parameter references should be removed from cache hash calculations

[mr-c]

this becomes a problem when these parameter references end up in the generated command line

An extreme example: https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl/blob/master/tools/ipr_stats.cwl

[mr-c]

This is still an issue, for example $(runtime.outdir) which varies