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
		];
		tumor_sample_name	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 164 403.5 164 422.5 284 422.5 284 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 224 410.5 0 104 17 -tumor_sample_name ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=tumor_sample_name,
			pos="224,413",
			rects="164,403.5,284,422.5",
			width=1.6667];
		somatic_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 84 403.5 84 422.5 160 422.5 160 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 122 410.5 0 60 11 -somatic_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=somatic_vcf,
			pos="122,413",
			rects="84,403.5,160,422.5",
			width=1.0556];
		normal_sample_name	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 288.5 403.5 288.5 422.5 413.5 422.5 413.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 351 410.5 0 109 18 -normal_sample_name ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=normal_sample_name,
			pos="351,413",
			rects="288.5,403.5,413.5,422.5",
			width=1.7361];
		reference	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 16.5 403.5 16.5 422.5 79.5 422.5 79.5 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 48 410.5 0 47 9 -reference ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=reference,
			pos="48,413",
			rects="16.5,403.5,79.5,422.5",
			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];
		germline_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 418 403.5 418 422.5 498 422.5 498 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 458 410.5 0 64 12 -germline_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=germline_vcf,
			pos="458,413",
			rects="418,403.5,498,422.5",
			width=1.1111];
		reference_dict	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 502 403.5 502 422.5 588 422.5 588 403.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 545 410.5 0 70 14 -reference_dict ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=reference_dict,
			pos="545,413",
			rects="502,403.5,588,422.5",
			width=1.1944];
	}
	subgraph cluster_outputs {
		graph [_draw_="S 6 -dashed c 7 -#000000 C 7 -#eeeeee P 4 399 8 399 63 507 63 507 8 ",
			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 453 15 0 92 16 -Workflow Outputs ",
			bb="399,8,507,63",
			label="Workflow Outputs",
			labelloc=b,
			lheight=0.15,
			lp="453,17.5",
			lwidth=1.28,
			rank=same,
			style=dashed
		];
		phased_vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 417 35.5 417 54.5 489 54.5 489 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 453 42.5 0 56 10 -phased_vcf ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=phased_vcf,
			pos="453,45",
			rects="417,35.5,489,54.5",
			width=1];
	}
	select_somatic_tumor_sample	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 93.5 350.5 93.5 369.5 252.5 369.5 252.5 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 173 357.5 0 143 29 -SelectVariants (GATK 4.1.8.1) ",
		height=0.27778,
		label="SelectVariants (GATK 4.1.8.1)",
		pos="173,360",
		rects="93.5,350.5,252.5,369.5",
		width=2.2083];
	tumor_sample_name -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 198.38 403.63 190.36 399.78 182.24 394.39 177 387 175.09 384.31 173.94 381.07 173.27 377.8 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 175.72 377.67 172.59 370.95 170.85 378.16 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 217.5 380.6 0 81 18 -samples_to_include ",
		label=samples_to_include,
		lp="217.5,382.5",
		pos="e,172.44,369.44 198.38,403.63 190.36,399.78 182.24,394.39 177,387 175.09,384.31 173.94,381.07 173.27,377.8"];
	rename_germline_vcf	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 286.5 350.5 286.5 369.5 409.5 369.5 409.5 350.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 348 357.5 0 107 19 -rename_germline_vcf ",
		height=0.27778,
		label=rename_germline_vcf,
		pos="348,360",
		rects="286.5,350.5,409.5,369.5",
		width=1.7083];
	tumor_sample_name -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 234.28 403.61 245.38 394.69 262.49 381.4 270 378 275.29 375.6 280.95 373.53 286.7 371.75 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 287.07 374.19 293.12 369.91 285.72 369.48 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 309.5 380.6 0 79 15 -new_sample_name ",
		label=new_sample_name,
		lp="309.5,382.5",
		pos="e,294.58,369.49 234.28,403.61 245.38,394.69 262.49,381.4 270,378 275.29,375.6 280.95,373.53 286.7,371.75"];
	somatic_vcf -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 130.04 403.52 136.66 396.58 146.33 386.55 155 378 156.01 377 157.06 375.98 158.12 374.96 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 159.66 376.87 163.04 370.27 156.28 373.32 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 161.5 380.6 0 13 3 -vcf ",
		label=vcf,
		lp="161.5,382.5",
		pos="e,164.14,369.23 130.04,403.52 136.66,396.58 146.33,386.55 155,378 156.01,377 157.06,375.98 158.12,374.96"];
	normal_sample_name -> rename_germline_vcf	[_draw_="c 7 -#000000 B 4 350.5 403.58 350.09 396.52 349.48 386.24 348.97 377.55 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 351.43 377.62 348.58 370.78 346.54 377.91 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 388.5 380.6 0 77 17 -sample_to_replace ",
		label=sample_to_replace,
		lp="388.5,382.5",
		pos="e,348.49,369.26 350.5,403.58 350.09,396.52 349.48,386.24 348.97,377.55"];
	reference -> select_somatic_tumor_sample	[_draw_="c 7 -#000000 B 7 59.92 403.65 71.3 396.03 89.15 384.91 106 378 111.78 375.63 117.97 373.52 124.18 371.66 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 124.49 374.12 130.56 369.86 123.16 369.41 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 126 380.6 0 40 9 -reference ",
		label=reference,
		lp="126,382.5",
		pos="e,132.02,369.45 59.925,403.65 71.302,396.03 89.154,384.91 106,378 111.78,375.63 117.97,373.52 124.18,371.66"];
	phase_vcf	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 392.5 125.5 392.5 144.5 513.5 144.5 513.5 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 453 132.5 0 105 19 -Read-backed phasing ",
		height=0.27778,
		label="Read-backed phasing",
		pos="453,135",
		rects="392.5,125.5,513.5,144.5",
		width=1.6806];
	reference -> phase_vcf	[_draw_="c 7 -#000000 B 10 49.84 403.74 51.91 393.7 55 376.19 55 361 55 361 55 361 55 179 55 146.29 270.3 138.43 384.2 136.57 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 384.08 139.02 391.04 136.46 384 134.12 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 75 268.1 0 40 9 -reference ",
		label=reference,
		lp="75,270",
		pos="e,392.55,136.44 49.839,403.74 51.913,393.7 55,376.19 55,361 55,361 55,361 55,179 55,146.29 270.3,138.43 384.2,136.57"];
	combine_variants	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 185.5 260.5 185.5 279.5 476.5 279.5 476.5 260.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 331 267.5 0 275 52 -Combine germline and somatic vcf for pVACseq phasing ",
		height=0.27778,
		label="Combine germline and somatic vcf for pVACseq phasing",
		pos="331,270",
		rects="185.5,260.5,476.5,279.5",
		width=4.0417];
	reference -> combine_variants	[_draw_="c 7 -#000000 B 7 51.73 403.5 57.98 390.22 71.8 364.56 91 350 141.6 311.63 211.71 291.39 263.09 281.05 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 263.28 283.51 269.68 279.77 262.34 278.7 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 135 335.6 0 40 9 -reference ",
		label=reference,
		lp="135,337.5",
		pos="e,271.17,279.48 51.733,403.5 57.983,390.22 71.795,364.56 91,350 141.6,311.63 211.71,291.39 263.09,281.05"];
	bam -> phase_vcf	[_draw_="c 7 -#000000 B 13 604.27 403.63 600.79 398.97 596.71 392.92 594 387 589.01 376.12 587 372.97 587 361 587 361 587 361 587 179 587 \
163.56 554.35 152.89 521.28 146.04 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 522.16 143.71 514.82 144.76 521.21 148.52 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 596.5 268.1 0 19 3 -bam ",
		label=bam,
		lp="596.5,270",
		pos="e,513.34,144.46 604.27,403.63 600.79,398.97 596.71,392.92 594,387 589.01,376.12 587,372.97 587,361 587,361 587,361 587,179 587,163.56 \
554.35,152.89 521.28,146.04"];
	germline_vcf -> rename_germline_vcf	[_draw_="c 7 -#000000 B 7 452.9 403.62 447.65 395.75 438.74 384.27 428 378 424.34 375.86 420.44 373.99 416.42 372.35 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 417.38 370.1 409.97 370.01 415.71 374.7 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 457.5 380.6 0 37 9 -input_vcf ",
		label=input_vcf,
		lp="457.5,382.5",
		pos="e,408.54,369.49 452.9,403.62 447.65,395.75 438.74,384.27 428,378 424.34,375.86 420.44,373.99 416.42,372.35"];
	sort	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 423.5 215.5 423.5 234.5 482.5 234.5 482.5 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 453 222.5 0 43 8 -Sort VCF ",
		height=0.27778,
		label="Sort VCF",
		pos="453,225",
		rects="423.5,215.5,482.5,234.5",
		width=0.81944];
	reference_dict -> sort	[_draw_="c 7 -#000000 B 10 529.02 403.58 515.05 394.95 497 380.09 497 361 497 361 497 361 497 269 497 256.33 487.55 246.17 477.41 238.91 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 478.87 236.93 471.66 235.18 476.2 241.05 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 526.5 313.1 0 59 14 -reference_dict ",
		label=reference_dict,
		lp="526.5,315",
		pos="e,470.39,234.36 529.02,403.58 515.05,394.95 497,380.09 497,361 497,361 497,361 497,269 497,256.33 487.55,246.17 477.41,238.91"];
	bgzip_and_index_phased_vcf	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 395 80.5 395 99.5 511 99.5 511 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 453 87.5 0 100 19 -bgzip and index VCF ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label="bgzip and index VCF",
		pos="453,90",
		rects="395,80.5,511,99.5",
		width=1.6111];
	bgzip_and_index_phased_vcf -> phased_vcf	[_draw_="c 7 -#000000 B 4 453 80.71 453 75.59 453 68.85 453 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 455.45 62.78 453 55.78 450.55 62.78 ",
		pos="e,453,54.265 453,80.709 453,75.593 453,68.848 453,62.666"];
	bgzip_and_index	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 395 170.5 395 189.5 511 189.5 511 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 453 177.5 0 100 19 -bgzip and index VCF ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label="bgzip and index VCF",
		pos="453,180",
		rects="395,170.5,511,189.5",
		width=1.6111];
	bgzip_and_index -> phase_vcf	[_draw_="c 7 -#000000 B 4 453 170.71 453 165.59 453 158.85 453 152.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 455.45 152.78 453 145.78 450.55 152.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 459.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="459.5,157.5",
		pos="e,453,144.27 453,170.71 453,165.59 453,158.85 453,152.67"];
	index_filtered_somatic	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 223 305.5 223 324.5 285 324.5 285 305.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 254 312.5 0 46 9 -vcf index ",
		height=0.27778,
		label="vcf index",
		pos="254,315",
		rects="223,305.5,285,324.5",
		width=0.86111];
	select_somatic_tumor_sample -> index_filtered_somatic	[_draw_="c 7 -#000000 B 4 189 350.5 200.87 344.2 217.24 335.51 230.58 328.43 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 231.66 330.63 236.69 325.19 229.36 326.31 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 227.5 335.6 0 13 3 -vcf ",
		label=vcf,
		lp="227.5,337.5",
		pos="e,238.03,324.48 189,350.5 200.87,344.2 217.24,335.51 230.58,328.43"];
	index_filtered_somatic -> combine_variants	[_draw_="c 7 -#000000 B 7 262.67 305.66 268.81 300.09 277.44 292.92 286 288 289.44 286.02 293.15 284.19 296.92 282.53 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 297.71 284.85 303.25 279.91 295.85 280.32 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 310.5 290.6 0 49 11 -somatic_vcf ",
		label=somatic_vcf,
		lp="310.5,292.5",
		pos="e,304.65,279.34 262.67,305.66 268.81,300.09 277.44,292.92 286,288 289.44,286.02 293.15,284.19 296.92,282.53"];
	phase_vcf -> bgzip_and_index_phased_vcf	[_draw_="c 7 -#000000 B 4 453 125.71 453 120.59 453 113.85 453 107.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 455.45 107.78 453 100.78 450.55 107.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 459.5 110.6 0 13 3 -vcf ",
		label=vcf,
		lp="459.5,112.5",
		pos="e,453,99.265 453,125.71 453,120.59 453,113.85 453,107.67"];
	sort -> bgzip_and_index	[_draw_="c 7 -#000000 B 4 453 215.71 453 210.59 453 203.85 453 197.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 455.45 197.78 453 190.78 450.55 197.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 459.5 200.6 0 13 3 -vcf ",
		label=vcf,
		lp="459.5,202.5",
		pos="e,453,189.27 453,215.71 453,210.59 453,203.85 453,197.67"];
	index_renamed_germline	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 312 305.5 312 324.5 374 324.5 374 305.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 343 312.5 0 46 9 -vcf index ",
		height=0.27778,
		label="vcf index",
		pos="343,315",
		rects="312,305.5,374,324.5",
		width=0.86111];
	rename_germline_vcf -> index_renamed_germline	[_draw_="c 7 -#000000 B 4 347.04 350.71 346.44 345.59 345.66 338.85 344.94 332.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 347.38 332.44 344.14 325.77 342.51 333 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 352.5 335.6 0 13 3 -vcf ",
		label=vcf,
		lp="352.5,337.5",
		pos="e,343.96,324.27 347.04,350.71 346.44,345.59 345.66,338.85 344.94,332.67"];
	index_renamed_germline -> combine_variants	[_draw_="c 7 -#000000 B 4 340.69 305.71 339.23 300.47 337.29 293.53 335.53 287.24 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 337.95 286.81 333.71 280.72 333.24 288.12 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 365 290.6 0 52 12 -germline_vcf ",
		label=germline_vcf,
		lp="365,292.5",
		pos="e,333.31,279.27 340.69,305.71 339.23,300.47 337.29,293.53 335.53,287.24"];
	combine_variants -> sort	[_draw_="c 7 -#000000 B 4 355.1 260.5 373.99 253.85 400.42 244.53 421.06 237.26 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 421.73 239.62 427.52 234.98 420.1 235 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 409.5 245.6 0 13 3 -vcf ",
		label=vcf,
		lp="409.5,247.5",
		pos="e,428.95,234.48 355.1,260.5 373.99,253.85 400.42,244.53 421.06,237.26"];
	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 10 678.17 403.57 666.04 400.5 651.94 397.24 639 395 483.15 368.02 441.87 379.67 284 370 276.49 369.54 268.7 369.01 \
260.88 368.45 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 261.07 366 253.91 367.93 260.71 370.89 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 632.5 380.6 0 91 19 -output_vcf_basename ",
		label=output_vcf_basename,
		lp="632.5,382.5",
		pos="e,252.4,367.82 678.17,403.57 666.04,400.5 651.94,397.24 639,395 483.15,368.02 441.87,379.67 284,370 276.49,369.54 268.7,369.01 260.88,\
368.45"];
}