CLIA IDT Exome and AML Trio Assays

This is a 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 workflows

Beta release of precision medicine analysis-workflows

This is a beta release of workflows for enabling precision medicine to perform neoantigen predictions and subsequent personalized cancer vaccine designs.

Improvements

• Reorganized code into tools, sub-workflows and pipelines.
• Increase the use of task-specific docker images
• Additional and updated ResourceRequirements
• Numerous QC tools added for WGS, Exome and RNA-seq
• Structural Variant and Copy Number calls, ex. Lumpy/smoove, Manta, CNVkit
• Additional annotation: custom ClinVar, VEP --everything
• Option to limit variant calls to defined regions, ex. ACMG genes
• Numerous other changes to the order of steps, secondary files and exposure of tool parameters to the workflows.

Pipelines Supported

• Somatic WGS and Exome
• Germline WGS and Exome
• scRNA-seq and RNA-seq Expression/Abundance Estimates
• Whole-Genome Bisulfite (WGBS)
• pVACseq for neoantigen predictions

Version 1.2.0 release

1. add step for add_bam_reacount_to_vcf_helper.py
2. pindel improvement

Version 1.1.0 release

1. Add cle_annotated_vcf_filter step
2. add strelka_cpu_reserved parameter
3. Change strelka cpu requested "coresMin" to 4

Version 1.0.0 of the cancer-genomics-workflow CWL

The CWL contained within the cancer-genomics-workflow at version 1.0.0. This release can be tested, validated and used for consistent reproducible workflow execution.