In your output, the Command executed: shows correct substitution of the files coming from output channels of STAR_ALIGN_CONTROL & STAR_ALIGN_TREATMENT.

So it seems that might not be the issue. Can you provide the contents of the work directory of DESEQ process? If the files are present in the work dir, it might be unrelated to channels passing the files incorrectly and might be Rscript problem.

  Error: object 'Control' not found
  Execution halted