Note: cnvkit batch is a complex command that is capable of running all or part of the cnvkit internal pipeline, depending on the combination of inputs provided to it. In order to take advantage of this, most inputs to this cwl are optional, so that different workflows can use different forms of the command while still using a single cwl file. For further reading, see the relevant cnvkit docs at https://cnvkit.readthedocs.io/en/stable/quickstart.html#build-a-reference-from-normal-samples-and-infer-tumor-copy-ratios https://cnvkit.readthedocs.io/en/stable/pipeline.html#batch In our pipelines, the command form is mainly determined by the components of the reference input. The somatic_exome cwl pipeline provides a fasta file and a normal bam, which causes the batch pipeline to construct a copy number reference (.cnn file) based on the normal bam. The germline_wgs cwl pipeline does not provide a normal bam; instead it passes a cnn reference file as an optional input. This file is intended to be manually generated from a reference normal sample for use in the pipeline. If it is not provided, cnvkit will automatically generate a flat reference file.