Wdlupdate (#18)

* updated HC to match fivedollar wdl. add jes bug fix for gathertranches in JD

* minor edits, added docker variable for gathertranches and importgvcf

* minor format change

* minor edits

* minor changes

* replaced fc.wdl with local.wdl in Readme. Removed runtime paramters from local json

* minor edit

* added logic to keep the .g.vcf.gz extension if the task is run in GVCF mode

* minor: removed quotes from int

* made gvcf extention for mergeGVCF output naming optional

* made make_gvcf variable optional

* select first

* update gatk

haplotypecaller-gvcf-gatk4.hg38.wgs.inputs.json

@@ -12,7 +12,7 @@
   "HaplotypeCallerGvcf_GATK4.scattered_calling_intervals_list": "gs://gatk-test-data/intervals/hg38_wgs_scattered_calling_intervals.txt",
 
   "##_COMMENT4": "DOCKERS", 
-  "HaplotypeCallerGvcf_GATK4.gatk_docker": "broadinstitute/gatk:4.0.0.0",
+  "HaplotypeCallerGvcf_GATK4.gatk_docker": "broadinstitute/gatk:4.0.1.0",
 
   "##_COMMENT5": "PATHS", 
   "HaplotypeCallerGvcf_GATK4.gatk_path": "/gatk/gatk",

joint-discovery-gatk4-local.hg38.wgs.inputs.json

@@ -39,7 +39,7 @@
 
   "##_COMMENT4": "DOCKERS", 
   "JointGenotyping.python_docker": "python:2.7",
-  "JointGenotyping.gatk_docker": "broadinstitute/gatk:4.0.0.0",
+  "JointGenotyping.gatk_docker": "broadinstitute/gatk:4.0.1.0",
 
   "##_COMMENT5": "PATHS", 
   "JointGenotyping.gatk_path": "/gatk/gatk",

joint-discovery-gatk4.hg38.wgs.inputs.json

@@ -37,7 +37,7 @@
 
   "##_COMMENT4": "DOCKERS", 
   "JointGenotyping.python_docker": "python:2.7",
-  "JointGenotyping.gatk_docker": "broadinstitute/gatk:4.0.0.0",
+  "JointGenotyping.gatk_docker": "broadinstitute/gatk:4.0.1.0",
 
   "##_COMMENT5": "PATHS", 
   "JointGenotyping.gatk_path": "/gatk/gatk",