Overhauled MuTect2 workflow

README.md

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 ## Info
 
-- Docker used: broadinstitute/gatk:4.1.4.1
-- Reference files - including PON, come from [GATK-best-practice bundle](https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-b37)
+- Docker used: `gcr.io/broad-getzlab-workflows/gatk4_wolf:v6`
+- Reference files - Most come from [GATK-best-practice bundle](https://console.cloud.google.com/storage/browser/gatk-best-practices/). See `wolF/reference_files.py` for details.
 - Original WDL for [GATK 4.1.4.1 Best Practice](https://github.com/gatk-workflows/gatk4-somatic-snvs-indels/tree/2.7.0)
-- Genome build: hg19
-- Disk image: 
-    - NAME: mutect2-wolf
-    - PROJECT: broad-cga-qing-gdac 
+- Genome build: hg38 *or* hg19
 
 ## News
 
-A minimal implementation tested work, will add 
-
-- [x] Build a disk image for all reference files, ~~potentially as another task~~
-- [ ] Cross-validate on Terra with same input
-- [ ] Cost estimate
-- [ ] Incorporates more optional arguments (bells and whistles)
+2024-03. Reimplemented the workflow with modern wolF design patterns
 
 ## Acknowledgement
 

__init__.py

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+from .wolF import *

wolF/__init__.py

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+from .tasks import *
+from .workflow import mutect2_workflow, mutect2_workflow_w_localization