genome/analysis-workflows: CLIA IDT Exome and AML Trio Assays

This is an official release of the CLIA Licensed Environment (CLE) IDT Exome and AML Trio assay workflow that is validated. Other workflows for enabling precision medicine that enable neoantigen predictions and subsequent personalized cancer vaccine design are still considered a beta release. Validation of additional workflows are ongoing. Improvements Added support for non-Human workflows, tools, and annotation, ex. Mouse Continued migration from large Docker images to task-specific, versioned Docker images Various changes to CWL ResourceRequirements for executing workflows with Cromwell on local HPC Other changes including the order of pipeline steps, naming of (secondary) files, and exposure of tool parameters and inputs to (sub)workflows Somatic DNA CLIA Licensed Environment (CLE) IDT Exome workflow and report CLIA Licensed Environment (CLE) AML Trio Exome workflow and report Numeruos improvement to false-positive filters including additional filters Ability to ignore DoCM caller/variants Sample concordance check with SOMALIER MANTA-SV for targeted regions Optimized parallel Pindel subworkflow Better handling of VEP versioning and updated VEP version Germline DNA Single-sample SV subworkflow Merged SV VCFs using SURVIVOR Annotation of SV VCFs with VEP and custom population allele frequencies Preliminary filters for SV calls ** Support for new germline VEP plugins Immunoworkflows and neoantigen predictions Continued integration and updates to use pVACtools and VAtools Larger combined workflow for executing multiple subworkflows Initial HLA-typing subworkflow Phasing of variants subworkflow Whole Genome Bisulfite (WGBS) ** Initial release of a quality assurance subworkflow RNA-seq and scRNA-seq scRNA-seq subworkflow with lineage inference Add duplicate marking to RNA-seq ** Fix the strand options and compatibility with the order of FASTQs in RNA-seq CWL workflow