Avoid pipes in python in AdapterRemoval node.

Previously, the script attempted to match the file-open order of AR,
which led to deadlocks if this order changed. This patch makes gzip or
bzip responsible for opening the fifo, avoiding this issue as this does
not block the main process.
Don't attempt to detect changes after the run.

This led to some suprising behavior when it worked, but was also
somewhat buggy.
Fix whitespace in prefix path breaking Bowtie2.