Wilms 06 module: Update and re-render 04 notebook

[sjspielman]

Towards #810

This PR updates the next step in the wilms-06 module, the 04_annotation_Across_Samples_exploration.Rmd notebook. Changes include:

• In the Rmd, I fixed a small looping bug as well as several typos.
  • I also added some words to the dictionary along the way
  • This file also got styled, so again recommended to turn off whitespace during review
• I updated the 00_run_workflow.sh script to include all remaining workflow steps
  • The remaining if [[ $IS_CI -eq 0 ]]; then will be removed in the next PR (details below), but the code there should be ready to go to run it through CI.

Here's what to expect next:

1. Updates related to copyKAT and inferCNV
   • We should change scripts/explore-cnv-methods.R into a shell script, since this currently uses system() to call other R commands, and we've seen that is not a robust strategy to ensure the whole script fails if a step fails.
   • Some bugs in the copyKat and inferCNV scripts need to be addressed, one of which was 100% my bad for previously missing - we go through some effort in the 04 notebook in this PR to look at thresholds for using scores, and then we proceeded not to actually use those thresholds 🤦‍♀️ . Cells used as normal reference need to meet the threshold! There are also several samples which do not have any cells to use as a normal reference, so these will be run through the workflow without a reference.
2. Updates related to the final annotation notebook (very small), and re-render it!