Bug in Stage index_bams

[nadiadavidson]

index_complete.txt can't be found (but is placed in the working directory).

replace
exec "touch index_complete.txt"
with
exec "touch $output.dir/index_complete.txt"
in clinker.pipe ?

[breons]

Makes sense! Shall fix.

[yelekley]

@nadiadavidson I've changed the code and it makes the file in the correct location, but it produces the same error: the file can't be found.