cutadapt trimming commented until we can properly use it.
Some unneeded prints removed
default tmpdir moved from /tmp to None
Unused import removed
Task added to TODO
Refactor: TrimChimeras moved to TrimMatePairChimeras
trim_chimeras binary renamed as trim_mp_chimeras
typo fixed
Unused imports removed
larger packet size for trim_mp_chimeras
Refactor. The bwa index is created before using it
Task added to TODO