Wdlupdate (#5)

* increased default memory
* Updated contact us message in ReadMe

README.md

@@ -11,17 +11,18 @@ Workflows for validating sequence data
  - Set of .txt files containing the validation reports, one per input file
 
 ### Cromwell version support 
- - Successfully tested on v33
+ - Successfully tested on v49
  - Does not work on versions < v23 due to output syntax
 
-### Important Note :
-- The provided JSON is meant to be a ready to use example JSON template of the workflow. It is the user’s responsibility to correctly set the reference and resource input variables using the [GATK Tool and Tutorial Documentations](https://software.broadinstitute.org/gatk/documentation/).
-- Relevant reference and resources bundles can be accessed in [Resource Bundle](https://software.broadinstitute.org/gatk/download/bundle).
+### Important Notes :
 - Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
+- The provided JSON is a ready to use example JSON template of the workflow. Users are responsible for reviewing the [GATK Tool and Tutorial Documentations](https://gatk.broadinstitute.org/hc/en-us/categories/360002310591) to properly set the reference and resource variables. 
 - 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://software.broadinstitute.org/gatk/documentation/article?id=12521).
-- The following material is provided by the GATK Team. Please post any questions or concerns to one of our forum sites : [GATK](https://gatkforums.broadinstitute.org/gatk/categories/ask-the-team/) , [FireCloud](https://gatkforums.broadinstitute.org/firecloud/categories/ask-the-firecloud-team) or [Terra](https://broadinstitute.zendesk.com/hc/en-us/community/topics/360000500432-General-Discussion) , [WDL/Cromwell](https://gatkforums.broadinstitute.org/wdl/categories/ask-the-wdl-team).
-- Please visit the [User Guide](https://software.broadinstitute.org/gatk/documentation/) site for further documentation on our workflows and tools.
+view the following tutorial [(How to) Execute Workflows from the gatk-workflows Git Organization](https://gatk.broadinstitute.org/hc/en-us/articles/360035530952).
+- Relevant reference and resources bundles can be accessed in [Resource Bundle](https://gatk.broadinstitute.org/hc/en-us/articles/360036212652).
+
+### 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).
 
 ### LICENSING :
 Copyright Broad Institute, 2019 | BSD-3

validate-bam.inputs.json

@@ -1,15 +1,6 @@
 {
-  "##Comment1":"Input",
   "ValidateBamsWf.bam_array": [ 
   	"gs://gatk-test-data/wgs_bam/NA12878_24RG_hg38/NA12878_24RG_small.hg38.bam",
   	"gs://gatk-test-data/wgs_bam/NA12878_24RG_hg38/NA12878_24RG_med.hg38.bam"
-  ],
-  "##Comment2":"Parameter",
-  "#ValidateBamsWf.ValidateBAM.validation_mode": "String (optional)",
-
-  "##Comment3":"Runtime - uncomment the lines below and supply a valid docker container to override the default",
-  "#ValidateBamsWf.ValidateBAM.machine_mem_gb": "Int? (optional)",  
-  "#ValidateBamsWf.ValidateBAM.disk_space_gb": "Int? (optional)",
-  "#ValidateBamsWf.ValidateBAM.gatk_path_override": "String (optional)",
-  "#ValidateBamsWf.gatk_docker_override": "String (optional)"
+  ]
 }

validate-bam.wdl

@@ -1,3 +1,4 @@
+version 1.0
 ## Copyright Broad Institute, 2017
 ## 
 ## This WDL performs format validation on SAM/BAM files in a list
@@ -26,11 +27,11 @@
 
 # WORKFLOW DEFINITION
 workflow ValidateBamsWf {
-  Array[File] bam_array 
-  String? gatk_docker_override
-  String gatk_docker = select_first([gatk_docker_override, "broadinstitute/gatk:latest"])
-  String? gatk_path_override
-  String gatk_path = select_first([gatk_path_override, "/gatk/gatk"])
+  input {
+    Array[File] bam_array 
+    String gatk_docker = "broadinstitute/gatk:latest"
+    String gatk_path = "/gatk/gatk"
+  }
 
   # Process the input files in parallel
   scatter (input_bam in bam_array) {
@@ -58,18 +59,20 @@ workflow ValidateBamsWf {
 
 # Validate a SAM or BAM using Picard ValidateSamFile
 task ValidateBAM {
-  # Command parameters
-  File input_bam
-  String output_basename
-  String? validation_mode
-  String gatk_path
+  input {
+    # Command parameters
+    File input_bam
+    String output_basename
+    String? validation_mode
+    String gatk_path
 
-  # Runtime parameters
-  String docker
-  Int? machine_mem_gb
-  Int? disk_space_gb
-  Int disk_size = ceil(size(input_bam, "GB")) + 20
-
+    # Runtime parameters
+    String docker
+    Int machine_mem_gb = 4
+    Int addtional_disk_space_gb = 50
+  }
+
+  Int disk_size = ceil(size(input_bam, "GB")) + addtional_disk_space_gb
   String output_name = "${output_basename}_${validation_mode}.txt"
 
   command {
@@ -81,9 +84,8 @@ task ValidateBAM {
   }
   runtime {
     docker: docker
-    memory: select_first([machine_mem_gb, 1]) + " GB"
-    cpu: "1"
-    disks: "local-disk " + select_first([disk_space_gb, disk_size]) + " HDD"
+    memory: machine_mem_gb + " GB"
+    disks: "local-disk " + disk_size + " HDD"
   }
   output {
     File validation_report = "${output_name}"