#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.b2c2951c" && echo "/cromwell_root/tmp.b2c2951c")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root

)
outdf4eac3a="${tmpDir}/out.$$" errdf4eac3a="${tmpDir}/err.$$"
mkfifo "$outdf4eac3a" "$errdf4eac3a"
trap 'rm "$outdf4eac3a" "$errdf4eac3a"' EXIT
tee '/cromwell_root/stdout' < "$outdf4eac3a" &
tee '/cromwell_root/stderr' < "$errdf4eac3a" >&2 &
(
cd /cromwell_root


set -euo pipefail

/src/normalize_clinical_cptac.py \
    --tumor_type CPTAC3-LUAD-TP \
     \
    /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/ecb32781-b744-498f-ade0-f0012afc3c1a/aggregate_data_workflow/b0727dba-dbb6-4983-84df-22e71cba2a89/call-aggregate_data/CPTAC3-LUAD-TP.clin.merged.txt

if true; then
    /src/package.sh -x broad-institute-gdac/\* normalize_clinical_cptac
fi
)  > "$outdf4eac3a" 2> "$errdf4eac3a"
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
