#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.82a42def" && echo "/cromwell_root/tmp.82a42def")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root

)
out38e22308="${tmpDir}/out.$$" err38e22308="${tmpDir}/err.$$"
mkfifo "$out38e22308" "$err38e22308"
trap 'rm "$out38e22308" "$err38e22308"' EXIT
tee '/cromwell_root/stdout' < "$out38e22308" &
tee '/cromwell_root/stderr' < "$err38e22308" >&2 &
(
cd /cromwell_root


set -euo pipefail

/src/MutationAssessorReport.R /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/facd4ecb-0fe6-4879-adb2-822d9aa6ce65/mutation_assessor/38e22308-ca03-4c5d-bd09-e956e92afff5/call-tool_mutation_assessor/CPTAC3-LUAD-TP.ma.maf /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/9e0520c9-8e20-4cc6-84e9-7a0dbcc09d77/mutation_mutsig2cv/feac43f0-aca5-408c-8251-fa2fda0291a8/call-tool_mutsig2cv/sig_genes.txt CPTAC3-LUAD-TP

zip -D nozzle_report * -x exec.sh

if true; then
	cp /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/facd4ecb-0fe6-4879-adb2-822d9aa6ce65/mutation_assessor/38e22308-ca03-4c5d-bd09-e956e92afff5/call-tool_mutation_assessor/mutation_assessor.zip .
	zip -r mutation_assessor.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]/*" \
		exec.sh \
		nozzle_report.zip
fi
)  > "$out38e22308" 2> "$err38e22308"
echo $? > /cromwell_root/rc.tmp
(
# add a .file in every empty directory to facilitate directory delocalization on the cloud
cd /cromwell_root
find . -type d -exec sh -c '[ -z "$(ls -A '"'"'{}'"'"')" ] && touch '"'"'{}'"'"'/.file' \;
)
(
cd /cromwell_root
sync


)
mv /cromwell_root/rc.tmp /cromwell_root/rc
