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Showing content from https://github.com/common-workflow-language/cwltool/issues/1304 below:

cwltool validate will pass workflows with fatal issues in included processes · Issue #1304 · common-workflow-language/cwltool · GitHub

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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