Kids First DNA Tumor Only Workflow v1.0.0

Release Notes

Filtration Updates

• Added README on Mutect2 Tumor Only Filtration recommendations: docs/MUTECT2_TUMOR_ONLY_FILTERING.md
• Updated README with new recommended gatk_filter_name and gatk_filter_expression values
• Added new default to filtermutectcalls_extra_args to filter calls with AF < 0.01

Annotation Updates

• Annotation workflow upgraded to version 1.2.1

Workflow Optimization

• ControlFREEC pileup creation now handled by a GNU parallel samtools implementation; no longer performing pileup on ALT contigs
• Interval creation and handling now matches what we have in the somatic workflow; user provides calling_regions, blacklist_regions, and cnv_blacklist_regions which are then processed by prepare_regions.cwl
• Added interval manipulation tools: awk_chrlen_builder.cwl, gatk_bedtointervallist.cwl, gatk_intervallisttobed.cwl, and gatk_intervallisttools.cwl
• Added switches to enable/disable all subworkflows of the tumor only workflow
• Move AnnotSV inside Manta subworkflow
• samtools calmd now only runs when the input is CRAM or if user specifies run_calmd_bam
• Styling cleanup for some tools and workflows

Quality of Life

• Added default of [2,3,4] to cfree_ploidy
• Reference input simplified to a single input with secondaryFile indexes rather than separate inputs for FASTA, FAI, and DICT
• Added suggestedFiles for indexed_reference_fasta, gem_mappability_file, panel_of_normals, blacklist_regions, and cnv_blacklist_regions

What's Changed

• ✨ Upgrade Annotation for Tumor Only by @dmiller15 in #10
• 🤖 Update Annotation Submodule for Release v1.2.0 by @migbro in #12
• 📚 add filter docs by @dmiller15 in #14
• 🚧 update tumor only workflow by @dmiller15 in #16
• 🧹 v1.0 release prep by @dmiller15 in #19

Full Changelog: v0.4.1-beta...v1.0.0