#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.346d790b" && echo "/cromwell_root/tmp.346d790b")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root

)
out22f8b2c7="${tmpDir}/out.$$" err22f8b2c7="${tmpDir}/err.$$"
mkfifo "$out22f8b2c7" "$err22f8b2c7"
trap 'rm "$out22f8b2c7" "$err22f8b2c7"' EXIT
tee '/cromwell_root/stdout' < "$out22f8b2c7" &
tee '/cromwell_root/stderr' < "$err22f8b2c7" >&2 &
(
cd /cromwell_root


set -euo pipefail

Rscript /src/sample_by_features.R  \
--mergedfile CPTAC3-LUAD-TP \
--maf /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/9e0520c9-8e20-4cc6-84e9-7a0dbcc09d77/mutation_mutsig2cv/feac43f0-aca5-408c-8251-fa2fda0291a8/call-tool_mutsig2cv/CPTAC3-LUAD-TP.final_analysis_set.maf \
--mutcateg /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/9e0520c9-8e20-4cc6-84e9-7a0dbcc09d77/mutation_mutsig2cv/feac43f0-aca5-408c-8251-fa2fda0291a8/call-tool_mutsig2cv/mutcategs.txt \
--genelist /cromwell_root/broad-institute-gdac/reference/scna_cosmic_genes/cancergene_scna_all_2014_10_16.tsv \
--clinical /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/39eab10a-1791-41cf-866c-13e6472ce02e/normalize_clinical_cptac/df4eac3a-77b6-4ce7-961f-e1027c1ad609/call-normalize_clinical_cptac_task_1/CPTAC3-LUAD-TP.clin.merged.picked.txt \
--clusters /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/69dd18b3-97fe-4143-b0f4-32e5d55e929d/aggregate_clusters_workflow/d44c315a-761b-4b72-be1f-cb969be36102/call-aggregate_clusters/CPTAC3-LUAD-TP.mergedcluster.txt \
--cnfocal /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/ba1a026a-1f61-4edb-af03-265ba4ac43e5/copy_number_gistic2/e341778e-2a5c-4d9c-b17a-bd3126ba4440/call-tool_gistic2/all_lesions.txt \
--cnbroad /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/ba1a026a-1f61-4edb-af03-265ba4ac43e5/copy_number_gistic2/e341778e-2a5c-4d9c-b17a-bd3126ba4440/call-tool_gistic2/broad_values_by_arm.txt \
 \
 \
 \
 \
 \
--broadq /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/ba1a026a-1f61-4edb-af03-265ba4ac43e5/copy_number_gistic2/e341778e-2a5c-4d9c-b17a-bd3126ba4440/call-tool_gistic2/broad_significance_results.txt \
--coverage /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/9e0520c9-8e20-4cc6-84e9-7a0dbcc09d77/mutation_mutsig2cv/feac43f0-aca5-408c-8251-fa2fda0291a8/call-tool_mutsig2cv/patient_counts_and_rates.txt \
 \
 \
--qthresh 0.1 \
 \
--sigfilemerged /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 \
--cnamp /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/ba1a026a-1f61-4edb-af03-265ba4ac43e5/copy_number_gistic2/e341778e-2a5c-4d9c-b17a-bd3126ba4440/call-tool_gistic2/amp_genes.txt \
--cndel /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/ba1a026a-1f61-4edb-af03-265ba4ac43e5/copy_number_gistic2/e341778e-2a5c-4d9c-b17a-bd3126ba4440/call-tool_gistic2/del_genes.txt \
 \
 \
 \
 \


echo "Finished aggregate feature table."
echo "Generating iComut table."

Rscript /src/generate_comut.R -s "/src" \
-f CPTAC3-LUAD-TP.samplefeatures.txt \
-t CPTAC3-LUAD-TP \
 \
-x 0.1

echo "Generating report."

Rscript /src/ft_report.R \
--feature_table CPTAC3-LUAD-TP.samplefeatures.txt \
--libdir "/src" \
 \
 \
 \
 \
 \
 \
 \
--tumor CPTAC3-LUAD-TP

zip -r nozzle_report.zip . -i *.png *.html *.txt *.RData

if true
	then zip -r aggregate_feature_table . -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
)  > "$out22f8b2c7" 2> "$err22f8b2c7"
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
