I tried that but it did not work either;
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
MultipleInputFeatureRequirement: {}
ScatterFeatureRequirement: {}
StepInputExpressionRequirement: {}
InlineJavascriptRequirement: {}
SubworkflowFeatureRequirement: {}
inputs:
maf_file:
type: File
bams:
type:
type: array
items:
type: record
fields:
bam_file:
type: File
secondaryFiles:
- ^.bai
sample_id: string
I get error messages that look like this;
ERROR Tool definition failed validation:
cwl/fillout_workflow.cwl:3:1: Object `cwl/fillout_workflow.cwl` is not valid because
tried `Workflow` but
cwl/fillout_workflow.cwl:15:1: the `inputs` field is not valid because
cwl/fillout_workflow.cwl:19:3: item is invalid because
cwl/fillout_workflow.cwl:20:5: the `type` field is not valid because
- tried InputRecordSchema but
cwl/fillout_workflow.cwl:21:7: * the `type` field is not valid because
the value 'array' is not a valid Record_symbol,
expected 'record'
cwl/fillout_workflow.cwl:22:7: * invalid field `items`, expected one of: 'fields',
'type', 'label'
cwl/fillout_workflow.cwl:20:5: - tried InputEnumSchema but
* missing required field `symbols`
cwl/fillout_workflow.cwl:21:7: * the `type` field is not valid because
the value 'array' is not a valid Enum_symbol,
expected 'enum'
cwl/fillout_workflow.cwl:22:7: * invalid field `items`, expected one of: 'symbols',
'type', 'label', 'inputBinding'
cwl/fillout_workflow.cwl:20:5: - tried InputArraySchema but
cwl/fillout_workflow.cwl:22:7: the `items` field is not valid because
- tried InputRecordSchema but
cwl/fillout_workflow.cwl:24:9: the `fields` field is not valid because
tried array of <InputRecordField> but
cwl/fillout_workflow.cwl:25:11: item is invalid because
cwl/fillout_workflow.cwl:27:13: invalid field `secondaryFiles`, expected one
of: 'name', 'doc', 'type', 'inputBinding', 'label'
cwl/fillout_workflow.cwl:22:7: - tried InputEnumSchema but
* missing required field `symbols`
cwl/fillout_workflow.cwl:23:9: * the `type` field is not valid because
the value 'record' is not a valid Enum_symbol,
expected 'enum'
cwl/fillout_workflow.cwl:24:9: * invalid field `fields`, expected one of:
'symbols', 'type', 'label', 'inputBinding'
cwl/fillout_workflow.cwl:22:7: - tried InputArraySchema but
* missing required field `items`
cwl/fillout_workflow.cwl:23:9: * the `type` field is not valid because
the value 'record' is not a valid Array_symbol,
expected 'array'
cwl/fillout_workflow.cwl:24:9: * invalid field `fields`, expected one of: 'items',
'type', 'label', 'inputBinding'