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
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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 4 133.5 395 133.5 450 763.5 450 763.5 395 ",
			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 183.5 438 0 84 15 -Workflow Inputs ",
			bb="133.5,395,763.5,450",
			label="Workflow Inputs",
			lheight=0.15,
			lp="183.5,440.5",
			lwidth=1.17,
			rank=same,
			style=dashed
		];
		bam	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 717.5 403.5 717.5 422.5 755.5 422.5 755.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 736.5 410.5 0 22 3 -bam ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=bam,
			pos="736.5,413",
			rects="717.5,403.5,755.5,422.5",
			width=0.52778];
		somatic_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 209.5 403.5 209.5 422.5 285.5 422.5 285.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 247.5 410.5 0 60 11 -somatic_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=somatic_vcf,
			pos="247.5,413",
			rects="209.5,403.5,285.5,422.5",
			width=1.0556];
		normal_sample_name	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 498 403.5 498 422.5 623 422.5 623 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 560.5 410.5 0 109 18 -normal_sample_name ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=normal_sample_name,
			pos="560.5,413",
			rects="498,403.5,623,422.5",
			width=1.7361];
		germline_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 413.5 403.5 413.5 422.5 493.5 422.5 493.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 453.5 410.5 0 64 12 -germline_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=germline_vcf,
			pos="453.5,413",
			rects="413.5,403.5,493.5,422.5",
			width=1.1111];
		reference_dict	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 627.5 403.5 627.5 422.5 713.5 422.5 713.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 670.5 410.5 0 70 14 -reference_dict ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=reference_dict,
			pos="670.5,413",
			rects="627.5,403.5,713.5,422.5",
			width=1.1944];
		tumor_sample_name	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 289.5 403.5 289.5 422.5 409.5 422.5 409.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 349.5 410.5 0 104 17 -tumor_sample_name ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=tumor_sample_name,
			pos="349.5,413",
			rects="289.5,403.5,409.5,422.5",
			width=1.6667];
		reference	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 142 403.5 142 422.5 205 422.5 205 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 173.5 410.5 0 47 9 -reference ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=reference,
			pos="173.5,413",
			rects="142,403.5,205,422.5",
			width=0.875];
	}
	subgraph cluster_outputs {
		graph [_draw_="S 6 -dashed c 7 -#000000 C 7 -#eeeeee P 4 519.5 8 519.5 63 627.5 63 627.5 8 ",
			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 573.5 15 0 92 16 -Workflow Outputs ",
			bb="519.5,8,627.5,63",
			label="Workflow Outputs",
			labelloc=b,
			lheight=0.15,
			lp="573.5,17.5",
			lwidth=1.28,
			rank=same,
			style=dashed
		];
		phased_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 537.5 35.5 537.5 54.5 609.5 54.5 609.5 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 573.5 42.5 0 56 10 -phased_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=phased_vcf,
			pos="573.5,45",
			rects="537.5,35.5,609.5,54.5",
			width=1];
	}
	phase_vcf	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 513 125.5 513 144.5 634 144.5 634 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 573.5 132.5 0 105 19 -Read-backed phasing ",
		height=0.27778,
		label="Read-backed phasing",
		pos="573.5,135",
		rects="513,125.5,634,144.5",
		width=1.6806];
	bam -> phase_vcf	[_draw_="c 7 -#000000 B 10 732.67 403.53 728.53 393.57 722.5 376.43 722.5 361 722.5 361 722.5 361 722.5 179 722.5 160.84 681.12 149.88 641.98 \
143.57 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 642.46 141.17 635.17 142.53 641.72 146.01 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 732 268.1 0 19 3 -bam ",
		label=bam,
		lp="732,270",
		pos="e,633.67,142.3 732.67,403.53 728.53,393.57 722.5,376.43 722.5,361 722.5,361 722.5,361 722.5,179 722.5,160.84 681.12,149.88 641.98,\
143.57"];
	select_somatic_tumor_sample	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 187 350.5 187 369.5 346 369.5 346 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 266.5 357.5 0 143 29 -SelectVariants (GATK 4.1.8.1) ",
		height=0.27778,
		label="SelectVariants (GATK 4.1.8.1)",
		pos="266.5,360",
		rects="187,350.5,346,369.5",
		width=2.2083];
	somatic_vcf -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 247.87 403.57 248.45 396.49 249.89 386.23 253.5 378 253.71 377.53 253.93 377.07 254.16 376.6 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 256.19 377.97 257.93 370.76 252.08 375.31 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 260 380.6 0 13 3 -vcf ",
		label=vcf,
		lp="260,382.5",
		pos="e,258.75,369.49 247.87,403.57 248.45,396.49 249.89,386.23 253.5,378 253.71,377.53 253.93,377.07 254.16,376.6"];
	rename_germline_vcf	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 366 350.5 366 369.5 489 369.5 489 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 427.5 357.5 0 107 19 -rename_germline_vcf ",
		height=0.27778,
		label=rename_germline_vcf,
		pos="427.5,360",
		rects="366,350.5,489,369.5",
		width=1.7083];
	normal_sample_name -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 543.81 403.61 528.79 396.27 506.01 385.61 485.5 378 479.62 375.82 473.33 373.73 467.13 371.81 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 468.23 369.58 460.82 369.91 466.82 374.27 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 544 380.6 0 77 17 -sample_to_replace ",
		label=sample_to_replace,
		lp="544,382.5",
		pos="e,459.37,369.47 543.81,403.61 528.79,396.27 506.01,385.61 485.5,378 479.62,375.82 473.33,373.73 467.13,371.81"];
	germline_vcf -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 452.19 403.74 450.8 396.58 448.15 386.11 443.5 378 443.06 377.23 442.57 376.46 442.05 375.71 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 444.13 374.38 437.8 370.53 440.35 377.49 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 466 380.6 0 37 9 -input_vcf ",
		label=input_vcf,
		lp="466,382.5",
		pos="e,436.84,369.36 452.19,403.74 450.8,396.58 448.15,386.11 443.5,378 443.06,377.23 442.57,376.46 442.05,375.71"];
	sort	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 544 215.5 544 234.5 603 234.5 603 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 573.5 222.5 0 43 8 -Sort VCF ",
		height=0.27778,
		label="Sort VCF",
		pos="573.5,225",
		rects="544,215.5,603,234.5",
		width=0.81944];
	reference_dict -> sort	[_draw_="c 7 -#000000 B 10 662.55 403.74 654.27 394.23 642.5 377.77 642.5 361 642.5 361 642.5 361 642.5 269 642.5 251.9 627.04 241.35 610.76 \
234.99 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 611.61 232.69 604.19 232.69 609.99 237.31 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 672 313.1 0 59 14 -reference_dict ",
		label=reference_dict,
		lp="672,315",
		pos="e,602.76,232.19 662.55,403.74 654.27,394.23 642.5,377.77 642.5,361 642.5,361 642.5,361 642.5,269 642.5,251.9 627.04,241.35 610.76,\
234.99"];
	tumor_sample_name -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 350.75 403.79 352.36 396.04 355.92 384.65 363.5 378 365.53 376.22 367.73 374.62 370.05 373.19 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 370.91 375.5 375.96 370.07 368.63 371.17 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 403 380.6 0 79 15 -new_sample_name ",
		label=new_sample_name,
		lp="403,382.5",
		pos="e,377.3,369.37 350.75,403.79 352.36,396.04 355.92,384.65 363.5,378 365.53,376.22 367.73,374.62 370.05,373.19"];
	tumor_sample_name -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 314.17 403.54 297.66 398.95 280.35 392.99 274.5 387 271.9 384.34 270.14 380.86 268.96 377.31 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 271.4 377 267.43 370.74 266.63 378.11 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 315 380.6 0 81 18 -samples_to_include ",
		label=samples_to_include,
		lp="315,382.5",
		pos="e,267.09,369.26 314.17,403.54 297.66,398.95 280.35,392.99 274.5,387 271.9,384.34 270.14,380.86 268.96,377.31"];
	reference -> phase_vcf	[_draw_="c 7 -#000000 B 16 152.66 403.51 144.86 400.54 135.86 397.36 127.5 395 110.05 390.06 102.78 396.76 87.5 387 75.44 379.29 68.5 375.31 \
68.5 361 68.5 361 68.5 361 68.5 179 68.5 157.37 366.44 143.6 504.62 138.38 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 504.67 140.83 511.57 138.12 504.49 135.93 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 88.5 268.1 0 40 9 -reference ",
		label=reference,
		lp="88.5,270",
		pos="e,513.09,138.06 152.66,403.51 144.86,400.54 135.86,397.36 127.5,395 110.05,390.06 102.78,396.76 87.5,387 75.439,379.29 68.5,375.31 \
68.5,361 68.5,361 68.5,361 68.5,179 68.5,157.37 366.44,143.6 504.62,138.38"];
	reference -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 180.37 403.56 187.06 395.86 197.88 384.7 209.5 378 213.15 375.89 217.09 374.03 221.13 372.37 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 221.84 374.72 227.55 369.99 220.13 370.13 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 229.5 380.6 0 40 9 -reference ",
		label=reference,
		lp="229.5,382.5",
		pos="e,228.97,369.46 180.37,403.56 187.06,395.86 197.88,384.7 209.5,378 213.15,375.89 217.09,374.03 221.13,372.37"];
	combine_variants	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 219 260.5 219 279.5 510 279.5 510 260.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 364.5 267.5 0 275 52 -Combine germline and somatic vcf for pVACseq phasing ",
		height=0.27778,
		label="Combine germline and somatic vcf for pVACseq phasing",
		pos="364.5,270",
		rects="219,260.5,510,279.5",
		width=4.0417];
	reference -> combine_variants	[_draw_="c 7 -#000000 B 7 173.03 403.81 172.72 390.95 173.94 365.87 186.5 350 216.44 312.18 268.29 291.98 308.34 281.5 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 308.77 283.92 314.96 279.84 307.58 279.17 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 221.5 335.6 0 40 9 -reference ",
		label=reference,
		lp="221.5,337.5",
		pos="e,316.43,279.47 173.03,403.81 172.72,390.95 173.94,365.87 186.5,350 216.44,312.18 268.29,291.98 308.34,281.5"];
	index_renamed_germline	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 364.5 305.5 364.5 324.5 426.5 324.5 426.5 305.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 395.5 312.5 0 46 9 -vcf index ",
		height=0.27778,
		label="vcf index",
		pos="395.5,315",
		rects="364.5,305.5,426.5,324.5",
		width=0.86111];
	index_renamed_germline -> combine_variants	[_draw_="c 7 -#000000 B 4 389.52 305.71 385.49 300.12 380.06 292.58 375.28 285.96 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 377.42 284.74 371.34 280.49 373.45 287.6 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 408.5 290.6 0 52 12 -germline_vcf ",
		label=germline_vcf,
		lp="408.5,292.5",
		pos="e,370.46,279.27 389.52,305.71 385.49,300.12 380.06,292.58 375.28,285.96"];
	index_filtered_somatic	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 284.5 305.5 284.5 324.5 346.5 324.5 346.5 305.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 315.5 312.5 0 46 9 -vcf index ",
		height=0.27778,
		label="vcf index",
		pos="315.5,315",
		rects="284.5,305.5,346.5,324.5",
		width=0.86111];
	index_filtered_somatic -> combine_variants	[_draw_="c 7 -#000000 B 7 317.27 305.84 318.86 300.22 321.7 292.9 326.5 288 328 286.46 329.67 285.06 331.45 283.77 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 332.69 285.88 337.39 280.15 330.14 281.69 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 351 290.6 0 49 11 -somatic_vcf ",
		label=somatic_vcf,
		lp="351,292.5",
		pos="e,338.68,279.36 317.27,305.84 318.86,300.22 321.7,292.9 326.5,288 328,286.46 329.67,285.06 331.45,283.77"];
	rename_germline_vcf -> index_renamed_germline	[_draw_="c 7 -#000000 B 4 421.33 350.71 417.17 345.12 411.56 337.58 406.63 330.96 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 408.7 329.63 402.55 325.48 404.77 332.56 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 420 335.6 0 13 3 -vcf ",
		label=vcf,
		lp="420,337.5",
		pos="e,401.65,324.27 421.33,350.71 417.17,345.12 411.56,337.58 406.63,330.96"];
	bgzip_and_index	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 515.5 170.5 515.5 189.5 631.5 189.5 631.5 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 573.5 177.5 0 100 19 -bgzip and index VCF ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label="bgzip and index VCF",
		pos="573.5,180",
		rects="515.5,170.5,631.5,189.5",
		width=1.6111];
	sort -> bgzip_and_index	[_draw_="c 7 -#000000 B 4 573.5 215.71 573.5 210.59 573.5 203.85 573.5 197.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 575.95 197.78 573.5 190.78 571.05 197.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 580 200.6 0 13 3 -vcf ",
		label=vcf,
		lp="580,202.5",
		pos="e,573.5,189.27 573.5,215.71 573.5,210.59 573.5,203.85 573.5,197.67"];
	bgzip_and_index_phased_vcf	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 515.5 80.5 515.5 99.5 631.5 99.5 631.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 573.5 87.5 0 100 19 -bgzip and index VCF ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label="bgzip and index VCF",
		pos="573.5,90",
		rects="515.5,80.5,631.5,99.5",
		width=1.6111];
	phase_vcf -> bgzip_and_index_phased_vcf	[_draw_="c 7 -#000000 B 4 573.5 125.71 573.5 120.59 573.5 113.85 573.5 107.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 575.95 107.78 573.5 100.78 571.05 107.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 580 110.6 0 13 3 -vcf ",
		label=vcf,
		lp="580,112.5",
		pos="e,573.5,99.265 573.5,125.71 573.5,120.59 573.5,113.85 573.5,107.67"];
	bgzip_and_index -> phase_vcf	[_draw_="c 7 -#000000 B 4 573.5 170.71 573.5 165.59 573.5 158.85 573.5 152.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 575.95 152.78 573.5 145.78 571.05 152.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 580 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="580,157.5",
		pos="e,573.5,144.27 573.5,170.71 573.5,165.59 573.5,158.85 573.5,152.67"];
	bgzip_and_index_phased_vcf -> phased_vcf	[_draw_="c 7 -#000000 B 4 573.5 80.71 573.5 75.59 573.5 68.85 573.5 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 575.95 62.78 573.5 55.78 571.05 62.78 ",
		pos="e,573.5,54.265 573.5,80.709 573.5,75.593 573.5,68.848 573.5,62.666"];
	select_somatic_tumor_sample -> index_filtered_somatic	[_draw_="c 7 -#000000 B 4 275.95 350.71 282.73 344.76 292.02 336.61 299.89 329.7 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 301.3 331.72 304.94 325.26 298.07 328.04 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 301 335.6 0 13 3 -vcf ",
		label=vcf,
		lp="301,337.5",
		pos="e,306.08,324.27 275.95,350.71 282.73,344.76 292.02,336.61 299.89,329.7"];
	combine_variants -> sort	[_draw_="c 7 -#000000 B 4 405.79 260.5 443.73 252.7 499.46 241.23 536.11 233.69 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 536.24 236.17 542.6 232.36 535.25 231.37 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 494 245.6 0 13 3 -vcf ",
		label=vcf,
		lp="494,247.5",
		pos="e,544.08,232.05 405.79,260.5 443.73,252.7 499.46,241.23 536.11,233.69"];
	default1	[_draw_="c 7 -#000000 C 7 -#d5aefc P 4 0 403.5 0 422.5 125 422.5 125 403.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 62.5 410.5 0 109 20 -\"somatic_tumor_only\" ",
		fillcolor="#D5AEFC",
		height=0.27778,
		label="\"somatic_tumor_only\"",
		pos="62.5,413",
		rects="0,403.5,125,422.5",
		width=1.7361];
	default1 -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 69.94 403.66 77.69 395.59 90.63 383.74 104.5 378 118.35 372.27 148.52 368.36 179.11 365.76 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 179.02 368.23 185.8 365.22 178.62 363.34 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 150 380.6 0 91 19 -output_vcf_basename ",
		label=output_vcf_basename,
		lp="150,382.5",
		pos="e,187.31,365.1 69.938,403.66 77.692,395.59 90.631,383.74 104.5,378 118.35,372.27 148.52,368.36 179.11,365.76"];
}