Count reads, rm debug stuff from combined decontamination task

[aofarrel]

Changes

• User can no longer define the counts out TSV file name
• User can set max_retries (default: 0) to take advantage of Terra's retry with more memory feature
• All reads are sized, even if not subsampling, to throw a warning if there's less than a thousand
• Remove some outdated debugging prints
• Parses the counts file to count the number of reads that were determined to be contamination, unmapped, reference, and remaining.
• Clarify the timers are in seconds, and remove the ones no one cares about

[aofarrel]

Tested and passes on Terra, although it might be good to test the subsampling part a bit more closely... will do so when writing a proper checker workflow for myco.