Update picard docker

[sickler-alex]

Description

Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change.

Update all picard tools to use the pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R docker.

Fixes # https://app.zenhub.com/workspaces/d3b-bfx-5cdd720eed0dce4209e0b8a5/issues/d3b-center/bixu-tracker/1102

Type of change

Please delete options that are not relevant.

• [ ] Bug fix (non-breaking change which fixes an issue)
• [ ] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
• [ ] This change requires a documentation update

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

• [X] WGS runs previous version, test run with updated docker
• [X] WXS runs previous version, test run with updated docker

Test Configuration:

• Environment:
• Test files:

Checklist:

• [X] My code follows the style guidelines of this project
• [X] I have performed a self-review of my own code
• [X] I have commented my code, particularly in hard-to-understand areas
• [X] I have made corresponding changes to the documentation
• [X] My changes generate no new warnings
• [ X I have added tests that prove my fix is effective or that my feature works
• [ ] New and existing unit tests pass locally with my changes
• [X] Any dependent changes have been merged and published in downstream modules
• [X] I have checked my code and corrected any misspellings
• [X] I have committed any related changes to the PR

[sickler-alex]

To compare the runs, I pulled the qc metrics for these runs and compared them. Attached is the excel file with the metrics and the comparison. metrics_comp.xlsx

[sickler-alex]

@migbro did I miss a place for the version number? The last commit updates the link to the new tag that will get created once this is approved.

[migbro]

@migbro did I miss a place for the version number? The last commit updates the link to the new tag that will get created once this is approved.

Ah, so I was referring to the github release version, sorry. So in the scripts workflows/kfdrc_alignment_wf.cwl and workflows/kfdrc-gatk-haplotypecaller-wf.cwl, these lines:

- id: 'https://github.com/kids-first/kf-alignment-workflow/releases/tag/v2.7.0'
  label: github-release

- id: 'https://github.com/kids-first/kf-alignment-workflow/releases/tag/v2.6.0'
  label: github-release

Just increment increment each by 0.0.1 please. Thanks!