Update data release analysis process workflow scripts

[ewafula]

Purpose/implementation Section

What scientific question is your analysis addressing?

Update data release analysis process workflow scripts

What was your approach?

• update generate-analysis-files.sh to include generate cnv consensus file
• clean up run-for-subtyping.sh to match the current molecular subtyping process that also includes generating additional release files - full histologies file and independent sample lists

What GitHub issue does your pull request address?

• Update workflow scripts associated with the data release analysis process ticket-tracker-OPC#561

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

Which areas should receive a particularly close look?

Test the scripts on EC2

Is there anything that you want to discuss further?

No

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)?

Tables

What is your summary of the results?

Module results and releases and release files

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.

[jharenza]

Hi @ewafula thanks for updating this- can you check out my comment below. Also odd- those errors did not occur in the latest EPN and NBL PRs. 🤔

[jharenza]

merge without GA, these are not run in GA