Update chromothripsis panels to use new cancer group palette (Fig 3)

[jaclyn-taroni]

⚠️ downstream of #1193

Working towards PDF versions of individual panels in directories figures/pdfs/<figure number>/panels using the new color palette in #1193.

This is regarding Figure 3 (placeholder image). Here I am:

• Adding a shell script to make it easy to run the entirety of the chromothripsis module
• Saving the CNV breaks vs. SV breaks scatter plot panel as a PDF (in addition to a PNG) in the notebook where that plot was originally made
• Adding the chromothripsis figure steps to figures/generate-figures.sh
  • Running the module in its entirety via the new shell script for that module
  • Copying over the PDF of the scatter plot panel to figures/pdfs/fig3/panels
  • Adding an Rscript, adapted from analyses/chromothripsis/04-plot-chromothripsis-and-breakpoint-data.Rmd, to make the bar plot panel with the new cancer group palette introduced in #1193

The new publication ready plot specific Rscript seemed like a quicker path to getting this panel done (and tweaked as necessary) because I haven't removed the older palette (figures/palettes/histology_label_color_table.tsv) yet.

[jaclyn-taroni]

Most recent changes are in figure scripts that aren't covered by CI, so going to merge without it to keep things moving.