V20 ci files

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

Create subset files for CI for v20 release

What was your approach?

1. Start AWS instance with >=150 GB RAM
2. Clone OpenPBTA-analysis
3. Create a new branch off of v20-ci
4. Update the release to release-v20-20210726 and add pbta-snv-scavenged-hotspots.maf.tsv.gz beb47c1
5. Run bash analyses/create-subset-files/create_subset_files.sh
6. Commit the biospecimen RDS file to v20-ci
7. Zip up the subset files zip -r testing_v20.zip testing/release-v20-20210726
8. Download testing_v20.zip
9. File a pull request from v20-ci

What GitHub issue does your pull request address?

#1048

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

Which areas should receive a particularly close look?

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)?

tables

What is your summary of the results?

Zip file uploaded in s3://kf-openaccess-us-east-1-prd-pbta/data/testing_v20.zip

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.

[jaclyn-taroni]

The changes to the code along LGTM! Is your plan to upload these to an S3 bucket you have access to and then change:

OpenPBTA-analysis/.circleci/config.yml

Line 13 in c66d5c5

command: OPENPBTA_URL=https://open-pbta.s3.amazonaws.com/data OPENPBTA_RELEASE=testing ./scripts/run_in_ci.sh bash download-data.sh

to reflect that? Can also talk via Slack tomorrow.

[jaclyn-taroni]

This module is upstream of/not tested by CI and the tests passed in #1121, so I am going to merge this.