Part3 Freec as default: Oncoprint update

[kgaonkar6]

⚠️ Staggered PR, please merge #987 #988 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 .
A re-run focal-cn-file-preparation updated results/consensus_seg_most_focal_cn_status.tsv.gz in #988 .
In this PR we will use the updated consensus_seg_most_focal_cn_status.tsv.gz as input and re-create the oncoplots.

What was your approach?

Just run run-oncoprint.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?

Is this something that was seen before ?

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?

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.