Call ggsashimi to plot converted bams

[pj-sullivan]

Closes #5

Calls ggsashimi script after converting cram to bam.
** Will add control conversion in a separate PR

The ATM patient has multiple cram files, and thus multiple bams are produced. In this script, these should all be collapsed into one sashimi plot.

These plots aren't pretty (yet). For now, the transcript plot produced from the gencode gtf is quite crowded.

cd analyses
bash run-ggsashimi.sh -i input/test-input.tsv -m input/manifest.tsv
md5sum -c results/bams/md5sum.txt 

[rjcorb]

The plots look great! The gencode annotation is always tricky--maybe we can just limit to protein-coding transcripts?

I think the comments I made on the previous PR are also applicable here.

Another thing to think about: right now this shell script is creating a separate sashimi plot for every row in test-input.tsv. But in many cases we will be interested in plotting multiple samples in the same sashimi plot. I think we can keep this PR's scope to this single sample plotting, and make new tickets to expand functionality to multi-sample plotting.

[rjcorb]

Can you make some of these parameters command line arguments? I think the --shrink and -M arguments would be useful, and any parameters that control annotation height