#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.487ed4c8" && echo "/cromwell_root/tmp.487ed4c8")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root

)
outca6ef43d="${tmpDir}/out.$$" errca6ef43d="${tmpDir}/err.$$"
mkfifo "$outca6ef43d" "$errca6ef43d"
trap 'rm "$outca6ef43d" "$errca6ef43d"' EXIT
tee '/cromwell_root/stdout' < "$outca6ef43d" &
tee '/cromwell_root/stderr' < "$errca6ef43d" >&2 &
(
cd /cromwell_root


set -euo pipefail
Rscript /src/generate_APOBEC_for_clinical.correlation.input.R --apobec.file /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/53b59b4a-b38d-4dfd-9ded-fd5171ac2ee1/mutation_apobec/ca6ef43d-ce49-4015-b418-a9b28606bbcb/call-tool_apobec/work/Mutsig_maf_modified.maf_sorted_sum_all_fisher_Pcorr.txt

if true; then
	mv /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/53b59b4a-b38d-4dfd-9ded-fd5171ac2ee1/mutation_apobec/ca6ef43d-ce49-4015-b418-a9b28606bbcb/call-tool_apobec/mutation_apobec.zip .
	zip -r mutation_apobec.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
fi
)  > "$outca6ef43d" 2> "$errca6ef43d"
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
