v2.0.0-rc1

This is a pre-release workflow. Please do not depend on this for production analysis.

This release is not supported by the PacBio Tech Support or Field Support teams. Please only use this if you are already in contact with PacBio R&D and providing active feedback on performance and results.

This is a major rewrite of the v1 workflow. Please read the documentation before filing issues.

Structural changes:

• There are two entrypoints, singleton.wdl and family.wdl.
  • singleton has a flattened input/output structure that should have better compatibility with platforms like Terra.
  • family includes joint calling tasks for small variants and structural variants.
  • phenotype field has been changed from Array[String] to String, a comma-delimited string, e.g., "HP:0000118,HP:0000001"
• Static inputs like reference FASTA and BED files are now referenced through new "map" files to simplify inputs.json structure.
• Most tasks have been moved to the wdl-common submodule for reuse.
• AWS AGC has been deprecated by AWS, and support has been removed.
• AWS HealthOmics support has been added (needs improved documentation).

New features:

• HiPhase now jointly phases small variants (DeepVariant), structural variants (PBSV), and tandem repeats (TRGT).
• Pharmacogenomics analysis with StarPhase and PharmCat.
• Updated tertiary analysis with gnomAD v4.1 and CoLoRSdb population datasets.
• High level summary statistics (e.g., mean depth, variant counts by type, etc) output directly by workflow.
• Plots for read length and quality histograms.
• Inferred sex by relative chrY aligned depth. This will never override user-defined sex, but is used if the sex is not provided by user.

Tool updates:

• Paraphase v3.1.1
• TRGT v1.0.0
• HiPhase v1.4.2
• HiFiCNV v1.0.0

Full Changelog: v1.1.1...v2.0.0-rc1

Contributors:
@juniper-lake
@gconcepcion
@amwenger