Add simple diploid variant calling workflow

[mvdbeek]

FOR CONTRIBUTOR:

• I have read the Adding workflows guidelines
• License permits unrestricted use (educational + commercial)
• Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

• .dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
• Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
• In workflow: annotation field contains short description of what the workflow does. Should start with This workflow does/runs/performs … xyz … to generate/analyze/etc …
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• In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
• Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
• Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
• Changelog contains appropriate entries
• Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

[mvdbeek]

@wm75 @SaimMomin12 would you have a moment to review @nekrut's workflow ?

[d-callan]

notice a haploid tag on it

[wm75]

Looks good to me. I would only add a bcftools norm step at the end with "Left-align and normalize indels?" set to Yes. This will also fix some minor VCF standard violations by freebayes.

If you want to make things a bit more sophisticated, you could make the "Atomize" setting of bcftools norm user-configurable. Atomized calls are easier to annotate with downstream tools (cmp https://github.com/freebayes/freebayes/blob/master/README.md#normalizing-variant-representation, which shows the same thing using vcflib), but you're losing haplotype info.