Customize battenberg_wgs.R wrapper

[Faizal-Eeman]

Description

Closes #17

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: ILHNLNEV000009-N001-B01-F , ILHNLNEV000009-T002-L01-F
  • normal: /hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/pipelines/call-gSNP/2020-12-22/ILHNLNEV000009-T002-L01-F//gSNP/2021-01-22_11.01.06/ILHNLNEV000009/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/ILHNLNEV000009-N001-B01-F_realigned_recalibrated_reheadered.bam
  • tumor: /hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/pipelines/call-gSNP/2020-12-22/ILHNLNEV000009-T002-L01-F//gSNP/2021-01-22_11.01.06/ILHNLNEV000009/SAMtools-1.10_Picard-2.23.3/recalibrated_reheadered_bam_and_bai/ILHNLNEV000009-T002-L01-F_realigned_recalibrated_reheadered.bam
  • sbatch: /hot/software/image/docker-Battenberg/Docker/development/2.2.9/test_run_battenberg.sh
  • output: /hot/software/image/docker-Battenberg/Docker/development/2.2.9/mmootor-customize-battenberg-wgs-wrapper/ILHNLNEV000009-T002-L01-F_subclones.txt

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

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