dx-cwl-compile.txt

ResourceNotFound: The specified folder could not be found in project-F6vf5fj0BV9650154B13Vk9j, code 404. Request Time=1507085723.48, Request ID=1507085723834-786503
The destination folder does not exist

Compiling tools/workflows for each step in the workflow
    alignment_to_rec
    alignment
ResourceNotFound: The specified folder could not be found in project-F6vf5fj0BV9650154B13Vk9j, code 404. Request Time=1507085741.25, Request ID=1507085741568-372221
The destination folder does not exist

Compiling tools/workflows for each step in the workflow
    prep_align_inputs
    process_alignment
    merge_split_alignments
Compiling CWL workflow to DNAnexus
{'folder': '/dx-cwl-prep/wf-alignment',
 'name': 'wf-alignment',
 'project': 'project-F6vf5fj0BV9650154B13Vk9j',
 'stages': [{'executable': u'applet-F7B4qQ80BV93VBkP1PzZ8b3y',
             'id': 'prep_align_inputs',
             'input': {u'alignment_rec': {u'$dnanexus_link': {'workflowInputField': u'alignment_rec'}}},
             'name': 'prep_align_inputs'},
            {'executable': u'applet-F7B4qpQ0BV92qfJv0ZFkV7p5',
             'id': 'scatter-process_alignment',
             'input': {u'alignment_rec': {u'$dnanexus_link': {'workflowInputField': u'alignment_rec'}},
                       u'process_alignment_rec': {u'$dnanexus_link': {'outputField': u'process_alignment_rec',
                                                                      'stage': u'prep_align_inputs'}}},
             'name': 'scatter-process_alignment'},
            {'executable': u'applet-F7B4qk80BV9FKY5Z2gk895GF',
             'id': 'merge_split_alignments',
             'input': {u'align_bam_toolinput': {u'$dnanexus_link': {'outputField': u'align_bam',
                                                                    'stage': 'scatter-process_alignment'}},
                       u'alignment_rec': {u'$dnanexus_link': {'workflowInputField': u'alignment_rec'}},
                       u'hla__fastq_toolinput': {u'$dnanexus_link': {'outputField': u'hla__fastq',
                                                                     'stage': 'scatter-process_alignment'}},
                       u'work_bam': {u'$dnanexus_link': {'outputField': u'work_bam',
                                                         'stage': 'scatter-process_alignment'}},
                       u'work_bam_plus__disc_toolinput': {u'$dnanexus_link': {'outputField': u'work_bam_plus__disc',
                                                                              'stage': 'scatter-process_alignment'}},
                       u'work_bam_plus__sr_toolinput': {u'$dnanexus_link': {'outputField': u'work_bam_plus__sr',
                                                                            'stage': 'scatter-process_alignment'}}},
             'name': 'merge_split_alignments'}],
 'title': 'wf-alignment',
 'workflowInputSpec': [{'class': 'hash',
                        'name': 'alignment_rec',
                        'optional': False}],
 'workflowOutputSpec': [{'class': 'hash',
                         'name': 'align_bam',
                         'optional': False,
                         'outputSource': {u'$dnanexus_link': {'outputField': u'align_bam',
                                                              'stage': u'merge_split_alignments'}}},
                        {'class': 'hash',
                         'name': 'work_bam_plus__disc',
                         'optional': True,
                         'outputSource': {u'$dnanexus_link': {'outputField': u'work_bam_plus__disc',
                                                              'stage': u'merge_split_alignments'}}},
                        {'class': 'hash',
                         'name': 'work_bam_plus__sr',
                         'optional': True,
                         'outputSource': {u'$dnanexus_link': {'outputField': u'work_bam_plus__sr',
                                                              'stage': u'merge_split_alignments'}}},
                        {'class': 'array:file',
                         'name': 'hla__fastq',
                         'optional': True,
                         'outputSource': {u'$dnanexus_link': {'outputField': u'hla__fastq',
                                                              'stage': u'merge_split_alignments'}}}]}
Traceback (most recent call last):
  File "/home/chapmanb/drive/az/nexus/dx-cwl/dx-cwl", line 1147, in <module>
    args.func(args)
  File "/home/chapmanb/drive/az/nexus/dx-cwl/dx-cwl", line 892, in compile_workflow
    compile_workflow_internal(args.workflow, args.assets, args.token, args.project)
  File "/home/chapmanb/drive/az/nexus/dx-cwl/dx-cwl", line 926, in compile_workflow_internal
    executable_id[sname] = executable_id.get(sname, compile_workflow_internal(tooldef_fname(step), assets, token, project))
  File "/home/chapmanb/drive/az/nexus/dx-cwl/dx-cwl", line 1064, in compile_workflow_internal
    wfinfo = dxpy.api.workflow_new(input_params, headers={"Authorization": "Bearer {}".format(token)})
  File "/home/chapmanb/install/bcbio-vm/anaconda/lib/python2.7/site-packages/dxpy/api.py", line 1376, in workflow_new
    return DXHTTPRequest('/workflow/new', input_params_cp, always_retry=always_retry, **kwargs)
  File "/home/chapmanb/install/bcbio-vm/anaconda/lib/python2.7/site-packages/dxpy/__init__.py", line 626, in DXHTTPRequest
    raise error_class(content, response.status, time_started, req_id)
dxpy.exceptions.InvalidInput: A stage refers to workflow input field alignment_rec, but the 'inputs' is not specified for the workflow, code 422. Request Time=1507085803.71, Request ID=1507085804037-100022