Output in the format of an input schema

Hi, I have an input schema that I’ve built several tools around, some of which I want to chain together. For example fastqc and cutadapt accept reads in this schema. I want to be able to chain the output from cutadapt (trimmed paired end fatq file) to fastqc using the input schema. How do I get the trimmed reads output by cutadapt into the input schema format? The bentene language server syas I can’t using mappings in the output of a command line tool.



Hi @DiDeoxy, could you post a snippet of the CWL you are using? Is the input schema in a different file? Thanks!