Update Picard to 3.0.0

[bethneilsen]

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/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:

docker run --rm -u $(id -u):$(id -g) picard:3.0.0 picard BuildBamIndex --version

Description

Closes # 23: Update Picard to 3.0.0

Testing Results

• Case 1
  • sample:
  • input files:
  • config:
  • output:

[yashpatel6]

Looks good! You can merge the PR but hold off on making a release; this repo doesn't seem to have the auto-build action for Docker images so we'll want to add that before making a release (I'll create a separate issue with more details)