Merge pull request #3 from mr-c/patch-1

don't rely on CLASSPATH
heliumdatacommons · Sep 5, 2018 · 6011878 · 6011878
2 parents 578066e + 4d080b9
commit 6011878
Showing 1 changed file with 3 additions and 9 deletions.
diff --git a/topmed-workflows/TOPMed_RNAseq_pipeline/markduplicates.cwl b/topmed-workflows/TOPMed_RNAseq_pipeline/markduplicates.cwl
@@ -11,13 +11,12 @@ doc: |
 cwlVersion: v1.0
 class: CommandLineTool
 label: "run-MarkDuplicates"
-baseCommand: [java]
+baseCommand: [picard, MarkDuplicates]
 
-requirements: # turn back into a hint when the biocontainer has its classpath
-              #   updated
+hints:
   EnvVarRequirement:
     envDef:
-      CLASSPATH: /usr/local/share/picard-2.9.2-2/picard.jar
+      JAVA_TOOL_OPTIONS: "-Xmx$(runtime.ram)M" 
   DockerRequirement:
     dockerPull: quay.io/biocontainers/picard:2.9.2--2
 
@@ -28,11 +27,6 @@ inputs:
     type: string
 
 arguments:
-  - prefix: -Xmx
-    valueFrom: $(runtime.ram)M
-    separate: false
-  - picard.cmdline.PicardCommandLine
-  - MarkDuplicates
   - I=$(inputs.input_bam.path)
   - O=$(runtime.outdir)/$(inputs.input_bam.nameroot).md.bam
   - M=$(runtime.outdir)/$(inputs.prefix_str).marked_dup_metrics.txt