I don’t think this command is running as you expect it:
- valueFrom: |-
gatk HaplotypeCallerSpark -R $(inputs.Reference2bitGenome.path) -I $(inputs.inputBAM.path) -O $(inputs.output_filename)
Will actually run as “gatk HaplotypeCallerSpark -R …” rather than “gatk” “HaplotypeCallerSpark” “-R” …
I would consider using the ‘inputBinding’ for each of your inputs and a ‘baseCommand’ set to
For the reference, you have put it in as a listing (can you justify why this is necessary), but have specified the
.path attribute. If you wish to reference the file that you have listing in the working directory, you should use the
.basename attribute instead.