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Remove unneeded params in CWL #23

Description

@junjun-zhang

These two parameters are not really needed:
download_reference_files

download_reference_files:
type: string
inputBinding:
position: 11
prefix: --download-reference-files
doc: should we attempt to download the reference files ["true", "false"]

output_dir

output_dir:
type: string
inputBinding:
position: 9
prefix: --output-dir
doc: the output directory

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