#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.c03988d7" && echo "/cromwell_root/tmp.c03988d7")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root

)
out6ec6d793="${tmpDir}/out.$$" err6ec6d793="${tmpDir}/err.$$"
mkfifo "$out6ec6d793" "$err6ec6d793"
trap 'rm "$out6ec6d793" "$err6ec6d793"' EXIT
tee '/cromwell_root/stdout' < "$out6ec6d793" &
tee '/cromwell_root/stderr' < "$err6ec6d793" >&2 &
(
cd /cromwell_root


set -euo pipefail

# Generate file of localized stick figure paths
if true; then
	cp /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_stick_figures/headers.txt generatedStickFigurePaths.txt
	sort /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_stick_figures/SIGNIFICANT_GENE.txt > stick_figure_genes.txt
	sort /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-report_mutsig/write_lines_974be3760b470f878adcc04aa44c7d00.tmp > stick_figure_txt.txt
	sort /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-report_mutsig/write_lines_15b5fde6a14fe598d69d598c7b67c87e.tmp > stick_figure_jpg.txt
	sort /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-report_mutsig/write_lines_aad8ff43adfd36033bdcde1974a0a95a.tmp > stick_figure_pdf.txt
	paste stick_figure_genes.txt \
		  stick_figure_txt.txt \
		  stick_figure_jpg.txt \
		  stick_figure_pdf.txt \
	>> generatedStickFigurePaths.txt
fi

/src/Mutsig_Report.R \
	 \
	 \
	--categories_table_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_mutsig2cv/mutcategs.txt \
	 \
	 \
	 \
	 \
	 \
	 \
	--patients_counts_rates_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_mutsig2cv/patient_counts_and_rates.txt \
	--coMut_plot_png_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_comut/PanCan_coMut.png \
	--coMut_plot_pdf_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_comut/PanCan_coMut.pdf \
	--stick_figures_path generatedStickFigurePaths.txt \
	--maf_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_mutsig2cv/PanCan.final_analysis_set.maf \
	 \
	 \
	--lego_plotter_mut_profile_png_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_lego_plotter/PanCan.final_analysis_set.maf.mutation_profile.png \
	--lego_plotter_mut_profile_AF_png_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_lego_plotter/PanCan.final_analysis_set.maf.mutation_profile_AF.png \
	--lego_plotter_mut_profile_ai_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_lego_plotter/PanCan.final_analysis_set.maf.mutation_profile.ai \
	--lego_plotter_mut_profile_AF_ai_path /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_lego_plotter/PanCan.final_analysis_set.maf.mutation_profile_AF.ai \
	PanCan /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-filter_sig_genes/sig_genes.txt /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_mutsig2cv/MutSig_version.txt

if true; then
	cat /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_mutsig2cv/tool_mutsig2cv.zip /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_comut/tool_comut.zip /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_lego_plotter/tool_lego_plotter.zip /cromwell_root/fc-1ae64e4d-153a-4446-836a-0ce1c97737d3/dde1b0c6-4363-483d-8d92-657f5e39e93c/mutation_mutsig2cv/6ec6d793-f3a8-4221-a0ab-4927e39f42b9/call-tool_stick_figures/tool_stick_figures.zip > tmp.zip
	zip -FF tmp.zip --out report_mutsig.zip > /dev/null 2>&1
	rm tmp.zip
	zip -r report_mutsig.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]/*" \
		"fc-secure-[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 \
		generatedStickFigurePaths.txt \
		stick_figure_\*.txt
fi
)  > "$out6ec6d793" 2> "$err6ec6d793"
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