Updated docker versions (#28)

* Updated docker versions, added dockstore yml

.dockstore.yml

@@ -0,0 +1,9 @@
+
+version: 1.2
+workflows:
+   - name: processing-for-variant-discovery-gatk4
+     subclass: WDL
+     primaryDescriptorPath: /processing-for-variant-discovery-gatk4
+     testParameterFiles:
+     -  /processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json
+     -  /processing-for-variant-discovery-gatk4.b37.wgs.inputs.json

README.md

@@ -30,7 +30,7 @@ The processing-for-variant-discovery-gatk4 WDL pipeline implements data pre-proc
 - Samtools 1.3.1 (using htslib 1.3.1)
 - Python 2.7
 - Cromwell version support 
-  - Successfully tested on v52 
+  - Successfully tested on v59 
 
 ### Important Notes :
 - Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
@@ -44,7 +44,7 @@ view the following tutorial [(How to) Execute Workflows from the gatk-workflows
 
 
 ### LICENSING :
-Copyright Broad Institute, 2019 | BSD-3
+Copyright Broad Institute, 2021 | BSD-3
 This script is released under the WDL open source code license (BSD-3) (full license text at https://github.com/openwdl/wdl/blob/master/LICENSE). Note however that the programs it calls may be subject to different licenses. Users are responsible for checking that they are authorized to run all programs before running this script.
 - [GATK](https://software.broadinstitute.org/gatk/download/licensing.php)
 - [BWA](http://bio-bwa.sourceforge.net/bwa.shtml#13)

processing-for-variant-discovery-gatk4.wdl

@@ -1,6 +1,6 @@
 version 1.0
 
-## Copyright Broad Institute, 2019
+## Copyright Broad Institute, 2021
 ## 
 ## This WDL pipeline implements data pre-processing according to the GATK Best Practices.  
 ##
@@ -24,8 +24,7 @@ version 1.0
 ## - Python 2.7
 ##
 ## Cromwell version support 
-## - Successfully tested on v37
-## - Does not work on versions < v23 due to output syntax
+## - Successfully tested on v59
 ##
 ## Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
 ##
@@ -62,9 +61,9 @@ workflow PreProcessingForVariantDiscovery_GATK4 {
     String bwa_commandline = "bwa mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta"
     Int compression_level = 5
 
-    String gatk_docker = "broadinstitute/gatk:4.1.8.1"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.2.0.0"
     String gatk_path = "/gatk/gatk"
-    String gotc_docker = "broadinstitute/genomes-in-the-cloud:2.3.1-1512499786"
+    String gotc_docker = "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.7-1603303710"
     String gotc_path = "/usr/gitc/"
     String python_docker = "python:2.7"