🚧 update tumor only workflow

[dmiller15]

Description

Part of https://d3b.atlassian.net/browse/BIXU-2125
Part of https://d3b.atlassian.net/browse/BIXU-3672

Filtration Updates

• 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

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

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

Type of change

Please delete options that are not relevant.

• New feature (non-breaking change which adds functionality)
• Documentation update

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

• https://cavatica.sbgenomics.com/u/d3b-bixu/kfdrc-snv-benchmarking/tasks/18e51983-47a9-4216-a1e0-adc1492128db/#
• Draft task pulling in the new suggested files: https://cavatica.sbgenomics.com/u/d3b-bixu/kfdrc-snv-benchmarking/tasks/4a25b745-e662-45b1-8066-8133dc125646/#set-input-data

Test Configuration:

• Environment:
• Test files:

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules
• I have checked my code and corrected any misspellings
• I have committed any related changes to the PR

[migbro]

Looks great! Could look into replacing verbatim tool copies with raw git links, but at this point, probably not worth fawning over. Do we want to throw in the release version now, or later?

[dmiller15]

Could look into replacing verbatim tool copies with raw git links, but at this point, probably not worth fawning over.

Yeah probably worth looking into during the strategic week next month. Perhaps we should make a ticket @migbro

Do we want to throw in the release version now, or later?

Later. I think there's a couple more things that we'll need to go over like workflow/output naming.