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
	];
	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
		];
		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];
		normal_sample_name	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 190.5 403.5 190.5 422.5 315.5 422.5 315.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 253 410.5 0 109 18 -normal_sample_name ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=normal_sample_name,
			pos="253,413",
			rects="190.5,403.5,315.5,422.5",
			width=1.7361];
		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];
		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];
		germline_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 106 403.5 106 422.5 186 422.5 186 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 146 410.5 0 64 12 -germline_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=germline_vcf,
			pos="146,413",
			rects="106,403.5,186,422.5",
			width=1.1111];
		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];
		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];
	}
	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];
	}
	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 10 555.7 403.64 555.01 391.41 552.69 368.11 545 350 531.69 318.66 527.63 307.89 500 288 497.34 286.08 494.45 284.38 \
491.45 282.86 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 492.57 280.68 485.18 280.08 490.58 285.16 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 561 335.6 0 40 9 -reference ",
		label=reference,
		lp="561,337.5",
		pos="e,483.79,279.47 555.7,403.64 555.01,391.41 552.69,368.11 545,350 531.69,318.66 527.63,307.89 500,288 497.34,286.08 494.45,284.38 \
491.45,282.86"];
	select_somatic_tumor_sample	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 403.5 350.5 403.5 369.5 544.5 369.5 544.5 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 474 357.5 0 125 25 -SelectVariants (GATK 3.6) ",
		height=0.27778,
		label="SelectVariants (GATK 3.6)",
		pos="474,360",
		rects="403.5,350.5,544.5,369.5",
		width=1.9583];
	reference -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 538.26 403.68 529.03 399.12 517.67 393.15 508 387 502.09 383.24 495.93 378.73 490.5 374.52 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 492.28 372.81 485.27 370.39 489.23 376.65 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 528 380.6 0 40 9 -reference ",
		label=reference,
		lp="528,382.5",
		pos="e,484.08,369.45 538.26,403.68 529.03,399.12 517.67,393.15 508,387 502.09,383.24 495.93,378.73 490.5,374.52"];
	rename_germline_vcf	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 199.5 350.5 199.5 369.5 322.5 369.5 322.5 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 261 357.5 0 107 19 -rename_germline_vcf ",
		height=0.27778,
		label=rename_germline_vcf,
		pos="261,360",
		rects="199.5,350.5,322.5,369.5",
		width=1.7083];
	normal_sample_name -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 236.77 403.7 226.29 397.18 215.7 387.62 222 378 222.81 376.77 223.72 375.62 224.73 374.56 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 226.16 376.56 230.13 370.29 223.12 372.72 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 260.5 380.6 0 77 17 -sample_to_replace ",
		label=sample_to_replace,
		lp="260.5,382.5",
		pos="e,231.31,369.35 236.77,403.7 226.29,397.18 215.7,387.62 222,378 222.81,376.77 223.72,375.62 224.73,374.56"];
	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 70.61 403.66 81.78 394.56 97 378.89 97 361 97 361 97 361 97 269 97 237.91 317.92 229.07 408.23 226.76 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 408.09 229.21 415.03 226.59 407.97 224.31 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 126.5 313.1 0 59 14 -reference_dict ",
		label=reference_dict,
		lp="126.5,315",
		pos="e,416.55,226.55 70.608,403.66 81.783,394.56 97,378.89 97,361 97,361 97,361 97,269 97,237.91 317.92,229.07 408.23,226.76"];
	tumor_sample_name -> rename_germline_vcf	[_draw_="c 7 -#000000 B 10 347.33 403.54 334.33 399.48 319.52 393.97 307 387 301.48 383.93 301.32 381.4 296 378 293.4 376.34 290.61 374.73 \
287.79 373.2 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 289.03 371.08 281.68 370.08 286.8 375.45 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 346.5 380.6 0 79 15 -new_sample_name ",
		label=new_sample_name,
		lp="346.5,382.5",
		pos="e,280.33,369.39 347.33,403.54 334.33,399.48 319.52,393.97 307,387 301.48,383.93 301.32,381.4 296,378 293.4,376.34 290.61,374.73 \
287.79,373.2"];
	tumor_sample_name -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 381.18 403.71 382.74 395.9 386.25 384.46 394 378 396.07 376.27 398.28 374.71 400.59 373.29 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 401.41 375.63 406.44 370.18 399.11 371.3 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 434.5 380.6 0 81 18 -samples_to_include ",
		label=samples_to_include,
		lp="434.5,382.5",
		pos="e,407.78,369.47 381.18,403.71 382.74,395.9 386.25,384.46 394,378 396.07,376.27 398.28,374.71 400.59,373.29"];
	germline_vcf -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 152.5 403.65 159.08 395.79 169.98 384.33 182 378 186.29 375.74 190.87 373.78 195.58 372.08 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 196.26 374.44 202.15 369.93 194.73 369.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 200.5 380.6 0 37 9 -input_vcf ",
		label=input_vcf,
		lp="200.5,382.5",
		pos="e,203.58,369.46 152.5,403.65 159.08,395.79 169.98,384.33 182,378 186.29,375.74 190.87,373.78 195.58,372.08"];
	somatic_vcf -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 4 480.68 403.58 479.57 396.52 477.96 386.24 476.6 377.55 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 479.04 377.3 475.53 370.76 474.2 378.06 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 484.5 380.6 0 13 3 -vcf ",
		label=vcf,
		lp="484.5,382.5",
		pos="e,475.3,369.26 480.68,403.58 479.57,396.52 477.96,386.24 476.6,377.55"];
	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"];
	index_filtered_somatic	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 422 305.5 422 324.5 484 324.5 484 305.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 453 312.5 0 46 9 -vcf index ",
		height=0.27778,
		label="vcf index",
		pos="453,315",
		rects="422,305.5,484,324.5",
		width=0.86111];
	index_filtered_somatic -> combine_variants	[_draw_="c 7 -#000000 B 4 451.65 305.71 450.82 300.59 449.72 293.85 448.71 287.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 451.13 287.27 447.59 280.76 446.3 288.06 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 474.5 290.6 0 49 11 -somatic_vcf ",
		label=somatic_vcf,
		lp="474.5,292.5",
		pos="e,447.35,279.27 451.65,305.71 450.82,300.59 449.72,293.85 448.71,287.67"];
	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_renamed_germline	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 311 305.5 311 324.5 373 324.5 373 305.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 342 312.5 0 46 9 -vcf index ",
		height=0.27778,
		label="vcf index",
		pos="342,315",
		rects="311,305.5,373,324.5",
		width=0.86111];
	index_renamed_germline -> combine_variants	[_draw_="c 7 -#000000 B 7 357.52 305.7 367.95 300.29 382.1 293.29 395 288 400.05 285.93 405.45 283.92 410.78 282.05 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 411.22 284.49 417.06 279.91 409.64 279.85 ",
		_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,418.49,279.42 357.52,305.7 367.95,300.29 382.1,293.29 395,288 400.05,285.93 405.45,283.92 410.78,282.05"];
	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	[_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];
	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"];
	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 4 277 350.5 288.87 344.2 305.24 335.51 318.58 328.43 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 319.66 330.63 324.69 325.19 317.36 326.31 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 314.5 335.6 0 13 3 -vcf ",
		label=vcf,
		lp="314.5,337.5",
		pos="e,326.03,324.48 277,350.5 288.87,344.2 305.24,335.51 318.58,328.43"];
	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 491.5 200.6 0 13 3 -vcf ",
		label=vcf,
		lp="491.5,202.5",
		pos="e,499.79,189.48 459.24,215.5 468.78,209.38 481.84,201 492.7,194.03"];
	select_somatic_tumor_sample -> index_filtered_somatic	[_draw_="c 7 -#000000 B 4 469.95 350.71 467.34 345.36 463.85 338.22 460.72 331.81 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 462.97 330.84 457.7 325.63 458.57 332.99 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 471.5 335.6 0 13 3 -vcf ",
		label=vcf,
		lp="471.5,337.5",
		pos="e,457.04,324.27 469.95,350.71 467.34,345.36 463.85,338.22 460.72,331.81"];
	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 7 675.23 403.55 663.75 400.74 650.84 397.66 639 395 600.98 386.47 557.85 377.61 525.23 371.08 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 526 368.73 518.65 369.76 525.04 373.54 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 643.5 380.6 0 91 19 -output_vcf_basename ",
		label=output_vcf_basename,
		lp="643.5,382.5",
		pos="e,517.17,369.47 675.23,403.55 663.75,400.74 650.84,397.66 639,395 600.98,386.47 557.85,377.61 525.23,371.08"];
}