Use temporary filenames in the pipeline

[morungos]

This is a serious one. Basically, the pipeline uses temporary files with names that are keyed to the alignment alone, and within $TMPDIR. This means there is a hugely significant risk of file name conflicts between different processes handling different samples, if the same alignment is used. Much better to use a filename provided by the system, at least as part of the name, reducing the change of temporary file conflicts.

I cannot confirm that this will corrupt data, but it seems very likely when run in a cluster/cloud-type environment that temporary files will get entangled.