Merge branch 'release/1.4.0'

DataBiosphere · Apr 30, 2018 · 9c25a97 · 9c25a97
2 parents 029c1a9 + 7386cc0
commit 9c25a97
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Showing 2 changed files with 7 additions and 11 deletions.
diff --git a/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl b/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl
@@ -1,10 +1,10 @@
 import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/topmed-firecloud-demo/functional-equivalence-wdl/FunctionalEquivalence.wdl" as TopMed_aligner
-import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/develop/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker
+import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.4.0/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker
 
 workflow checkerWorkflow {
   #File referenceFasta
   Int expectedNumofReads
-  File docker_image
+  String docker_image
 
   File wgs_evaluation_interval_list
   File wgs_coverage_interval_list
@@ -37,9 +37,6 @@ workflow checkerWorkflow {
   Int preemptible_tries
   Int agg_preemptible_tries
 
-  # Get the size of the standard reference files
-  Float ref_size = size(ref_fasta, "GB") + size(ref_fasta_index, "GB")
-
  call TopMed_aligner.PairedEndSingleSampleWorkflow as aligner { 
    input: 
      #docker_image = docker_image,
@@ -77,7 +74,6 @@ workflow checkerWorkflow {
 
   }
 
- Float total_size = ref_size + size(aligner.output_cram, "GB")
 
- call checker.checkerTask { input: inputCRAMFile=aligner.output_cram, referenceFasta=ref_fasta , expectedNumofReads=expectedNumofReads, docker_image=docker_image, total_size=total_size }
+ call checker.checkerTask { input: inputCRAMFile=aligner.output_cram, expectedNumofReads=expectedNumofReads, docker_image=docker_image}
 }
diff --git a/functional-equivalence-checker/topmed-alignment-checker.wdl b/functional-equivalence-checker/topmed-alignment-checker.wdl
@@ -1,9 +1,9 @@
 task checkerTask {
   File inputCRAMFile
-  File referenceFasta
   Int expectedNumofReads
-  File docker_image
-  Float total_size
+  String docker_image
+
+  Float disk_size = size(inputCRAMFile, "GB")
 
   command {
     printf "The CRAM file is ${inputCRAMFile}"
@@ -29,6 +29,6 @@ task checkerTask {
 
   runtime {
     docker: docker_image
-    disk_size = total_size
+    disks: "local-disk " + sub(disk_size, "\\..*", "") + " HDD"
   }
 }