KFDRC Genotyping Production Workflow

Changes in this release:

• BWA index tool now stages the reference fasta in the working directory. This change has no effect on the current workflow as BWA index is not run.
• The Joint Genotyping workflow has received public app formatting: reference files now load automatically in Cavatica, the workflow now has a number of descriptive tags, formatting in general has been cleaned up for readability.
• Single sample and old non-public-app-formatted Joint Genotyping workflows have been moved to a folder called workflows-deprecated. The workflows still perform as in previous releases but from now on will receive no future updates.

KFDRC Genotyping Production Workflows

This release unifies the code used in our production and public app workflows. Previously these workflows had existed as separate workflows on separate branches.

Major workflow changes:

• Input references for the joint and single sample genotyping workflows no longer have secondaryFiles for their associated indexes
• Indexes are now handed in as their own inputs (e.g. dbsnp_vcf has an associated input for its index in dbsnp_index)
• Steps are added early into the pipeline to conditionally index and stage the input references.

Other changes:

• New tools and subworkflows were added to aid in the indexing process.
• GATK Dockers changed to pull from KFDRC
• Expanded documentation for single sample genotyping workflow
• Added example runtime and cost estimates to the README

Fix shellQuote for script

If edited in cavatica, the editor will automatically add shellQuote: false, which can break certain tools that don't have a declaration for shellQuote. This release explicitly states shellQuote: true for those tools.

Production Stable Release

This spring (of 2019) we had updated out production workflow, harmonized GATK versions to all 4.0.12.0*

• Except for Variant Annotation tool, which is GATK 3.8. This tool was still beta for that GATK 4 release.

Early Production Beta Workflow

This workflow included many beta versions of GATK 4, and was used for many earlier iterations of X01 joint genotyping projects (pre-spring 2019). The output results should be considered of more than usable quality, but we have since harmonized software version usage.