Simplify and fix trinity scratch dir handling

[mvdbeek]

This is currently failing on usegalaxy.org with

cp: -r not specified; omitting directory 'trinity_out_dir/Trinity.tmp.fasta.salmon.idx'

we now use the same logic throughout tool regardless of whether an admin has set TRINITY_SCRATCH_DIR.
We should never introduce these tool specific variables, this should've just used $TMPDIR and then the admin / tpv can set this to special values if needed.
The upside is that this now gets tested.

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[natefoo]

We should never introduce these tool specific variables, this should've just used $TMPDIR and then the admin / tpv can set this to special values if needed.

Agreed, but this was much more tedious before TPV since it meant another destination or some custom implementation in a dynamic rule.