Update table generation notebook and excel files

[sjspielman]

Purpose/implementation Section

What scientific question is your analysis addressing?

From issue #1268 , supplementary tables for mutational signatures had been using the wrong file. The correct file is now used and results are re-generated. Several other changes were implemented in this notebook:

• Updated other formatting aspects to increase code modularity
• Updated incorrect file paths to TMB files in data/
• Knitting the notebook in the docker

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

NA

Is there anything that you want to discuss further?

NA

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

yes

Results

What types of results are included (e.g., table, figure)?

Updated output tables to use in manuscript

Reproducibility Checklist

• [ ] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• [ ] This analysis has been added to continuous integration.

Documentation Checklist

• [ ] This analysis module has a README and it is up to date.
• [ ] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• [ ] The analytical code is documented and contains comments.

[sjspielman]

Question for @jaclyn-taroni during review - I am realizing this notebook is not in .circleci/config.yaml which would have caught the other file path bugs, presumably. I'm not sure if it should be in CI (e.g.,generate_figures.sh is not there), but this notebook seems good to add in anyways?

[jaclyn-taroni]

generate_figures.sh would need to be modified to be able to run on a machine with 8GB to work on CI and, presumably, many of the modules that get re-run in that script are already tested. To me, this scenario seems different because I expect it will run on a machine that size without issue (but I live to be wrong about such matters).

[jaclyn-taroni]

@sjspielman we need to use a param to be able to have this work in CI. I think we can make it more general than in CI y/n – we could instead make it the release where the default is the current release. In CI, perhaps you'd pass "testing" and if the param is "testing", construct the path to be data/<file> instead of data/<release param>/<file>