Release docker-Battenberg v2.2.9

[Faizal-Eeman]

Description

PR to release docker-Battenberg image v2.2.9.
README updated with Battenberg GRCh37 and GRCh38 resources on the cluster.

Closes #10

Testing Results

Docker Image Testing

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

$ docker run -it --rm -u $(id -u):$(id -g) -v /hot/:/hot/ -w $(pwd) ghcr.io/uclahs-cds/battenberg:dev
$ Rscript /usr/local/bin/battenberg_wgs.R --help
Usage: /usr/local/bin/battenberg_wgs.R [options]

Options:
	-t CHARACTER, --tumourname=CHARACTER
		Samplename of the tumour

	-n CHARACTER, --normalname=CHARACTER
		Samplename of the normal

	--tb=CHARACTER
		Tumour BAM file

	--nb=CHARACTER
		Normal BAM file

	--sex=CHARACTER
		Sex of the sample

	-o CHARACTER, --output=CHARACTER
		Directory where output will be written

	--skip_allelecount
		Provide when alleles don't have to be counted. This expects allelecount files on disk

	--skip_preprocessing
		Provide when pre-processing has previously completed. This expects the files on disk

	--skip_phasing
		Provide when phasing has previously completed. This expects the files on disk

	--cpu=CHARACTER
		The number of CPU cores to be used by the pipeline (Default: 8)

	--bp=CHARACTER
		Optional two column file (chromosome and position) specifying prior breakpoints to be used during segmentation

	-h, --help
		Show this help message and exit

Test Cases from PR #9

• 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/user/mmootor/temp_files/battenberg/run/test_run_battenberg.sh
  • output: /hot/user/mmootor/temp_files/battenberg/run/ILHNLNEV000009-T002-L01-F_subclones.txt
  • Germline plot: /hot/user/mmootor/temp_files/battenberg/run/ILHNLNEV000009-T002-L01-F.germline.png
  • Tumor plot: /hot/user/mmootor/temp_files/battenberg/run/ILHNLNEV000009-T002-L01-F.tumour.png

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.

[tyamaguchi-ucla]

Looks good. Did you want to enable GitHub discussions and update the README using the latest template? https://github.com/uclahs-cds/template-docker

Also, we want to use /hot/software/image for image development as much as possible.

[Faizal-Eeman]

Did you want to enable GitHub discussions and update the README using the latest template? https://github.com/uclahs-cds/template-docker

Added Discussion and updated README.

/hot/software/image

/hot/software/image/docker-Battenberg/Docker/development

[tyamaguchi-ucla]

Added a few minor suggestions but otherwise looks good to me. Anything else to add @yashpatel6 ?

[yashpatel6]

One small comment but otherwise looks good!