Hard coding /scratch for picard / arrg tmpdir

mskcc · Jan 30, 2020 · 14a783b · 14a783b
1 parent 07e0d12
commit 14a783b
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diff --git a/cwl_tools/picard/AddOrReplaceReadGroups.cwl b/cwl_tools/picard/AddOrReplaceReadGroups.cwl
@@ -7,6 +7,7 @@ arguments:
 - -Xmx4g
 - -jar
 - $(inputs.arrg)
+- TMP_DIR=/scratch
 
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/cwl_tools/picard/FixMateInformation.cwl b/cwl_tools/picard/FixMateInformation.cwl
@@ -7,6 +7,7 @@ arguments:
 - -Xmx24g
 - -jar
 - $(inputs.fix_mate_information)
+- TMP_DIR=/scratch
 
 requirements:
   InlineJavascriptRequirement: {}