Update to SAMTools 1.20

[kiarod]

Description

Closes #16

Testing Results

Docker Image Testing

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

Testing version:

docker run --rm -u $(id -u):$(id -g) samtools:latest samtools --version
samtools 1.20
Using htslib 1.20
Copyright (C) 2024 Genome Research Ltd.

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:

ln -s /hot/ref/mitochondria_ref/mt_test_bams/tcga_test_file_normal.bam ./
docker run --workdir $(pwd) --rm --user $(id -u):$(id -g) --volume $(pwd):$(pwd) --volume /hot/ref/mitochondria_ref/mt_test_bams/:/hot/ref/mitochondria_ref/mt_test_bams/ samtools samtools index tcga_test_file_normal.bam

successfully creates:
tcga_test_file_normal.bam.bai

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.

[yashpatel6]

Looks good!