digraph workflow {
	graph [_draw_="c 9 -#fffffe00 C 7 -#eeeeee P 4 0 0 0 458 771.5 458 771.5 0 ",
		bb="0,0,771.5,458",
		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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		fillcolor=lightgoldenrodyellow,
		fontcolor=black,
		fontname=Helvetica,
		fontsize=10,
		height=0,
		label="\N",
		shape=record,
		style=filled,
		width=0
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	edge [arrowsize=0.7,
		color=black,
		fontcolor=black,
		fontname=Helvetica,
		fontsize=8
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	subgraph cluster_inputs {
		graph [_draw_="S 6 -dashed c 7 -#000000 C 7 -#eeeeee P 4 8 395 8 450 638 450 638 395 ",
			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 58 438 0 84 15 -Workflow Inputs ",
			bb="8,395,638,450",
			label="Workflow Inputs",
			lheight=0.15,
			lp="58,440.5",
			lwidth=1.17,
			rank=same,
			style=dashed
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		reference	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 566.5 403.5 566.5 422.5 629.5 422.5 629.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 598 410.5 0 47 9 -reference ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=reference,
			pos="598,413",
			rects="566.5,403.5,629.5,422.5",
			width=0.875];
		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];
		somatic_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 486 403.5 486 422.5 562 422.5 562 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 524 410.5 0 60 11 -somatic_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=somatic_vcf,
			pos="524,413",
			rects="486,403.5,562,422.5",
			width=1.0556];
		germline_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 278 403.5 278 422.5 358 422.5 358 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 318 410.5 0 64 12 -germline_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=germline_vcf,
			pos="318,413",
			rects="278,403.5,358,422.5",
			width=1.1111];
		tumor_sample_name	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 362 403.5 362 422.5 482 422.5 482 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 422 410.5 0 104 17 -tumor_sample_name ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=tumor_sample_name,
			pos="422,413",
			rects="362,403.5,482,422.5",
			width=1.6667];
		normal_sample_name	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 148.5 403.5 148.5 422.5 273.5 422.5 273.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 211 410.5 0 109 18 -normal_sample_name ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=normal_sample_name,
			pos="211,413",
			rects="148.5,403.5,273.5,422.5",
			width=1.7361];
		reference_dict	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 58 403.5 58 422.5 144 422.5 144 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 101 410.5 0 70 14 -reference_dict ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=reference_dict,
			pos="101,413",
			rects="58,403.5,144,422.5",
			width=1.1944];
	}
	subgraph cluster_outputs {
		graph [_draw_="S 6 -dashed c 7 -#000000 C 7 -#eeeeee P 4 144 8 144 63 252 63 252 8 ",
			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 198 15 0 92 16 -Workflow Outputs ",
			bb="144,8,252,63",
			label="Workflow Outputs",
			labelloc=b,
			lheight=0.15,
			lp="198,17.5",
			lwidth=1.28,
			rank=same,
			style=dashed
		];
		phased_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 162 35.5 162 54.5 234 54.5 234 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 198 42.5 0 56 10 -phased_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=phased_vcf,
			pos="198,45",
			rects="162,35.5,234,54.5",
			width=1];
	}
	select_somatic_tumor_sample	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 445.5 350.5 445.5 369.5 586.5 369.5 586.5 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 516 357.5 0 125 25 -SelectVariants (GATK 3.6) ",
		height=0.27778,
		label="SelectVariants (GATK 3.6)",
		pos="516,360",
		rects="445.5,350.5,586.5,369.5",
		width=1.9583];
	reference -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 580.26 403.68 571.03 399.12 559.67 393.15 550 387 544.09 383.24 537.93 378.73 532.5 374.52 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 534.28 372.81 527.27 370.39 531.23 376.65 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 570 380.6 0 40 9 -reference ",
		label=reference,
		lp="570,382.5",
		pos="e,526.08,369.45 580.26,403.68 571.03,399.12 559.67,393.15 550,387 544.09,383.24 537.93,378.73 532.5,374.52"];
	phase_vcf	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 137.5 125.5 137.5 144.5 258.5 144.5 258.5 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 198 132.5 0 105 19 -Read-backed phasing ",
		height=0.27778,
		label="Read-backed phasing",
		pos="198,135",
		rects="137.5,125.5,258.5,144.5",
		width=1.6806];
	reference -> phase_vcf	[_draw_="c 7 -#000000 B 10 611.92 403.76 624.81 394.95 642 379.71 642 361 642 361 642 361 642 179 642 141.76 391.39 136.21 266.73 135.75 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 266.86 133.3 259.86 135.73 266.85 138.2 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 662 268.1 0 40 9 -reference ",
		label=reference,
		lp="662,270",
		pos="e,258.34,135.72 611.92,403.76 624.81,394.95 642,379.71 642,361 642,361 642,361 642,179 642,141.76 391.39,136.21 266.73,135.75"];
	combine_variants	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 319.5 260.5 319.5 279.5 610.5 279.5 610.5 260.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 465 267.5 0 275 52 -Combine germline and somatic vcf for pVACseq phasing ",
		height=0.27778,
		label="Combine germline and somatic vcf for pVACseq phasing",
		pos="465,270",
		rects="319.5,260.5,610.5,279.5",
		width=4.0417];
	reference -> combine_variants	[_draw_="c 7 -#000000 B 10 598.06 403.89 597.83 391.56 596.12 367.68 587 350 569.27 315.65 559.3 307.63 526 288 522.36 285.86 518.45 283.97 \
514.41 282.32 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 515.4 280.07 507.98 279.95 513.7 284.67 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 602 335.6 0 40 9 -reference ",
		label=reference,
		lp="602,337.5",
		pos="e,506.56,279.42 598.06,403.89 597.83,391.56 596.12,367.68 587,350 569.27,315.65 559.3,307.63 526,288 522.36,285.86 518.45,283.97 \
514.41,282.32"];
	bam -> phase_vcf	[_draw_="c 7 -#000000 B 10 45.65 403.7 59.79 392.25 83 371.82 83 361 83 361 83 361 83 179 83 164.77 114.3 153.68 144.25 146.33 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 144.49 148.79 150.75 144.8 143.37 144.02 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 92.5 268.1 0 19 3 -bam ",
		label=bam,
		lp="92.5,270",
		pos="e,152.22,144.45 45.653,403.7 59.794,392.25 83,371.82 83,361 83,361 83,361 83,179 83,164.77 114.3,153.68 144.25,146.33"];
	somatic_vcf -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 4 522.68 403.58 521.57 396.52 519.96 386.24 518.6 377.55 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 521.04 377.3 517.53 370.76 516.2 378.06 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 526.5 380.6 0 13 3 -vcf ",
		label=vcf,
		lp="526.5,382.5",
		pos="e,517.3,369.26 522.68,403.58 521.57,396.52 519.96,386.24 518.6,377.55"];
	rename_germline_vcf	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 261.5 350.5 261.5 369.5 384.5 369.5 384.5 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 323 357.5 0 107 19 -rename_germline_vcf ",
		height=0.27778,
		label=rename_germline_vcf,
		pos="323,360",
		rects="261.5,350.5,384.5,369.5",
		width=1.7083];
	germline_vcf -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 310.57 403.56 305.43 396.64 300.14 386.62 304 378 304.32 377.29 304.68 376.6 305.08 375.93 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 306.89 377.58 309.49 370.64 303.13 374.45 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 322.5 380.6 0 37 9 -input_vcf ",
		label=input_vcf,
		lp="322.5,382.5",
		pos="e,310.46,369.47 310.57,403.56 305.43,396.64 300.14,386.62 304,378 304.32,377.29 304.68,376.6 305.08,375.93"];
	tumor_sample_name -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 423.18 403.71 424.74 395.9 428.25 384.46 436 378 438.07 376.27 440.28 374.71 442.59 373.29 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 443.41 375.63 448.44 370.18 441.11 371.3 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 476.5 380.6 0 81 18 -samples_to_include ",
		label=samples_to_include,
		lp="476.5,382.5",
		pos="e,449.78,369.47 423.18,403.71 424.74,395.9 428.25,384.46 436,378 438.07,376.27 440.28,374.71 442.59,373.29"];
	tumor_sample_name -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 388.04 403.52 375.54 399.57 361.62 394.13 350 387 344.78 383.8 339.75 379.44 335.48 375.21 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 337.46 373.73 330.87 370.34 333.91 377.11 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 389.5 380.6 0 79 15 -new_sample_name ",
		label=new_sample_name,
		lp="389.5,382.5",
		pos="e,329.82,369.24 388.04,403.52 375.54,399.57 361.62,394.13 350,387 344.78,383.8 339.75,379.44 335.48,375.21"];
	normal_sample_name -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 212.13 403.64 213.64 395.78 217.13 384.31 225 378 230.13 373.88 240.89 370.71 253.47 368.29 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 253.54 370.76 260.01 367.14 252.69 365.94 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 263.5 380.6 0 77 17 -sample_to_replace ",
		label=sample_to_replace,
		lp="263.5,382.5",
		pos="e,261.5,366.87 212.13,403.64 213.64,395.78 217.13,384.31 225,378 230.13,373.88 240.89,370.71 253.47,368.29"];
	sort	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 168.5 215.5 168.5 234.5 227.5 234.5 227.5 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 198 222.5 0 43 8 -Sort VCF ",
		height=0.27778,
		label="Sort VCF",
		pos="198,225",
		rects="168.5,215.5,227.5,234.5",
		width=0.81944];
	reference_dict -> sort	[_draw_="c 7 -#000000 B 10 119.54 403.53 134.82 395.13 154 380.67 154 361 154 361 154 361 154 269 154 256.33 163.45 246.17 173.59 238.91 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 174.8 241.05 179.34 235.18 172.13 236.93 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 183.5 313.1 0 59 14 -reference_dict ",
		label=reference_dict,
		lp="183.5,315",
		pos="e,180.61,234.36 119.54,403.53 134.82,395.13 154,380.67 154,361 154,361 154,361 154,269 154,256.33 163.45,246.17 173.59,238.91"];
	index_filtered_somatic	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 453 305.5 453 324.5 515 324.5 515 305.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 484 312.5 0 46 9 -vcf index ",
		height=0.27778,
		label="vcf index",
		pos="484,315",
		rects="453,305.5,515,324.5",
		width=0.86111];
	select_somatic_tumor_sample -> index_filtered_somatic	[_draw_="c 7 -#000000 B 4 509.83 350.71 505.67 345.12 500.06 337.58 495.13 330.96 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 497.2 329.63 491.05 325.48 493.27 332.56 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 508.5 335.6 0 13 3 -vcf ",
		label=vcf,
		lp="508.5,337.5",
		pos="e,490.15,324.27 509.83,350.71 505.67,345.12 500.06,337.58 495.13,330.96"];
	bgzip_and_index	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 140 170.5 140 189.5 256 189.5 256 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 198 177.5 0 100 19 -bgzip and index VCF ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label="bgzip and index VCF",
		pos="198,180",
		rects="140,170.5,256,189.5",
		width=1.6111];
	sort -> bgzip_and_index	[_draw_="c 7 -#000000 B 4 198 215.71 198 210.59 198 203.85 198 197.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 200.45 197.78 198 190.78 195.55 197.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 204.5 200.6 0 13 3 -vcf ",
		label=vcf,
		lp="204.5,202.5",
		pos="e,198,189.27 198,215.71 198,210.59 198,203.85 198,197.67"];
	index_renamed_germline	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 342 305.5 342 324.5 404 324.5 404 305.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 373 312.5 0 46 9 -vcf index ",
		height=0.27778,
		label="vcf index",
		pos="373,315",
		rects="342,305.5,404,324.5",
		width=0.86111];
	index_renamed_germline -> combine_variants	[_draw_="c 7 -#000000 B 7 386.39 305.68 395.41 300.26 407.68 293.25 419 288 423.15 286.07 427.59 284.21 432.01 282.46 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 432.79 284.78 438.46 280 431.05 280.21 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 445 290.6 0 52 12 -germline_vcf ",
		label=germline_vcf,
		lp="445,292.5",
		pos="e,439.87,279.46 386.39,305.68 395.41,300.26 407.68,293.25 419,288 423.15,286.07 427.59,284.21 432.01,282.46"];
	bgzip_and_index -> phase_vcf	[_draw_="c 7 -#000000 B 4 198 170.71 198 165.59 198 158.85 198 152.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 200.45 152.78 198 145.78 195.55 152.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 204.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="204.5,157.5",
		pos="e,198,144.27 198,170.71 198,165.59 198,158.85 198,152.67"];
	rename_germline_vcf -> index_renamed_germline	[_draw_="c 7 -#000000 B 4 332.64 350.71 339.56 344.76 349.04 336.61 357.07 329.7 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 358.53 331.67 362.24 325.25 355.34 327.96 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 359.5 335.6 0 13 3 -vcf ",
		label=vcf,
		lp="359.5,337.5",
		pos="e,363.39,324.27 332.64,350.71 339.56,344.76 349.04,336.61 357.07,329.7"];
	bgzip_and_index_phased_vcf	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 140 80.5 140 99.5 256 99.5 256 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 198 87.5 0 100 19 -bgzip and index VCF ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label="bgzip and index VCF",
		pos="198,90",
		rects="140,80.5,256,99.5",
		width=1.6111];
	phase_vcf -> bgzip_and_index_phased_vcf	[_draw_="c 7 -#000000 B 4 198 125.71 198 120.59 198 113.85 198 107.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 200.45 107.78 198 100.78 195.55 107.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 204.5 110.6 0 13 3 -vcf ",
		label=vcf,
		lp="204.5,112.5",
		pos="e,198,99.265 198,125.71 198,120.59 198,113.85 198,107.67"];
	bgzip_and_index_phased_vcf -> phased_vcf	[_draw_="c 7 -#000000 B 4 198 80.71 198 75.59 198 68.85 198 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 200.45 62.78 198 55.78 195.55 62.78 ",
		pos="e,198,54.265 198,80.709 198,75.593 198,68.848 198,62.666"];
	index_filtered_somatic -> combine_variants	[_draw_="c 7 -#000000 B 4 480.34 305.71 477.97 300.36 474.82 293.22 471.98 286.81 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 474.33 286.06 469.26 280.65 469.85 288.04 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 500.5 290.6 0 49 11 -somatic_vcf ",
		label=somatic_vcf,
		lp="500.5,292.5",
		pos="e,468.65,279.27 480.34,305.71 477.97,300.36 474.82,293.22 471.98,286.81"];
	combine_variants -> sort	[_draw_="c 7 -#000000 B 4 412.25 260.5 360.17 252.12 281.83 239.5 235.71 232.07 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 236.28 229.68 228.98 230.99 235.51 234.52 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 362.5 245.6 0 13 3 -vcf ",
		label=vcf,
		lp="362.5,247.5",
		pos="e,227.49,230.75 412.25,260.5 360.17,252.12 281.83,239.5 235.71,232.07"];
	default1	[_draw_="c 7 -#000000 C 7 -#d5aefc P 4 646.5 403.5 646.5 422.5 771.5 422.5 771.5 403.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 709 410.5 0 109 20 -\"somatic_tumor_only\" ",
		fillcolor="#D5AEFC",
		height=0.27778,
		label="\"somatic_tumor_only\"",
		pos="709,413",
		rects="646.5,403.5,771.5,422.5",
		width=1.7361];
	default1 -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 681.47 403.58 657.63 396.41 622.18 386.02 591 378 582.19 375.73 572.76 373.47 563.65 371.37 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 564.26 368.99 556.89 369.82 563.17 373.77 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 668.5 380.6 0 91 19 -output_vcf_basename ",
		label=output_vcf_basename,
		lp="668.5,382.5",
		pos="e,555.42,369.49 681.47,403.58 657.63,396.41 622.18,386.02 591,378 582.19,375.73 572.76,373.47 563.65,371.37"];
}