Open mvdbeek opened 11 months ago
cwltool --pack https://raw.githubusercontent.com/common-workflow-language/cwl-v1.1/main/tests/conflict-wf.cwl should resolve conflicts and output an equivalent workflow to cwlpack output:
$graph: - baseCommand: echo class: CommandLineTool id: echo inputs: text: inputBinding: {} type: string outputs: fileout: outputBinding: {glob: out.txt} type: File stdout: out.txt - baseCommand: cat class: CommandLineTool id: cat inputs: file1: inputBinding: {position: 1} type: File file2: inputBinding: {position: 2} type: File outputs: fileout: outputBinding: {glob: out.txt} type: File stdout: out.txt - class: Workflow id: collision inputs: {input_1: string, input_2: string} outputs: fileout: {outputSource: cat_step/fileout, type: File} steps: cat_step: in: file1: {source: echo_1/fileout} file2: {source: echo_2/fileout} out: [fileout] run: '#cat' echo_1: in: {text: input_1} out: [fileout] run: '#echo' echo_2: in: {text: input_2} out: [fileout] run: '#echo' cwlVersion: v1.1
cwltool --pack https://raw.githubusercontent.com/common-workflow-language/cwl-v1.1/main/tests/conflict-wf.cwl swallows the workflow (without any error):
{ "$graph": [ { "id": "#main/cat", "class": "CommandLineTool", "inputs": [ { "type": "File", "inputBinding": { "position": 1 }, "id": "#main/cat/file1" }, { "type": "File", "inputBinding": { "position": 2 }, "id": "#main/cat/file2" } ], "baseCommand": "cat", "stdout": "out.txt", "outputs": [ { "type": "File", "outputBinding": { "glob": "out.txt" }, "id": "#main/cat/fileout" } ] }, { "id": "#main/echo", "class": "CommandLineTool", "inputs": [ { "type": "string", "inputBinding": {}, "id": "#main/echo/text" } ], "outputs": [ { "type": "File", "outputBinding": { "glob": "out.txt" }, "id": "#main/echo/fileout" } ], "baseCommand": "echo", "stdout": "out.txt" } ], "cwlVersion": "v1.1" }
3.1.20231020140206.dev3+g4337bee3.d20231105
Thank you @mvdbeek for the report; does using cwlpack from https://github.com/rabix/sbpack work for you?
cwlpack
Yes, that's what I generated the expected version with
Expected Behavior
cwltool --pack https://raw.githubusercontent.com/common-workflow-language/cwl-v1.1/main/tests/conflict-wf.cwl should resolve conflicts and output an equivalent workflow to cwlpack output:
Actual Behavior
cwltool --pack https://raw.githubusercontent.com/common-workflow-language/cwl-v1.1/main/tests/conflict-wf.cwl swallows the workflow (without any error):
Your Environment
3.1.20231020140206.dev3+g4337bee3.d20231105