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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	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 8 450 638 450 638 395 ",
			_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
		];
		somatic_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 444 403.5 444 422.5 520 422.5 520 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 482 410.5 0 60 11 -somatic_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=somatic_vcf,
			pos="482,413",
			rects="444,403.5,520,422.5",
			width=1.0556];
		reference	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 524.5 403.5 524.5 422.5 587.5 422.5 587.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 556 410.5 0 47 9 -reference ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=reference,
			pos="556,413",
			rects="524.5,403.5,587.5,422.5",
			width=0.875];
		bam	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 592 403.5 592 422.5 630 422.5 630 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 611 410.5 0 22 3 -bam ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=bam,
			pos="611,413",
			rects="592,403.5,630,422.5",
			width=0.52778];
		tumor_sample_name	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 320 403.5 320 422.5 440 422.5 440 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 380 410.5 0 104 17 -tumor_sample_name ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=tumor_sample_name,
			pos="380,413",
			rects="320,403.5,440,422.5",
			width=1.6667];
		reference_dict	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 16 403.5 16 422.5 102 422.5 102 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 59 410.5 0 70 14 -reference_dict ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=reference_dict,
			pos="59,413",
			rects="16,403.5,102,422.5",
			width=1.1944];
		normal_sample_name	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 106.5 403.5 106.5 422.5 231.5 422.5 231.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 169 410.5 0 109 18 -normal_sample_name ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=normal_sample_name,
			pos="169,413",
			rects="106.5,403.5,231.5,422.5",
			width=1.7361];
		germline_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 236 403.5 236 422.5 316 422.5 316 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 276 410.5 0 64 12 -germline_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=germline_vcf,
			pos="276,413",
			rects="236,403.5,316,422.5",
			width=1.1111];
	}
	subgraph cluster_outputs {
		graph [_draw_="S 6 -dashed c 7 -#000000 C 7 -#eeeeee P 4 546 8 546 63 654 63 654 8 ",
			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 600 15 0 92 16 -Workflow Outputs ",
			bb="546,8,654,63",
			label="Workflow Outputs",
			labelloc=b,
			lheight=0.15,
			lp="600,17.5",
			lwidth=1.28,
			rank=same,
			style=dashed
		];
		phased_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 564 35.5 564 54.5 636 54.5 636 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 600 42.5 0 56 10 -phased_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=phased_vcf,
			pos="600,45",
			rects="564,35.5,636,54.5",
			width=1];
	}
	select_somatic_tumor_sample	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 385.5 350.5 385.5 369.5 544.5 369.5 544.5 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 465 357.5 0 143 29 -SelectVariants (GATK 4.1.8.1) ",
		height=0.27778,
		label="SelectVariants (GATK 4.1.8.1)",
		pos="465,360",
		rects="385.5,350.5,544.5,369.5",
		width=2.2083];
	somatic_vcf -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 480.66 403.72 479.39 396.73 477.2 386.52 474 378 473.87 377.64 473.72 377.28 473.58 376.92 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 475.89 376.08 470.67 370.82 471.47 378.19 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 483.5 380.6 0 13 3 -vcf ",
		label=vcf,
		lp="483.5,382.5",
		pos="e,470.02,369.45 480.66,403.72 479.39,396.73 477.2,386.52 474,378 473.87,377.64 473.72,377.28 473.58,376.92"];
	phase_vcf	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 539.5 125.5 539.5 144.5 660.5 144.5 660.5 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 600 132.5 0 105 19 -Read-backed phasing ",
		height=0.27778,
		label="Read-backed phasing",
		pos="600,135",
		rects="539.5,125.5,660.5,144.5",
		width=1.6806];
	reference -> phase_vcf	[_draw_="c 7 -#000000 B 10 569.92 403.76 582.81 394.95 600 379.71 600 361 600 361 600 361 600 179 600 170.31 600 160.63 600 152.65 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 602.45 152.76 600 145.76 597.55 152.76 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 620 268.1 0 40 9 -reference ",
		label=reference,
		lp="620,270",
		pos="e,600,144.24 569.92,403.76 582.81,394.95 600,379.71 600,361 600,361 600,361 600,179 600,170.31 600,160.63 600,152.65"];
	combine_variants	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 300.5 260.5 300.5 279.5 591.5 279.5 591.5 260.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 446 267.5 0 275 52 -Combine germline and somatic vcf for pVACseq phasing ",
		height=0.27778,
		label="Combine germline and somatic vcf for pVACseq phasing",
		pos="446,270",
		rects="300.5,260.5,591.5,279.5",
		width=4.0417];
	reference -> combine_variants	[_draw_="c 7 -#000000 B 10 555.68 403.65 554.95 391.43 552.6 368.15 545 350 531.95 318.83 528.37 307.82 501 288 498.34 286.08 495.46 284.37 \
492.46 282.85 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 493.59 280.67 486.19 280.07 491.6 285.14 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 561 335.6 0 40 9 -reference ",
		label=reference,
		lp="561,337.5",
		pos="e,484.81,279.45 555.68,403.65 554.95,391.43 552.6,368.15 545,350 531.95,318.83 528.37,307.82 501,288 498.34,286.08 495.46,284.37 \
492.46,282.85"];
	reference -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 539.42 403.69 530.11 398.95 518.32 392.8 508 387 500.63 382.86 492.67 378.12 485.63 373.84 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 486.96 371.78 479.72 370.21 484.4 375.96 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 528 380.6 0 40 9 -reference ",
		label=reference,
		lp="528,382.5",
		pos="e,478.43,369.42 539.42,403.69 530.11,398.95 518.32,392.8 508,387 500.63,382.86 492.67,378.12 485.63,373.84"];
	bam -> phase_vcf	[_draw_="c 7 -#000000 B 10 622.3 403.59 633.18 394.44 648 378.72 648 361 648 361 648 361 648 179 648 165.88 637.92 155.75 627 148.63 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 628.38 146.6 621.1 145.15 625.89 150.82 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 657.5 268.1 0 19 3 -bam ",
		label=bam,
		lp="657.5,270",
		pos="e,619.8,144.39 622.3,403.59 633.18,394.44 648,378.72 648,361 648,361 648,361 648,179 648,165.88 637.92,155.75 627,148.63"];
	rename_germline_vcf	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 219.5 350.5 219.5 369.5 342.5 369.5 342.5 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 281 357.5 0 107 19 -rename_germline_vcf ",
		height=0.27778,
		label=rename_germline_vcf,
		pos="281,360",
		rects="219.5,350.5,342.5,369.5",
		width=1.7083];
	tumor_sample_name -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 343.81 403.56 331.25 399.67 317.45 394.27 306 387 303.21 385.23 298.48 380.51 293.87 375.56 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 295.81 374.04 289.29 370.51 292.18 377.34 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 345.5 380.6 0 79 15 -new_sample_name ",
		label=new_sample_name,
		lp="345.5,382.5",
		pos="e,288.27,369.39 343.81,403.56 331.25,399.67 317.45,394.27 306,387 303.21,385.23 298.48,380.51 293.87,375.56"];
	tumor_sample_name -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 380.69 403.77 381.79 396 384.63 384.6 392 378 393.82 376.37 395.76 374.89 397.8 373.55 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 398.84 375.77 403.75 370.21 396.45 371.5 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 432.5 380.6 0 81 18 -samples_to_include ",
		label=samples_to_include,
		lp="432.5,382.5",
		pos="e,405.07,369.47 380.69,403.77 381.79,396 384.63,384.6 392,378 393.82,376.37 395.76,374.89 397.8,373.55"];
	sort	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 416.5 215.5 416.5 234.5 475.5 234.5 475.5 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 446 222.5 0 43 8 -Sort VCF ",
		height=0.27778,
		label="Sort VCF",
		pos="446,225",
		rects="416.5,215.5,475.5,234.5",
		width=0.81944];
	reference_dict -> sort	[_draw_="c 7 -#000000 B 10 75.93 403.59 90.43 395.05 109 380.34 109 361 109 361 109 361 109 269 109 239.1 320.38 229.59 408.32 226.93 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 408.24 229.38 415.17 226.73 408.1 224.48 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 138.5 313.1 0 59 14 -reference_dict ",
		label=reference_dict,
		lp="138.5,315",
		pos="e,416.68,226.68 75.928,403.59 90.433,395.05 109,380.34 109,361 109,361 109,361 109,269 109,239.1 320.38,229.59 408.32,226.93"];
	normal_sample_name -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 170.13 403.64 171.64 395.78 175.13 384.31 183 378 188.13 373.88 198.89 370.71 211.47 368.29 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 211.54 370.76 218.01 367.14 210.69 365.94 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 221.5 380.6 0 77 17 -sample_to_replace ",
		label=sample_to_replace,
		lp="221.5,382.5",
		pos="e,219.5,366.87 170.13,403.64 171.64,395.78 175.13,384.31 183,378 188.13,373.88 198.89,370.71 211.47,368.29"];
	germline_vcf -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 268.57 403.56 263.43 396.64 258.14 386.62 262 378 262.32 377.29 262.68 376.6 263.08 375.93 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 264.89 377.58 267.49 370.64 261.13 374.45 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 280.5 380.6 0 37 9 -input_vcf ",
		label=input_vcf,
		lp="280.5,382.5",
		pos="e,268.46,369.47 268.57,403.56 263.43,396.64 258.14,386.62 262,378 262.32,377.29 262.68,376.6 263.08,375.93"];
	bgzip_and_index_phased_vcf	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 542 80.5 542 99.5 658 99.5 658 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 600 87.5 0 100 19 -bgzip and index VCF ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label="bgzip and index VCF",
		pos="600,90",
		rects="542,80.5,658,99.5",
		width=1.6111];
	phase_vcf -> bgzip_and_index_phased_vcf	[_draw_="c 7 -#000000 B 4 600 125.71 600 120.59 600 113.85 600 107.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 602.45 107.78 600 100.78 597.55 107.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 606.5 110.6 0 13 3 -vcf ",
		label=vcf,
		lp="606.5,112.5",
		pos="e,600,99.265 600,125.71 600,120.59 600,113.85 600,107.67"];
	index_filtered_somatic	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 423 305.5 423 324.5 485 324.5 485 305.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 454 312.5 0 46 9 -vcf index ",
		height=0.27778,
		label="vcf index",
		pos="454,315",
		rects="423,305.5,485,324.5",
		width=0.86111];
	index_filtered_somatic -> combine_variants	[_draw_="c 7 -#000000 B 4 452.46 305.71 451.48 300.47 450.19 293.53 449.02 287.24 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 451.5 287.19 447.81 280.75 446.69 288.08 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 475.5 290.6 0 49 11 -somatic_vcf ",
		label=somatic_vcf,
		lp="475.5,292.5",
		pos="e,447.54,279.27 452.46,305.71 451.48,300.47 450.19,293.53 449.02,287.24"];
	index_renamed_germline	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 290 305.5 290 324.5 352 324.5 352 305.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 321 312.5 0 46 9 -vcf index ",
		height=0.27778,
		label="vcf index",
		pos="321,315",
		rects="290,305.5,352,324.5",
		width=0.86111];
	index_renamed_germline -> combine_variants	[_draw_="c 7 -#000000 B 4 345.7 305.5 365.13 298.82 392.37 289.45 413.56 282.16 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 414.1 284.56 419.92 279.97 412.51 279.93 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 421 290.6 0 52 12 -germline_vcf ",
		label=germline_vcf,
		lp="421,292.5",
		pos="e,421.36,279.48 345.7,305.5 365.13,298.82 392.37,289.45 413.56,282.16"];
	bgzip_and_index	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 455 170.5 455 189.5 571 189.5 571 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 513 177.5 0 100 19 -bgzip and index VCF ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label="bgzip and index VCF",
		pos="513,180",
		rects="455,170.5,571,189.5",
		width=1.6111];
	sort -> bgzip_and_index	[_draw_="c 7 -#000000 B 4 459.24 215.5 468.78 209.38 481.84 201 492.7 194.03 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 493.95 196.14 498.52 190.3 491.3 192.01 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 492.5 200.6 0 13 3 -vcf ",
		label=vcf,
		lp="492.5,202.5",
		pos="e,499.79,189.48 459.24,215.5 468.78,209.38 481.84,201 492.7,194.03"];
	bgzip_and_index -> phase_vcf	[_draw_="c 7 -#000000 B 4 530.19 170.5 543.06 164.14 560.85 155.35 575.25 148.23 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 576.3 150.45 581.49 145.15 574.13 146.05 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 570.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="570.5,157.5",
		pos="e,582.85,144.48 530.19,170.5 543.06,164.14 560.85,155.35 575.25,148.23"];
	combine_variants -> sort	[_draw_="c 7 -#000000 B 4 446 260.71 446 255.59 446 248.85 446 242.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 448.45 242.78 446 235.78 443.55 242.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 452.5 245.6 0 13 3 -vcf ",
		label=vcf,
		lp="452.5,247.5",
		pos="e,446,234.27 446,260.71 446,255.59 446,248.85 446,242.67"];
	bgzip_and_index_phased_vcf -> phased_vcf	[_draw_="c 7 -#000000 B 4 600 80.71 600 75.59 600 68.85 600 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 602.45 62.78 600 55.78 597.55 62.78 ",
		pos="e,600,54.265 600,80.709 600,75.593 600,68.848 600,62.666"];
	rename_germline_vcf -> index_renamed_germline	[_draw_="c 7 -#000000 B 4 288.71 350.71 294.14 344.88 301.53 336.93 307.87 330.12 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 309.31 332.17 312.28 325.37 305.72 328.83 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 311.5 335.6 0 13 3 -vcf ",
		label=vcf,
		lp="311.5,337.5",
		pos="e,313.31,324.27 288.71,350.71 294.14,344.88 301.53,336.93 307.87,330.12"];
	select_somatic_tumor_sample -> index_filtered_somatic	[_draw_="c 7 -#000000 B 4 462.88 350.71 461.54 345.47 459.76 338.53 458.15 332.24 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 460.6 331.91 456.49 325.73 455.85 333.12 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 467.5 335.6 0 13 3 -vcf ",
		label=vcf,
		lp="467.5,337.5",
		pos="e,456.11,324.27 462.88,350.71 461.54,345.47 459.76,338.53 458.15,332.24"];
	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 7 675.6 403.56 664.04 400.73 650.97 397.62 639 395 599.06 386.25 553.71 377.43 519.33 370.96 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 520.1 368.61 512.77 369.73 519.19 373.43 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 645.5 380.6 0 91 19 -output_vcf_basename ",
		label=output_vcf_basename,
		lp="645.5,382.5",
		pos="e,511.28,369.45 675.6,403.56 664.04,400.73 650.97,397.62 639,395 599.06,386.25 553.71,377.43 519.33,370.96"];
}