Part2 Freec as default: Cnv focal files update

[kgaonkar6]

⚠️ Staggered PR, please merge #987 before this PR

Purpose/implementation Section

What scientific question is your analysis addressing?

We updated the consensus seg file creation in #987 to use freec CN calls as default. In this PR we will re-run focal-cn-file-preparation to identify changes in focal calls because of the update.

What was your approach?

Just run run-prepare-cn.sh

What GitHub issue does your pull request address?

related to #964

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

Which areas should receive a particularly close look?

🚨 I couldn't complete the plotting in the module.

I haven't run this module before, so I started with having 12GB memory in docker which killed 04-prepare-cn-file.R. I increased that to 15G and re-run the 04,05,06 but it seems rna-expression-validation.R would need more than 15G.

Is this something that was seen before ?

Is there anything that you want to discuss further?

🚨 plots are not complete for consensus calls because of the mem issue mentioned above.

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

NO

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.
• 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.