Update to v2.2.1_samtools-1.17 and add auto build function, update Dockerfile to meet current standards

[bethneilsen]

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/dependencies and added my name to the maintainer list in the Dockerfile.

• I have updated the version number/feature changes in the README.md.

• I have updated the version number and added my name to the contributors list in the metadata.yaml.

• 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.

• I have drafted the new version release with any additions/changes and have linked the CHANGELOG.md in the release.

Docker Hub Auto Build Rules

• I have created automated build rules following this page and I have not manually pushed this Docker image to the blcdsdockerregistry on Docker Hub.

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:

Case 1: docker run --rm -u $(id -u):$(id -g) hisat2:latest hisat2 version

Case 2: docker run --rm -u $(id -u):$(id -g) hisat2:latest samtools version

Testing Results

Case 1:
HISAT2 version 2.2.1 by Daehwan Kim ([email protected], www.ccb.jhu.edu/people/infphilo)
Usage:
hisat2 [options]* -x {-1 -2 | -U } [-S ]

Index filename prefix (minus trailing .X.ht2).
Files with #1 mates, paired with files in .
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with #2 mates, paired with files in .
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
File for SAM output (default: stdout)

, , can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):
...

Case 2:
samtools 1.17
Using htslib 1.17
Copyright (C) 2023 Genome Research Ltd.

Description

Closes NA - Updates SAMTools to the latest version 1.17, added auto build Docker functionality, updated to use mamba to build to meet current Docker standards

Partially addresses issue #258 within pipeline-align-DNA

[yashpatel6]

Generally, looks good! A couple of comments:

[yashpatel6]

Looks good!