Informational: Support for Cram

Looks like you can add "cram support" into your tool description ie bamfiles could be bam or cram.  

Since you can't directly input the genome sequence, if users get this error (common if using cloud):
[E::fai_build3_core] Failed to open the file /path/to/genome/reference.fa

they can do this:
samtools view -@ $threads -C -T reference.fa -o C5752.repathrefseq.cram C5752.cram
