Version 21.9.2

• add cBioPortal SV file conversion for new SV file format requirements
• add data_mutations_uncalled.txt output for samples fillout workflow
• add parallel test case scripts and recipe to Makefile for faster dev & debug
• fix issues in some unit tests and integrations tests that were preventing CI from working
• refactor some test cases to use latest pluto module methods for better test case execution controls

Version 21.9.1

• fix output for data_CNA.txt file to use merged output
• add updateCaseList.cwl for updating cBioPortal case list files
• add extra_sample_ids for portal workflow and workflow with facets

Version 21.9.0

• merge in docs branch
• add cBioPortal compatible .maf output for fillout workflow
• fix some broken test cases
• fix germline filter for fillout workflow
• version bump helix filters container used throughout workflow
• add types.yml for CWL record type definitions for use throughout CWL workflows
• overhaul of test cases for fillout workflow
• clean up env.sh file
• remove pluto-cwl operators, run.py and run-json.py scripts; use the run-cwltool.sh and run-toil.sh scripts from pluto submodule instead

Version 21.8.1

• disable germline filter for sample fillout workflow
• update test cases

Version 21.8.0

• add differential handling for research and clinical samples in fillout workflow including conditional variant filtering
• add conditional handling for Facets workflow

Version 21.7.0

Updates for samples_fillout_index_workflow.cwl and samples_fillout_workflow.cwl:

• update input schema to use array of sample records
• add filtering for input sample records to apply cBioPortal filters for "indexed" samples prior to using them in fillout
• add sample normal_id as an input for each sample record and apply it correctly in the output maf file rows
• optional output fillout maf filename

Other:

• fixes for integration testing env and recipes
• added XL size integration test case

Version 21.6.0

• refactor test cases for workflow_with_facets.cwl and workflow.cwl to use new updates to pluto submodule library
• add medium sized test case for integration testing

Version 21.5.0

• add full-outer-join.cwl for merging CNA tables
• add data_CNA merge against extra input tables to pipeline, output under the file data_CNA.txt
• add basic HTML report to main workflow
• update pluto submodule to start using OFile and ODir classes for test cases

Version 21.4.5

• full refactor of samples fillout workflow to give cBio Portal compatible output
• various Docker container dependency updates including usage of helix filter Docker containers instead of cmo containers
• fixes for environment variables for Docker containers
• removal of some old deprecated cwl listings
• fix for array syntax in main workflow with facets
• lots of updates and tweaks for pluto submodule

Version 21.4.4

Update mem resource requirements in annotate-maf-wrapper.cwl and msi.cwl.