added requester pays option (#57)

* added requester pays option
* updated gatk to 4.1.8.1 for hc
* fix link for resource bundle in Readme

README.md

@@ -47,7 +47,7 @@ file with 50 or more GVCFs and produces a multisample VCF.
 - Samtools 1.3.1
 - Python 2.7
 - Cromwell version support 
-  - Successfully tested on v50
+  - Successfully tested on v53
 
 ### IMPORTANT NOTE : 
 - VQSR wiring. The SNP and INDEL models are built in parallel, but then the corresponding 
@@ -92,7 +92,7 @@ file with 50 or more GVCFs and produces a multisample VCF.
 - For help running workflows on the Google Cloud Platform or locally please
 view the following tutorial [(How to) Execute Workflows from the gatk-workflows Git Organization](https://gatk.broadinstitute.org/hc/en-us/articles/360035530952).
 - Please visit the [User Guide](https://gatk.broadinstitute.org/hc/en-us/categories/360002310591) site for further documentation on our workflows and tools.
-- Relevant reference and resources bundles can be accessed in [Resource Bundle](https://gatk.broadinstitute.org/hc/en-us/articles/360036212652).
+- Relevant reference and resources bundles can be accessed in [Resource Bundle](https://gatk.broadinstitute.org/hc/en-us/articles/360035890811).
 
 ### Contact Us :
 - The following material is provided by the Data Science Platforum group at the Broad Institute. Please direct any questions or concerns to one of our forum sites : [GATK](https://gatk.broadinstitute.org/hc/en-us/community/topics) or [Terra](https://support.terra.bio/hc/en-us/community/topics/360000500432).

haplotypecaller-gvcf-gatk4.wdl

@@ -40,7 +40,7 @@ workflow HaplotypeCallerGvcf_GATK4 {
 
     Boolean make_gvcf = true
     Boolean make_bamout = false
-    String gatk_docker = "broadinstitute/gatk:4.1.7.0"
+    String gatk_docker = "broadinstitute/gatk:4.1.8.1"
     String gatk_path = "/gatk/gatk"
     String gitc_docker = "broadinstitute/genomes-in-the-cloud:2.3.1-1500064817"
     String samtools_path = "samtools"
@@ -173,6 +173,8 @@ task HaplotypeCaller {
     Boolean make_bamout
     Int hc_scatter
 
+    String? gcs_project_for_requester_pays
+
     String gatk_path
     String? java_options
 
@@ -218,6 +220,7 @@ task HaplotypeCaller {
       -G StandardAnnotation -G StandardHCAnnotation ~{true="-G AS_StandardAnnotation" false="" make_gvcf} \
       -GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 50 -GQB 60 -GQB 70 -GQB 80 -GQB 90 \
       ~{true="-ERC GVCF" false="" make_gvcf} \
+      ~{if defined(gcs_project_for_requester_pays) then "--gcs-project-for-requester-pays ~{gcs_project_for_requester_pays}" else ""} \
       ~{bamout_arg}
 
     # Cromwell doesn't like optional task outputs, so we have to touch this file.