Fix build and add custom parameterization

[Faizal-Eeman]

Description

• fix the build failure in Docker build failing #22 using renv.lock file
• add Boutros Lab custom scripts for battenberg.R and battenberg_wgs.R

Closes #23

Testing Results

Docker Image Testing

• I have tested the Docker image with the docker run command as described below.

Test the Docker image with at least one sample. Verify the new Docker image works using:

docker run -u $(id -u):$(id -g) –w <working-directory> -v <directory-you-want-to-mount>:<how-you-want-to-mount-it-within-the-docker> --rm <docker-image-name> <command-to-the-docker-with-all-parameters>

My command:

sbatch /hot/software/image/docker-Battenberg/Docker/development/mmootor-add-custom-parameterization/test_run_battenberg.sh

Test Cases

• Case 1
  • sample: NA24149 (normal), NA24143 (tumor)
  • output: /hot/software/image/docker-Battenberg/Docker/development/mmootor-add-custom-parameterization

Checklist

Formatting

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• I have set up or verified the branch protection rule following the github standards before opening this pull request.

File Updates

• I have ensured that the version number update follows the versioning standards.

• I have updated the version number in the Dockerfile, README.md and metadata.yaml files.

• I have updated the dependencies and added my name to the maintainer list in the Dockerfile.

• I have updated the feature changes in the README.md (optional).

• I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

GitHub Packages Auto Build Rules

• I have not manually pushed this Docker image to the uclahs-cds container registry (ghcr.io/uclahs-cds) on GitHub.

• I have updated the image_name in the metadata.yaml which is required by GitHub action to automatically build and push the image.

[wiz-inc-8da00b022c]

Wiz Scan Summary

Scan Module						Total
IaC Misconfigurations	0	0	17	2	0	19
Vulnerabilities	0	0	0	0	0	0
Sensitive Data	0	0	0	0	0	0
Secrets	0	0	0	0	0	0
Total	0	0	17	2	0	19

View scan details in Wiz

To detect these findings earlier in the dev lifecycle, try using Wiz Code VS Code Extension.

[Faizal-Eeman]

I also realized, we'd have to make a sub-branch off of this branch in order to release docker-Battenberg v2.2.9-bl-parametrize-max-rho. That way the main branch is not affected and I can continue to make changes to the main branch later down the dev cycle.

[yashpatel6]

A couple of comments but otherwise looks good. Anything else from @tyamaguchi-ucla ?

[yashpatel6]

Generally ok with building from this, anything else to add from @tyamaguchi-ucla ?

[tyamaguchi-ucla]

Looks good to me! We can update the copyright year range and merge the branch into main.

[tyamaguchi-ucla]

Suggested change

	Copyright (C) 2021-2023 University of California Los Angeles ("Boutros Lab") All rights reserved.
	Copyright (C) 2021-2024 University of California Los Angeles ("Boutros Lab") All rights reserved.

I can't believe it's almost 2025..!