toil-bwa should throw error on wrong input

[Jeltje]

Jake and I both managed to run toil-bwa with tar files as input, instead of fastq.gz. The manifest line read
jake-test s3://cgl-driver-projects-encrypted/ucsf-pnoc/ucsf-WXS-fastq/C021_0006_T_WES.tar s3://cgl-driver-projects-encrypted/ucsf-pnoc/ucsf-WXS-fastq/C021_0006_C_WES.tar
(note also how that's not fwd and rev reads but tumor and control samples)

The program appeared to run just fine and output a very small bam file, which turned into an empty sam file.
I think there should be errors both on nonsensical input and on empty output.