common-workflow-language / common-workflow-language/cwltool
cwltool validate will pass workflows with fatal issues in included processes
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- Python
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Description
`cwltool 3.0.20200324120055`
Consider the following workflow: https://github.com/NCI-GDC/gdc-dnaseq-cwl/blob/18affdd927cc388fab2c113dc2ec6df782af2a52/workflows/bamfastq_align/transform.cwl
This passes `cwltool --validate`. However, there is an issue with an enclosed workflow: The workflow `gdc-dnaseq-cwl/workflows/bamfastq_align/fastq_clean_pe.cwl` does not supply a required input `reads_in_memory` to the tool `gdc-dnaseq-cwl/tools/fastq_cleaner_pe.cwl`
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