document, loader)
  File "/cluster/home/aalva/software/anaconda/envs/py2/lib/python2.7/site-packages/schema_salad/ref_resolver.py", line 639, in _resolve_idmap
    "and does not have a mapPredicate", k, v)
ValidationException: ("mapSubject '%s' value '%s' is not a dictand does not have a mapPredicate", '-class', None)

Your Environment

• cwltool version: Check using cwltool v1.0

[ranijames]

@mr-c Thanks its now working!

[ranijames]

@mr-c I did not get the results, the program is staring from the first step. Although few results are there