common-workflow-language / common-workflow-language/cwltool
Auto-casting single item to array fails
- 主要言語
- Python
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説明
Input
```
inputFileName_markDups:
type: File[]?
inputBinding:
position: 4
prefix: INPUT=
```
The call uses a _single_ BAM file from a previous step, not an array.
Causes the following error:
```
Workflow error, try again with --debug for more information:
Type mismatch between source 'file:///home/ubuntu/gitroot/common-workflow-language/workflows/workflows/GATK/GATK-complete-Workflow-h3abionet.cwl#samtools-sort/sorted' (File) and sink 'file:///home/ubuntu/gitroot/common-workflow-language/workflows/workflows/GATK/GATK-complete-Workflow-h3abionet.cwl#MarkDuplicates/inputFileName_markDups' ([u'null', {u'items': 'File', u'type': u'array'}])
```
But it works fine when markdup's input is:
```
inputFileName_markDups:
type: File[]
inputBinding:
position: 4
prefix: INPUT=
```
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