Comments (4)
The test cwl.json
{
"cwlVersion": "v1.2",
"$graph": [
{
"id": "main",
"class": "Workflow",
"inputs": [
{
"id": "command",
"type": "string"
},
{
"id": "wf_file_input",
"type": "File",
"secondaryFiles": [
{
"pattern": ".also",
"required": true
}
]
},
{
"id": "wf_file_input_array",
"type": {
"type": "array",
"items": "File"
},
"secondaryFiles": [
{
"pattern": ".also",
"required": true
}
]
}
],
"outputs": [
{
"id": "the_answer",
"type": "string",
"outputSource": "run_tool/the_answer"
}
],
"steps": [
{
"id": "run_tool",
"run": "#cwl_secondary_files_workflow_tool",
"in": {
"command": "command",
"f": "wf_file_input",
"fs": "wf_file_input_array"
},
"out": [
{
"id": "the_answer"
}
]
}
]
},
{
"id": "cwl_secondary_files_workflow_tool",
"class": "CommandLineTool",
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"hints": {
"DockerRequirement": {
"dockerPull": "debian:stretch-slim"
},
"NetworkAccess": {
"networkAccess": true
},
"LoadListingRequirement": {
"loadListing": "deep_listing"
}
},
"inputs": [
{
"id": "command",
"type": "string"
},
{
"id": "f",
"type": "File",
"inputBinding": {
"position": 2
}
},
{
"id": "fs",
"type": {
"type": "array",
"items": "File",
"inputBinding": {
"position": 3
}
}
}
],
"outputs": {
"the_answer": {
"type": "string",
"outputBinding": {
"outputEval": "${ return \"\\$(\" + 42 + \")\"; }"
}
}
},
"baseCommand": [],
"arguments": [
"bash",
"-c",
"$(inputs.command)"
]
}
]
}
from cwljava.
Please let me know if there is an estimated time for it to be fixed. Thanks!
from cwljava.
The cwljava package is the output of the schema-salad code generator from the CWL specification.
https://github.com/common-workflow-language/schema_salad/blob/main/schema_salad/java_codegen.py
So if there is a bug, it probably would need to be fixed upstream in the code generator, and the cwljava code re-generated.
from cwljava.
Thanks! @tetron
I filed a new issue in schema_salad and will close this one.
common-workflow-language/schema_salad#525
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Related Issues (20)
- parsing CWL v1.0 & v1.1 HOT 8
- Partial/lazy parse? HOT 3
- Supporting recursive expansion of `typeDSL`
- Incomplete $import support HOT 5
- Fails to parse conformance tests (ValidationException: Failed to match union type) HOT 4
- SchemaDefRequirement not parsed correctly HOT 2
- Fails to parse requirements correctly HOT 5
- No way to access custom metadata HOT 2
- Workflows are not parsed correctly HOT 1
- NullPointerException HOT 1
- Add Apache 2.0 license
- CWL version is not set when parsing a packed workflow HOT 4
- Workflow with imported schema is not parsable when packed HOT 1
- Add helper to upgrade documents to CWL v1.2
- WorkflowStepInput source IDs incorrect when parsing workflow packed with cwlpack HOT 5
- Embedded process ID is ignored HOT 2
- Enum types are not parsed correctly HOT 6
- explore rendering the markdown in the javadocs
- Using this SDK to generate CWL Documents HOT 5
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