add --no-same-owner to tar -x in WDL tasks

broadinstitute · Aug 21, 2018 · 8e70f50 · 8e70f50
1 parent 7eea977
commit 8e70f50
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/pipes/WDL/workflows/tasks/tasks_assembly.wdl b/pipes/WDL/workflows/tasks/tasks_assembly.wdl
@@ -184,7 +184,7 @@ task refine {
         # prep GATK
         mkdir gatk
         if [[ ${gatk_jar} == *.tar.bz2 ]]; then
-          tar -xjvf ${gatk_jar} -C gatk
+          tar -xjvf ${gatk_jar} -C gatk --no-same-owner
         else
           ln -s ${gatk_jar} gatk/GenomeAnalysisTK.jar
         fi
@@ -255,7 +255,7 @@ task refine_2x_and_plot {
         # prep GATK
         mkdir gatk
         if [[ ${gatk_jar} == *.tar.bz2 ]]; then
-          tar -xjvf ${gatk_jar} -C gatk
+          tar -xjvf ${gatk_jar} -C gatk --no-same-owner
         else
           ln -s ${gatk_jar} gatk/GenomeAnalysisTK.jar
         fi

diff --git a/pipes/WDL/workflows/tasks/tasks_reports.wdl b/pipes/WDL/workflows/tasks/tasks_reports.wdl
@@ -19,7 +19,7 @@ task plot_coverage {
     # prep GATK
     mkdir gatk
     if [[ ${gatk_jar} == *.tar.bz2 ]]; then
-      tar -xjvf ${gatk_jar} -C gatk
+      tar -xjvf ${gatk_jar} -C gatk --no-same-owner
     else
       ln -s ${gatk_jar} gatk/GenomeAnalysisTK.jar
     fi