digraph workflow {
	graph [_draw_="c 9 -#fffffe00 C 7 -#eeeeee P 4 0 0 0 458 770.5 458 770.5 0 ",
		bb="0,0,770.5,458",
		bgcolor="#eeeeee",
		clusterrank=local,
		color=black,
		dpi=96,
		fontsize=10,
		labeljust=left,
		nodesep=0.05,
		ranksep=0.22,
		xdotversion=1.7
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	node [color=black,
		fillcolor=lightgoldenrodyellow,
		fontcolor=black,
		fontname=Helvetica,
		fontsize=10,
		height=0,
		label="\N",
		shape=record,
		style=filled,
		width=0
	];
	edge [arrowsize=0.7,
		color=black,
		fontcolor=black,
		fontname=Helvetica,
		fontsize=8
	];
	subgraph cluster_inputs {
		graph [_draw_="S 6 -dashed c 7 -#000000 C 7 -#eeeeee P 4 8 395 8 450 637 450 637 395 ",
			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 58 438 0 84 15 -Workflow Inputs ",
			bb="8,395,637,450",
			label="Workflow Inputs",
			lheight=0.15,
			lp="58,440.5",
			lwidth=1.17,
			rank=same,
			style=dashed
		];
		reference	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 58.5 403.5 58.5 422.5 121.5 422.5 121.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 90 410.5 0 47 9 -reference ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=reference,
			pos="90,413",
			rects="58.5,403.5,121.5,422.5",
			width=0.875];
		tumor_sample_name	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 339 403.5 339 422.5 459 422.5 459 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 399 410.5 0 104 17 -tumor_sample_name ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=tumor_sample_name,
			pos="399,413",
			rects="339,403.5,459,422.5",
			width=1.6667];
		somatic_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 463 403.5 463 422.5 539 422.5 539 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 501 410.5 0 60 11 -somatic_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=somatic_vcf,
			pos="501,413",
			rects="463,403.5,539,422.5",
			width=1.0556];
		bam	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 16 403.5 16 422.5 54 422.5 54 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 35 410.5 0 22 3 -bam ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=bam,
			pos="35,413",
			rects="16,403.5,54,422.5",
			width=0.52778];
		reference_dict	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 543 403.5 543 422.5 629 422.5 629 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 586 410.5 0 70 14 -reference_dict ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=reference_dict,
			pos="586,413",
			rects="543,403.5,629,422.5",
			width=1.1944];
		normal_sample_name	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 125.5 403.5 125.5 422.5 250.5 422.5 250.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 188 410.5 0 109 18 -normal_sample_name ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=normal_sample_name,
			pos="188,413",
			rects="125.5,403.5,250.5,422.5",
			width=1.7361];
		germline_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 255 403.5 255 422.5 335 422.5 335 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 295 410.5 0 64 12 -germline_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=germline_vcf,
			pos="295,413",
			rects="255,403.5,335,422.5",
			width=1.1111];
	}
	subgraph cluster_outputs {
		graph [_draw_="S 6 -dashed c 7 -#000000 C 7 -#eeeeee P 4 25 8 25 63 133 63 133 8 ",
			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 79 15 0 92 16 -Workflow Outputs ",
			bb="25,8,133,63",
			label="Workflow Outputs",
			labelloc=b,
			lheight=0.15,
			lp="79,17.5",
			lwidth=1.28,
			rank=same,
			style=dashed
		];
		phased_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 43 35.5 43 54.5 115 54.5 115 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 79 42.5 0 56 10 -phased_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=phased_vcf,
			pos="79,45",
			rects="43,35.5,115,54.5",
			width=1];
	}
	combine_variants	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 123.5 260.5 123.5 279.5 414.5 279.5 414.5 260.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 269 267.5 0 275 52 -Combine germline and somatic vcf for pVACseq phasing ",
		height=0.27778,
		label="Combine germline and somatic vcf for pVACseq phasing",
		pos="269,270",
		rects="123.5,260.5,414.5,279.5",
		width=4.0417];
	reference -> combine_variants	[_draw_="c 7 -#000000 B 7 98.32 403.6 117.28 384.71 165.59 337.91 211 305 221.8 297.17 234.51 289.56 245.28 283.53 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 246.44 285.69 251.4 280.17 244.08 281.39 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 194 335.6 0 40 9 -reference ",
		label=reference,
		lp="194,337.5",
		pos="e,252.72,279.44 98.318,403.6 117.28,384.71 165.59,337.91 211,305 221.8,297.17 234.51,289.56 245.28,283.53"];
	phase_vcf	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 18.5 125.5 18.5 144.5 139.5 144.5 139.5 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 79 132.5 0 105 19 -Read-backed phasing ",
		height=0.27778,
		label="Read-backed phasing",
		pos="79,135",
		rects="18.5,125.5,139.5,144.5",
		width=1.6806];
	reference -> phase_vcf	[_draw_="c 7 -#000000 B 10 87.11 403.81 83.85 393.84 79 376.4 79 361 79 361 79 361 79 179 79 170.31 79 160.63 79 152.65 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 81.45 152.76 79 145.76 76.55 152.76 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 99 268.1 0 40 9 -reference ",
		label=reference,
		lp="99,270",
		pos="e,79,144.24 87.11,403.81 83.851,393.84 79,376.4 79,361 79,361 79,361 79,179 79,170.31 79,160.63 79,152.65"];
	select_somatic_tumor_sample	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 350.5 350.5 350.5 369.5 491.5 369.5 491.5 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 421 357.5 0 125 25 -SelectVariants (GATK 3.6) ",
		height=0.27778,
		label="SelectVariants (GATK 3.6)",
		pos="421,360",
		rects="350.5,350.5,491.5,369.5",
		width=1.9583];
	reference -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 13 104.22 403.64 110.64 400.3 118.48 396.82 126 395 151.72 388.78 340.05 398.24 364 387 368.84 384.73 367.55 380.97 \
372 378 374.91 376.06 378.06 374.31 381.31 372.75 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 382.18 375.05 387.64 370.03 380.24 370.55 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 392 380.6 0 40 9 -reference ",
		label=reference,
		lp="392,382.5",
		pos="e,389.03,369.44 104.22,403.64 110.64,400.3 118.48,396.82 126,395 151.72,388.78 340.05,398.24 364,387 368.84,384.73 367.55,380.97 \
372,378 374.91,376.06 378.06,374.31 381.31,372.75"];
	rename_germline_vcf	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 178.5 350.5 178.5 369.5 301.5 369.5 301.5 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 240 357.5 0 107 19 -rename_germline_vcf ",
		height=0.27778,
		label=rename_germline_vcf,
		pos="240,360",
		rects="178.5,350.5,301.5,369.5",
		width=1.7083];
	tumor_sample_name -> rename_germline_vcf	[_draw_="c 7 -#000000 B 13 369.5 403.56 358.7 400.63 346.35 397.47 335 395 314.29 390.5 307.47 395.37 288 387 281.88 384.37 281.71 381.44 \
276 378 273.22 376.32 270.24 374.69 267.24 373.14 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 268.53 371.04 261.16 370.14 266.36 375.44 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 327.5 380.6 0 79 15 -new_sample_name ",
		label=new_sample_name,
		lp="327.5,382.5",
		pos="e,259.81,369.47 369.5,403.56 358.7,400.63 346.35,397.47 335,395 314.29,390.5 307.47,395.37 288,387 281.88,384.37 281.71,381.44 276,\
378 273.22,376.32 270.24,374.69 267.24,373.14"];
	tumor_sample_name -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 404.12 403.89 406.99 399.1 410.49 392.85 413 387 414.3 383.96 415.49 380.63 416.53 377.4 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 418.85 378.22 418.48 370.81 414.15 376.83 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 456.5 380.6 0 81 18 -samples_to_include ",
		label=samples_to_include,
		lp="456.5,382.5",
		pos="e,418.91,369.36 404.12,403.89 406.99,399.1 410.49,392.85 413,387 414.3,383.96 415.49,380.63 416.53,377.4"];
	somatic_vcf -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 502.78 403.67 503.88 396.05 504.1 384.95 498 378 496.01 375.74 492.44 373.75 487.88 372.01 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 488.84 369.75 481.43 369.94 487.35 374.42 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 508.5 380.6 0 13 3 -vcf ",
		label=vcf,
		lp="508.5,382.5",
		pos="e,479.99,369.48 502.78,403.67 503.88,396.05 504.1,384.95 498,378 496.01,375.74 492.44,373.75 487.88,372.01"];
	bam -> phase_vcf	[_draw_="c 7 -#000000 B 10 37.36 403.78 40.03 393.76 44 376.28 44 361 44 361 44 361 44 179 44 167.34 51.84 157.09 60.09 149.52 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 61.4 151.62 65.2 145.25 58.26 147.86 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 53.5 268.1 0 19 3 -bam ",
		label=bam,
		lp="53.5,270",
		pos="e,66.364,144.28 37.365,403.78 40.031,393.76 44,376.28 44,361 44,361 44,361 44,179 44,167.34 51.835,157.09 60.091,149.52"];
	sort	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 239.5 215.5 239.5 234.5 298.5 234.5 298.5 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 269 222.5 0 43 8 -Sort VCF ",
		height=0.27778,
		label="Sort VCF",
		pos="269,225",
		rects="239.5,215.5,298.5,234.5",
		width=0.81944];
	reference_dict -> sort	[_draw_="c 7 -#000000 B 13 604.89 403.62 612.13 399.55 619.87 394.01 625 387 632.07 377.34 632 372.97 632 361 632 361 632 361 632 269 632 \
236.5 399.56 228.48 306.68 226.57 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 306.96 224.13 299.91 226.44 306.86 229.03 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 661.5 313.1 0 59 14 -reference_dict ",
		label=reference_dict,
		lp="661.5,315",
		pos="e,298.4,226.41 604.89,403.62 612.13,399.55 619.87,394.01 625,387 632.07,377.34 632,372.97 632,361 632,361 632,361 632,269 632,236.5 \
399.56,228.48 306.68,226.57"];
	normal_sample_name -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 171.2 403.64 159.97 396.93 148.51 387.16 156 378 158.59 374.83 163.96 372.23 170.79 370.12 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 171.11 372.57 177.24 368.39 169.84 367.83 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 194.5 380.6 0 77 17 -sample_to_replace ",
		label=sample_to_replace,
		lp="194.5,382.5",
		pos="e,178.7,368 171.2,403.64 159.97,396.93 148.51,387.16 156,378 158.59,374.83 163.96,372.23 170.79,370.12"];
	germline_vcf -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 271.27 403.52 258.94 398.61 245.69 392.36 242 387 240.14 384.31 239.18 381.06 238.74 377.79 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 241.2 377.91 238.63 370.95 236.3 377.99 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 260.5 380.6 0 37 9 -input_vcf ",
		label=input_vcf,
		lp="260.5,382.5",
		pos="e,238.6,369.44 271.27,403.52 258.94,398.61 245.69,392.36 242,387 240.14,384.31 239.18,381.06 238.74,377.79"];
	index_renamed_germline	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 213 305.5 213 324.5 275 324.5 275 305.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 244 312.5 0 46 9 -vcf index ",
		height=0.27778,
		label="vcf index",
		pos="244,315",
		rects="213,305.5,275,324.5",
		width=0.86111];
	rename_germline_vcf -> index_renamed_germline	[_draw_="c 7 -#000000 B 4 240.77 350.71 241.25 345.59 241.87 338.85 242.45 332.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 244.88 332.97 243.09 325.77 240 332.52 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 248.5 335.6 0 13 3 -vcf ",
		label=vcf,
		lp="248.5,337.5",
		pos="e,243.23,324.27 240.77,350.71 241.25,345.59 241.87,338.85 242.45,332.67"];
	combine_variants -> sort	[_draw_="c 7 -#000000 B 4 269 260.71 269 255.59 269 248.85 269 242.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 271.45 242.78 269 235.78 266.55 242.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 275.5 245.6 0 13 3 -vcf ",
		label=vcf,
		lp="275.5,247.5",
		pos="e,269,234.27 269,260.71 269,255.59 269,248.85 269,242.67"];
	index_filtered_somatic	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 334 305.5 334 324.5 396 324.5 396 305.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 365 312.5 0 46 9 -vcf index ",
		height=0.27778,
		label="vcf index",
		pos="365,315",
		rects="334,305.5,396,324.5",
		width=0.86111];
	index_filtered_somatic -> combine_variants	[_draw_="c 7 -#000000 B 7 348.11 305.52 337.52 300.3 323.56 293.56 311 288 306.86 286.17 302.47 284.3 298.13 282.51 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 299.29 280.33 291.88 279.96 297.43 284.87 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 354.5 290.6 0 49 11 -somatic_vcf ",
		label=somatic_vcf,
		lp="354.5,292.5",
		pos="e,290.48,279.39 348.11,305.52 337.52,300.3 323.56,293.56 311,288 306.86,286.17 302.47,284.3 298.13,282.51"];
	bgzip_and_index_phased_vcf	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 21 80.5 21 99.5 137 99.5 137 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 79 87.5 0 100 19 -bgzip and index VCF ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label="bgzip and index VCF",
		pos="79,90",
		rects="21,80.5,137,99.5",
		width=1.6111];
	bgzip_and_index_phased_vcf -> phased_vcf	[_draw_="c 7 -#000000 B 4 79 80.71 79 75.59 79 68.85 79 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 81.45 62.78 79 55.78 76.55 62.78 ",
		pos="e,79,54.265 79,80.709 79,75.593 79,68.848 79,62.666"];
	index_renamed_germline -> combine_variants	[_draw_="c 7 -#000000 B 4 248.82 305.71 252 300.24 256.27 292.9 260.06 286.38 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 262.03 287.86 263.43 280.57 257.8 285.39 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 284 290.6 0 52 12 -germline_vcf ",
		label=germline_vcf,
		lp="284,292.5",
		pos="e,264.19,279.27 248.82,305.71 252,300.24 256.27,292.9 260.06,286.38"];
	phase_vcf -> bgzip_and_index_phased_vcf	[_draw_="c 7 -#000000 B 4 79 125.71 79 120.59 79 113.85 79 107.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 81.45 107.78 79 100.78 76.55 107.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 85.5 110.6 0 13 3 -vcf ",
		label=vcf,
		lp="85.5,112.5",
		pos="e,79,99.265 79,125.71 79,120.59 79,113.85 79,107.67"];
	bgzip_and_index	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 148 170.5 148 189.5 264 189.5 264 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 206 177.5 0 100 19 -bgzip and index VCF ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label="bgzip and index VCF",
		pos="206,180",
		rects="148,170.5,264,189.5",
		width=1.6111];
	sort -> bgzip_and_index	[_draw_="c 7 -#000000 B 4 256.55 215.5 247.67 209.44 235.54 201.16 225.39 194.23 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 226.83 192.25 219.67 190.33 224.07 196.3 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 249.5 200.6 0 13 3 -vcf ",
		label=vcf,
		lp="249.5,202.5",
		pos="e,218.42,189.48 256.55,215.5 247.67,209.44 235.54,201.16 225.39,194.23"];
	bgzip_and_index -> phase_vcf	[_draw_="c 7 -#000000 B 4 180.91 170.5 161.17 163.82 133.49 154.45 111.96 147.16 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 112.89 144.89 105.47 144.96 111.32 149.53 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 159.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="159.5,157.5",
		pos="e,104.04,144.48 180.91,170.5 161.17,163.82 133.49,154.45 111.96,147.16"];
	select_somatic_tumor_sample -> index_filtered_somatic	[_draw_="c 7 -#000000 B 4 409.94 350.5 402.19 344.56 391.67 336.48 382.76 329.64 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 384.29 327.72 377.24 325.4 381.3 331.61 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 404.5 335.6 0 13 3 -vcf ",
		label=vcf,
		lp="404.5,337.5",
		pos="e,376.04,324.48 409.94,350.5 402.19,344.56 391.67,336.48 382.76,329.64"];
	default1	[_draw_="c 7 -#000000 C 7 -#d5aefc P 4 645.5 403.5 645.5 422.5 770.5 422.5 770.5 403.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 708 410.5 0 109 20 -\"somatic_tumor_only\" ",
		fillcolor="#D5AEFC",
		height=0.27778,
		label="\"somatic_tumor_only\"",
		pos="708,413",
		rects="645.5,403.5,770.5,422.5",
		width=1.7361];
	default1 -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 675.71 403.57 663.9 400.64 650.39 397.47 638 395 589.62 385.35 534.72 376.77 492.24 370.64 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 492.69 368.23 485.41 369.67 492 373.08 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 635.5 380.6 0 91 19 -output_vcf_basename ",
		label=output_vcf_basename,
		lp="635.5,382.5",
		pos="e,483.92,369.45 675.71,403.57 663.9,400.64 650.39,397.47 638,395 589.62,385.35 534.72,376.77 492.24,370.64"];
}