digraph workflow {
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			label=reference_sizes,
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			rects="53.5,313.5,146.5,332.5",
			width=1.2917];
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			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 293 320.5 0 70 11 -sample_name ",
			fillcolor="#94DDF4",
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			label=sample_name,
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			rects="250,313.5,336,332.5",
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			fillcolor="#94DDF4",
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			rects="1067,313.5,1153,332.5",
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		instrument_data_bams	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 611.5 313.5 611.5 332.5 740.5 332.5 740.5 313.5 ",
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			rects="611.5,313.5,740.5,332.5",
			width=1.7917];
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	subgraph cluster_outputs {
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			lwidth=1.28,
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		gathered_directory	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 419.5 35.5 419.5 54.5 528.5 54.5 528.5 35.5 ",
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			fillcolor="#94DDF4",
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			label=gathered_directory,
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			rects="419.5,35.5,528.5,54.5",
			width=1.5139];
		cram	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 337.5 35.5 337.5 54.5 378.5 54.5 378.5 35.5 ",
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			fillcolor="#94DDF4",
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			label=cram,
			pos="358,45",
			rects="337.5,35.5,378.5,54.5",
			width=0.56944];
		cpgs	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 294.5 35.5 294.5 54.5 333.5 54.5 333.5 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 314 42.5 0 23 4 -cpgs ",
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			label=cpgs,
			pos="314,45",
			rects="294.5,35.5,333.5,54.5",
			width=0.54167];
		vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 383 35.5 383 54.5 415 54.5 415 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 399 42.5 0 16 3 -vcf ",
			fillcolor="#94DDF4",
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		cpg_bedgraph	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 205.5 35.5 205.5 54.5 290.5 54.5 290.5 35.5 ",
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			fillcolor="#94DDF4",
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			rects="205.5,35.5,290.5,54.5",
			width=1.1806];
	}
	bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 554.5 260.5 554.5 279.5 797.5 279.5 797.5 260.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 676 267.5 0 227 44 -bam to trimmed fastqs and biscuit alignments ",
		fillcolor="#F3CEA1",
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		pos="676,270",
		rects="554.5,260.5,797.5,279.5",
		width=3.375];
	trimming_max_uncalled -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 1196.42 313.57 1167.39 305.42 1121 293.52 1080 288 988.69 275.7 884.82 271.54 805.27 270.41 ",
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		label=max_uncalled,
		lp="1156.5,292.5",
		pos="e,797.16,270.31 1196.4,313.57 1167.4,305.42 1121,293.52 1080,288 988.69,275.7 884.82,271.54 805.27,270.41"];
	trimming_adapter_min_overlap -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 4 804.57 313.58 778.49 304.94 737.8 291.47 709.19 281.99 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 710.32 279.78 702.9 279.91 708.78 284.44 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 796 290.6 0 86 19 -adapter_min_overlap ",
		label=adapter_min_overlap,
		lp="796,292.5",
		pos="e,701.47,279.43 804.57,313.58 778.49,304.94 737.8,291.47 709.19,281.99"];
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		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 484 177.5 0 67 14 -Biscuit pileup ",
		height=0.27778,
		label="Biscuit pileup",
		pos="484,180",
		rects="442.5,170.5,525.5,189.5",
		width=1.1528];
	reference_index -> pileup	[_draw_="c 7 -#000000 B 10 223.13 313.51 231.36 310.75 240.56 307.71 249 305 349.11 272.82 405.84 314.21 475 235 483.78 224.94 485.63 209.67 \
485.52 197.93 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 487.97 197.82 485.18 190.95 483.07 198.06 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 487 245.6 0 40 9 -reference ",
		label=reference,
		lp="487,247.5",
		pos="e,485.1,189.44 223.13,313.51 231.36,310.75 240.56,307.71 249,305 349.11,272.82 405.84,314.21 475,235 483.78,224.94 485.63,209.67 \
485.52,197.93"];
	reference_index -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 13 218.99 313.53 228.07 310.26 238.9 306.86 249 305 290.56 297.35 399.51 312.04 439 297 444.9 294.75 444.13 290.35 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 546.34 276.59 553.19 273.75 546.06 271.7 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 483 290.6 0 66 15 -reference_index ",
		label=reference_index,
		lp="483,292.5",
		pos="e,554.7,273.66 218.99,313.53 228.07,310.26 238.9,306.86 249,305 290.56,297.35 399.51,312.04 439,297 444.9,294.75 444.13,290.35 450,\
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	bam_to_cram	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 288 170.5 288 189.5 428 189.5 428 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 358 177.5 0 124 22 -BAM to CRAM conversion ",
		height=0.27778,
		label="BAM to CRAM conversion",
		pos="358,180",
		rects="288,170.5,428,189.5",
		width=1.9444];
	reference_index -> bam_to_cram	[_draw_="c 7 -#000000 B 4 207.53 313.6 234.16 290.13 309.55 223.69 342.39 194.75 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 343.95 196.64 347.59 190.18 340.71 192.97 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 307 245.6 0 40 9 -reference ",
		label=reference,
		lp="307,247.5",
		pos="e,348.72,189.18 207.53,313.6 234.16,290.13 309.55,223.69 342.39,194.75"];
	bisulfite_qc	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 433.5 125.5 433.5 144.5 534.5 144.5 534.5 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 484 132.5 0 85 18 -Bisulfite QC tools ",
		fillcolor="#F3CEA1",
		height=0.27778,
		label="Bisulfite QC tools",
		pos="484,135",
		rects="433.5,125.5,534.5,144.5",
		width=1.4028];
	reference_index -> bisulfite_qc	[_draw_="c 7 -#000000 B 16 221.15 313.52 229.81 310.55 239.78 307.37 249 305 289.7 294.55 435 313.02 435 271 435 271 435 271 435 201.5 435 \
187.16 434.45 182.19 442 170 447.14 161.7 455.05 154.52 462.62 148.93 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 463.78 151.11 468.15 145.12 461 147.08 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 455 223.1 0 40 9 -reference ",
		label=reference,
		lp="455,225",
		pos="e,469.39,144.26 221.15,313.52 229.81,310.55 239.78,307.37 249,305 289.7,294.55 435,313.02 435,271 435,271 435,271 435,201.5 435,\
187.16 434.45,182.19 442,170 447.14,161.7 455.05,154.52 462.62,148.93"];
	vcf2bed	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 7 125.5 7 144.5 389 144.5 389 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 198 132.5 0 366 77 -convert a biscuit pileup vcf to a bed and bedgraph file, via a wrapper script ",
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		label="convert a biscuit pileup vcf to a bed and bedgraph file, via a wrapper script",
		pos="198,135",
		rects="7,125.5,389,144.5",
		width=5.3056];
	reference_index -> vcf2bed	[_draw_="c 7 -#000000 B 10 198 313.7 198 303.6 198 286.05 198 271 198 271 198 271 198 179 198 170.31 198 160.63 198 152.65 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 200.45 152.76 198 145.76 195.55 152.76 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 218 223.1 0 40 9 -reference ",
		label=reference,
		lp="218,225",
		pos="e,198,144.24 198,313.7 198,303.6 198,286.05 198,271 198,271 198,271 198,179 198,170.31 198,160.63 198,152.65"];
	trimming_adapters -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 13 421.22 313.51 431.37 310.47 443.14 307.24 454 305 481.64 299.3 489.56 303.6 517 297 528.48 294.24 530.52 290.76 \
542 288 553.88 285.15 566.47 282.75 578.99 280.74 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 579.16 283.19 585.71 279.71 578.42 278.35 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 560.5 290.6 0 37 8 -adapters ",
		label=adapters,
		lp="560.5,292.5",
		pos="e,587.2,279.48 421.22,313.51 431.37,310.47 443.14,307.24 454,305 481.64,299.3 489.56,303.6 517,297 528.48,294.24 530.52,290.76 542,\
288 553.88,285.15 566.47,282.75 578.99,280.74"];
	QCannotation -> bisulfite_qc	[_draw_="c 7 -#000000 B 10 1321.07 313.59 1306.57 305.05 1288 290.34 1288 271 1288 271 1288 271 1288 179 1288 141.66 727.67 136.7 542.56 \
136.08 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 542.81 133.63 535.81 136.05 542.8 138.53 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1316.5 223.1 0 57 12 -QCannotation ",
		label=QCannotation,
		lp="1316.5,225",
		pos="e,534.29,136.05 1321.1,313.59 1306.6,305.05 1288,290.34 1288,271 1288,271 1288,271 1288,179 1288,141.66 727.67,136.7 542.56,136.08"];
	trimming_min_readlength -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 10 953.62 313.5 941.61 310.78 928.24 307.76 916 305 882.23 297.4 874.16 293.57 840 288 822.03 285.07 802.88 282.55 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 784.72 278 777.49 279.65 784.17 282.87 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 913 290.6 0 64 14 -min_readlength ",
		label=min_readlength,
		lp="913,292.5",
		pos="e,775.98,279.48 953.62,313.5 941.61,310.78 928.24,307.76 916,305 882.23,297.4 874.16,293.57 840,288 822.03,285.07 802.88,282.55 \
784.22,280.41"];
	trimming_adapter_trim_end -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 546.33 313.59 560.64 306.02 582.76 295.04 603 288 609.95 285.58 617.39 283.4 624.77 281.47 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 625.06 283.93 631.25 279.85 623.87 279.17 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 639 290.6 0 72 16 -adapter_trim_end ",
		label=adapter_trim_end,
		lp="639,292.5",
		pos="e,632.72,279.48 546.33,313.59 560.64,306.02 582.76,295.04 603,288 609.95,285.58 617.39,283.4 624.77,281.47"];
	bedgraph_to_bigwig	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 114 80.5 114 99.5 282 99.5 282 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 198 87.5 0 152 29 -bedGraph to bigwig conversion ",
		height=0.27778,
		label="bedGraph to bigwig conversion",
		pos="198,90",
		rects="114,80.5,282,99.5",
		width=2.3333];
	reference_sizes -> bedgraph_to_bigwig	[_draw_="c 7 -#000000 B 10 53.51 316.08 27.4 309.86 0 297.11 0 271 0 271 0 271 0 134 0 110.46 54.12 99.78 105.77 94.95 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 105.76 97.41 112.52 94.36 105.33 92.53 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 32.5 200.6 0 65 15 -reference_sizes ",
		label=reference_sizes,
		lp="32.5,202.5",
		pos="e,114.03,94.223 53.513,316.08 27.399,309.86 0,297.11 0,271 0,271 0,271 0,134 0,110.46 54.12,99.781 105.77,94.949"];
	read_group_id -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 1089.69 313.63 1081.51 310.54 1071.92 307.24 1063 305 978.89 283.91 881.66 275.43 805.69 272.21 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 806.08 269.77 798.99 271.94 805.88 274.67 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1050 290.6 0 58 13 -read_group_id ",
		label=read_group_id,
		lp="1050,292.5",
		pos="e,797.47,271.88 1089.7,313.63 1081.5,310.54 1071.9,307.24 1063,305 978.89,283.91 881.66,275.43 805.69,272.21"];
	instrument_data_bams -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 4 676 313.58 676 306.52 676 296.24 676 287.55 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 678.45 287.78 676 280.78 673.55 287.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 685.5 290.6 0 19 3 -bam ",
		label=bam,
		lp="685.5,292.5",
		pos="e,676,279.26 676,313.58 676,306.52 676,296.24 676,287.55"];
	merge	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 491 215.5 491 234.5 601 234.5 601 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 546 222.5 0 94 15 -Sambamba: merge ",
		height=0.27778,
		label="Sambamba: merge",
		pos="546,225",
		rects="491,215.5,601,234.5",
		width=1.5278];
	merge -> pileup	[_draw_="c 7 -#000000 B 7 536.06 215.62 528.39 209.21 518.38 200.99 514 198 511.78 196.48 509.41 194.97 507.01 193.51 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 508.46 191.52 501.18 190.11 505.99 195.75 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 534.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="534.5,202.5",
		pos="e,499.87,189.34 536.06,215.62 528.39,209.21 518.38,200.99 514,198 511.78,196.48 509.41,194.97 507.01,193.51"];
	merge -> bam_to_cram	[_draw_="c 7 -#000000 B 4 508.86 215.5 478.47 208.56 435.39 198.7 403.04 191.3 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 403.91 188.99 396.54 189.82 402.82 193.76 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 477.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="477.5,202.5",
		pos="e,395.07,189.48 508.86,215.5 478.47,208.56 435.39,198.7 403.04,191.3"];
	merge -> bisulfite_qc	[_draw_="c 7 -#000000 B 10 545.38 215.65 544.83 210.48 543.83 203.74 542 198 537.78 184.74 536.84 180.75 528 170 521.52 162.12 512.9 154.96 \
505 149.26 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 506.43 147.27 499.28 145.31 503.65 151.3 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 548.5 178.1 0 19 3 -bam ",
		label=bam,
		lp="548.5,180",
		pos="e,498.03,144.45 545.38,215.65 544.83,210.48 543.83,203.74 542,198 537.78,184.74 536.84,180.75 528,170 521.52,162.12 512.9,154.96 \
505,149.26"];
	bedgraph_to_bigwig -> cpg_bedgraph	[_draw_="c 7 -#000000 B 4 207.64 80.71 214.56 74.76 224.04 66.61 232.07 59.7 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 233.53 61.67 237.24 55.25 230.34 57.96 ",
		pos="e,238.39,54.265 207.64,80.709 214.56,74.76 224.04,66.609 232.07,59.701"];
	pileup -> vcf	[_draw_="c 7 -#000000 B 10 463.86 170.53 452.82 164.88 439.82 156.38 432 145 415.27 120.64 428.43 107.65 418 80 415.6 73.65 412.17 67.05 \
408.87 61.38 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 411.1 60.32 405.37 55.61 406.91 62.87 ",
		pos="e,404.58,54.322 463.86,170.53 452.82,164.88 439.82,156.38 432,145 415.27,120.64 428.43,107.65 418,80 415.6,73.65 412.17,67.052 408.87,\
61.378"];
	pileup -> bisulfite_qc	[_draw_="c 7 -#000000 B 4 484 170.71 484 165.59 484 158.85 484 152.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 486.45 152.78 484 145.78 481.55 152.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 490.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="490.5,157.5",
		pos="e,484,144.27 484,170.71 484,165.59 484,158.85 484,152.67"];
	pileup -> vcf2bed	[_draw_="c 7 -#000000 B 7 442.74 172.04 438.44 171.34 434.13 170.65 430 170 374.99 161.39 312.53 152.27 266.28 145.65 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 266.91 143.26 259.63 144.7 266.22 148.11 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 378.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="378.5,157.5",
		pos="e,258.14,144.48 442.74,172.04 438.44,171.34 434.13,170.65 430,170 374.99,161.39 312.53,152.27 266.28,145.65"];
	bam_to_trimmed_fastq_and_biscuit_alignments -> merge	[_draw_="c 7 -#000000 B 4 650.32 260.5 630.02 253.79 601.53 244.37 579.45 237.06 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 580.48 234.83 573.07 234.95 578.94 239.48 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 633.5 245.6 0 23 4 -bams ",
		label=bams,
		lp="633.5,247.5",
		pos="e,571.63,234.48 650.32,260.5 630.02,253.79 601.53,244.37 579.45,237.06"];
	index_cram	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 298.5 80.5 298.5 99.5 417.5 99.5 417.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 358 87.5 0 103 19 -samtools index cram ",
		height=0.27778,
		label="samtools index cram",
		pos="358,90",
		rects="298.5,80.5,417.5,99.5",
		width=1.6528];
	bam_to_cram -> index_cram	[_draw_="c 7 -#000000 B 10 377.02 170.52 380.46 168.2 383.69 165.38 386 162 395.31 148.38 394.96 140.38 389 125 386.08 117.45 380.61 110.55 \
375.07 104.97 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 377.05 103.47 370.26 100.49 373.71 107.05 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 403.5 133.1 0 21 4 -cram ",
		label=cram,
		lp="403.5,135",
		pos="e,369.15,99.46 377.02,170.52 380.46,168.2 383.69,165.38 386,162 395.31,148.38 394.96,140.38 389,125 386.08,117.45 380.61,110.55 \
375.07,104.97"];
	index_cram -> cram	[_draw_="c 7 -#000000 B 4 358 80.71 358 75.59 358 68.85 358 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 360.45 62.78 358 55.78 355.55 62.78 ",
		pos="e,358,54.265 358,80.709 358,75.593 358,68.848 358,62.666"];
	bisulfite_qc -> gathered_directory	[_draw_="c 7 -#000000 B 4 483.04 125.56 481.4 111.14 478.03 81.48 475.9 62.73 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 478.34 62.47 475.11 55.79 473.47 63.02 ",
		pos="e,474.94,54.284 483.04,125.56 481.4,111.14 478.03,81.476 475.9,62.727"];
	vcf2bed -> cpgs	[_draw_="c 7 -#000000 B 7 233.55 125.6 250 120.34 268.96 112.19 283 100 289.35 94.49 299.42 75.75 306.35 61.89 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 308.46 63.15 309.35 55.78 304.06 60.99 ",
		pos="e,310.02,54.426 233.55,125.6 250,120.34 268.96,112.19 283,100 289.35,94.49 299.42,75.753 306.35,61.889"];
	vcf2bed -> bedgraph_to_bigwig	[_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 218 110.6 0 40 8 -bedgraph ",
		label=bedgraph,
		lp="218,112.5",
		pos="e,198,99.265 198,125.71 198,120.59 198,113.85 198,107.67"];
}