Wdlupdate (#7)

* Update README.md

* Update germline_single_sample_workflow.hg38.inputs.json

minor format changes

* removed scattered intervals as its not being used in the workflow, corrected haplotype_scatter_count to 50. Add comment regarding exomes intervals in Readme

* added the new HaplotypeCaller tasks.

* added a generic options

* deleted old structure

* Update README.md

minor edit

* sub_strip_path replaced by basename() because hardcoding the gs:// component makes the WDL assume too much about the platform it will run on

* removed ceil() to pass Float type as disk_size for GatherBamFiles

* Fix for splitRG task. Disk sizing now takes place within tasks.

* removed empty haplotyp map file

germline_single_sample_workflow.hg38.inputs.json

@@ -37,7 +37,7 @@
   "germline_single_sample_workflow.dbSNP_vcf_index": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
   "germline_single_sample_workflow.wgs_coverage_interval_list": "gs://broad-references/hg38/v0/wgs_coverage_regions.hg38.interval_list",
   "germline_single_sample_workflow.wgs_evaluation_interval_list": "gs://broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
-  "##germline_single_sample_workflow.haplotype_database_file": "gs://gatk-aas-test-data/small/empty.vcf",
+  "##germline_single_sample_workflow.haplotype_database_file": "File (optional)",
 
   "##_COMMENT5": "Runtime Attributes",
   "germline_single_sample_workflow.flowcell_small_disk": 100,
@@ -52,3 +52,4 @@
   "germline_single_sample_workflow.break_bands_at_multiples_of": 1000000,
   "germline_single_sample_workflow.haplotype_scatter_count": 50 
 }
+