SPAdes fails for some small datasets (mostly at the final misassembly correction stage)
solution: fall back to the contigs before the correction
SPAdes creates empty files that pollute the server launch directory
This is dealt with by running arast_popen() with cwd set to self.outpath
The strange thing is when I globally modified arast_popen() to always call subprocess.Popen(cwd=self.outpath..., it failed on tagdust. Tagdust just generates empty files.
SPAdes v3.5.0 occassionally dumps to the directory from which the compute server is launched.
We may need to set cwd in Popen().. Also single files should be passed in as
--s#
as opposed to--pe#-s
?