Fix build and add custom parameterization (#24)

[Faizal-Eeman]

• add battenberg.R for customization

• add max.rho to battenberg_bl_custom.R

• add max rho default

• add custom battenberg wrapper

• add max rho to wrapper

• add max rho to wrapper

• add max rho to wrapper

• use battenberg.R from v2.2.9 and add max.rho

• rename battenberg_wgs.R battenberg_wgs_bl_custom.R

• resolve merge conflict again

• Add renv.lock file containining R package versions

• remove modify_reference_path.sh

• resolve merge conflict in Dockerfile

• resue ascat/battenberg version arg

• Update CHANGELOG.md

• Update changes

• commit to remove installer.R

• specify removal of files under /usr/local/src/

• verify checksum and set up workdir

• update CHANGELOG

• Update license year

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Description

Closes #...

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:

Provide the command you ran here

Test Cases

• Case 1
  • sample:
  • input csv:
  • config:
  • output:
• Case 2
  • sample:
  • input csv:
  • config:
  • output:

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

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