Create input files for TCI analysis - V2

[AntoniaChroni]

Purpose/implementation Section

What scientific question is your analysis addressing?

This addresses the previously closed #60

What was your approach?

What GitHub issue does your pull request address?

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

Which areas should receive a particularly close look?

1. To ensure the following file is in the respective folder: tmb-vaf-longitudinal/results/tmb_vaf_genomic.tsv
2. To edit to use the following data as input for the CNA: cnv-cnvkit-cns.tsv.gz

Is there anything that you want to discuss further?

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

Results

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

What is your summary of the results?

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.

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.