Clean up temp files

[ArtPoon]

Currently running the pipeline produces a lot of extra files:

art@orolo:~/git/micall/working$ ls
micall.fasta            SRS5100454_1.amino.csv   temp.fasta
reference.1.bt2         SRS5100454_1.conseq.csv  temp.fasta.1.bt2
reference.2.bt2         SRS5100454_1.fastq       temp.fasta.2.bt2
reference.3.bt2         SRS5100454_1.insert.csv  temp.fasta.3.bt2
reference.4.bt2         SRS5100454_1.nuc.csv     temp.fasta.4.bt2
reference.rev.1.bt2     SRS5100454_1.prelim.csv  temp.fasta.rev.1.bt2
reference.rev.2.bt2     SRS5100454_1.remap.csv   temp.fasta.rev.2.bt2
SRS5100454_1.align.csv  SRS5100454_2.fastq       temp.sam

[ArtPoon]

Implemented --keep flag:

art@orolo:~/git/micall/working$ ls
SRS5100454_1.align.csv   SRS5100454_1.fastq       SRS5100454_2.fastq
SRS5100454_1.amino.csv   SRS5100454_1.insert.csv
SRS5100454_1.conseq.csv  SRS5100454_1.nuc.csv