#!/bin/bash

cd /cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/execution
tmpDir=$(mkdir -p "/cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/tmp.a9e69d7f" && echo "/cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/tmp.a9e69d7f")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/execution

)
out79391cb8="${tmpDir}/out.$$" err79391cb8="${tmpDir}/err.$$"
mkfifo "$out79391cb8" "$err79391cb8"
trap 'rm "$out79391cb8" "$err79391cb8"' EXIT
tee '/cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/execution/stdout' < "$out79391cb8" &
tee '/cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/execution/stderr' < "$err79391cb8" >&2 &
(
cd /cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/execution


      set -euo pipefail

RunR.sh /src/ClinicalAnalysisAllGenesReport_nozzle.R \
  /src \
  -iR/cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/inputs/-480120836/clinical-results.txt \
  -iI/cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/inputs/-480120836/clinical-results.RData \
  -rN10 \
  -cP0.05 \
  -cQ0.3 \
  -OPMRNASEQ_EXPR \
   \
  

zip -r report.zip .
if true; then
	mv /cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/inputs/-480120836/correlate_clinical_vs_expression.zip .
	zip -r correlate_clinical_vs_expression.zip . -x \
		"fc-[a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9]-[a-f0-9][a-f0-9][a-f0-9][a-f0-9]-[a-f0-9][a-f0-9][a-f0-9][a-f0-9]-[a-f0-9][a-f0-9][a-f0-9][a-f0-9]-[a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9][a-f0-9]/*" \
		lost+found/\* \
		broad-institute-gdac/\* \
		"tmp.[a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9][a-zA-Z0-9]/*" \
		exec.sh \
		report.zip
fi
)  > "$out79391cb8" 2> "$err79391cb8"
echo $? > /cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/execution/rc.tmp
(
# add a .file in every empty directory to facilitate directory delocalization on the cloud
cd /cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/execution
find . -type d -exec sh -c '[ -z "$(ls -A '"'"'{}'"'"')" ] && touch '"'"'{}'"'"'/.file' \;
)
(
cd /cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/execution
sync


)
mv /cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/execution/rc.tmp /cromwell-executions/report_correlate_expression_clinical_workflow/79391cb8-4c75-490b-8f58-538f2066adad/call-report_correlate_expression_clinical/execution/rc
