Format changes (#1)

* Made docker image to variable.

* Updated Readme.

* Moved workflow block to the top of script.

README.md

@@ -1,2 +1,32 @@
 # gatk3-data-processing
+### Purpose :
 Workflows for processing high-throughput sequencing data for variant discovery with GATK3 and related tools
+
+### processing-for-variant-discovery-gatk3 :
+The processing-for-variant-discovery-gatk3 WDL pipeline implements data pre-processing according to the GATK Best Practices 
+(June 2016). Example JSONs are provided for the WGS use case but the workflow can be 
+applied to Exomes and Targeted Panels.
+
+#### Requirements/expectations 
+- Pair-end sequencing data in unmapped BAM (uBAM) format
+- One or more read groups, one per uBAM file, all belonging to a single sample (SM)
+- Input uBAM files must additionally comply with the following requirements:
+  - filenames all have the same suffix (we use ".unmapped.bam")
+  - files must pass validation by ValidateSamFile 
+  - reads are provided in query-sorted order
+  - all reads must have an RG tag
+
+#### Outputs 
+- A clean BAM file and its index, suitable for variant discovery analyses.
+
+### Software version requirements :
+- GATK 3 
+- Picard 2.x
+- Samtools (see gotc docker)
+- Python 2.7
+
+Cromwell version support 
+ - Successfully tested on v33
+ - Does not work on versions < v23 due to output syntax
+
+Runtime parameters are optimized for Broad's Google Cloud Platform implementation.

processing-for-variant-discovery-gatk3.hg38.wgs.inputs.json

@@ -32,7 +32,10 @@
     "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi"
   ],
 
-  "##_COMMENT4": "DISK SIZES + PREEMPTIBLES",
+  "##_COMMENT4": "DOCKER - uncomment the following line and supply a valid docker container to override the default",
+  "##GenericPreProcessingWorkflow.gitc_docker_override": "",
+
+  "##_COMMENT5": "DISK SIZES + PREEMPTIBLES",
   "GenericPreProcessingWorkflow.agg_small_disk": 200,
   "GenericPreProcessingWorkflow.agg_medium_disk": 300,
   "GenericPreProcessingWorkflow.agg_large_disk": 400,