Move check_station_mismatch logic from CWL file to script

Matthijs van der Wildrequested to merge
RAP-1065-check-station-mismatch into master

A script for the check_station_mismatch step already exists, but the input and output handling was embedded in the CWL step. I have moved this to the Python script, made the script executable, and updated the pipeline step.

Closes RAP-1066

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