Support IonTorrent .bam input

[fmaguire]

The IonTorrent platform provides reads in an unaligned .bam instead of .fastq.

Modify workflow to automatically convert supplied .bam to .fastq by adding a conditional to this rule: https://github.com/jaleezyy/covid-19-signal/blob/master/Snakefile#L245 (e.g., if the suffix of the sample sheet input is a bam then use samtools bamtofastq)
and update the sample sheet parser and validation to allow only a single file if .bam instead of r1 and r2.fastq