digraph workflow {
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			rects="468.5,313.5,603.5,332.5",
			width=1.875];
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			fillcolor="#94DDF4",
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			rects="608,313.5,718,332.5",
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		trimming_min_readlength	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 986.5 313.5 986.5 332.5 1129.5 332.5 1129.5 313.5 ",
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			rects="986.5,313.5,1129.5,332.5",
			width=1.9861];
	}
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			label="Workflow Outputs",
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			lheight=0.15,
			lp="326,17.5",
			lwidth=1.28,
			rank=same,
			style=dashed
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		gathered_directory	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 480.5 35.5 480.5 54.5 589.5 54.5 589.5 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 535 42.5 0 93 18 -gathered_directory ",
			fillcolor="#94DDF4",
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			label=gathered_directory,
			pos="535,45",
			rects="480.5,35.5,589.5,54.5",
			width=1.5139];
		cpgs	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 355.5 35.5 355.5 54.5 394.5 54.5 394.5 35.5 ",
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			label=cpgs,
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			rects="355.5,35.5,394.5,54.5",
			width=0.54167];
		cpg_bigwig	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 280.5 35.5 280.5 54.5 351.5 54.5 351.5 35.5 ",
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			label=cpg_bigwig,
			pos="316,45",
			rects="280.5,35.5,351.5,54.5",
			width=0.98611];
		cram	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 398.5 35.5 398.5 54.5 439.5 54.5 439.5 35.5 ",
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			label=cram,
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		vcf	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 444 35.5 444 54.5 476 54.5 476 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 460 42.5 0 16 3 -vcf ",
			fillcolor="#94DDF4",
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	}
	bisulfite_qc	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 493.5 125.5 493.5 144.5 594.5 144.5 594.5 125.5 ",
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		fillcolor="#F3CEA1",
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		label="Bisulfite QC tools",
		pos="544,135",
		rects="493.5,125.5,594.5,144.5",
		width=1.4028];
	QCannotation -> bisulfite_qc	[_draw_="c 7 -#000000 B 10 1409.39 313.68 1396.8 304.82 1380 289.53 1380 271 1380 271 1380 271 1380 179 1380 140.04 793.33 136.18 602.91 \
135.95 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 602.93 133.5 595.93 135.95 602.92 138.4 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1408.5 223.1 0 57 12 -QCannotation ",
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		pos="e,594.41,135.94 1409.4,313.68 1396.8,304.82 1380,289.53 1380,271 1380,271 1380,271 1380,179 1380,140.04 793.33,136.18 602.91,135.95"];
	bedgraph_to_bigwig	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 152 80.5 152 99.5 320 99.5 320 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 236 87.5 0 152 29 -bedGraph to bigwig conversion ",
		height=0.27778,
		label="bedGraph to bigwig conversion",
		pos="236,90",
		rects="152,80.5,320,99.5",
		width=2.3333];
	reference_sizes -> bedgraph_to_bigwig	[_draw_="c 7 -#000000 B 10 55.9 313.59 48.51 303.95 38 287.37 38 271 38 271 38 271 38 134 38 110.46 92.12 99.78 143.77 94.95 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 143.76 97.41 150.52 94.36 143.33 92.53 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 70.5 200.6 0 65 15 -reference_sizes ",
		label=reference_sizes,
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		pos="e,152.03,94.223 55.903,313.59 48.512,303.95 38,287.37 38,271 38,271 38,271 38,134 38,110.46 92.12,99.781 143.77,94.949"];
	pileup	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 453.5 170.5 453.5 189.5 536.5 189.5 536.5 170.5 ",
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		height=0.27778,
		label="Biscuit pileup",
		pos="495,180",
		rects="453.5,170.5,536.5,189.5",
		width=1.1528];
	reference_index -> pileup	[_draw_="c 7 -#000000 B 7 306.7 313.63 356.97 294.9 474.2 250.07 486 235 494.23 224.49 496.14 209.26 496.19 197.65 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 498.64 197.7 495.96 190.79 493.74 197.87 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 494 245.6 0 40 9 -reference ",
		label=reference,
		lp="494,247.5",
		pos="e,495.91,189.28 306.7,313.63 356.97,294.9 474.2,250.07 486,235 494.23,224.49 496.14,209.26 496.19,197.65"];
	vcf2bed	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 45 125.5 45 144.5 427 144.5 427 125.5 ",
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		label="convert a biscuit pileup vcf to a bed and bedgraph file, via a wrapper script",
		pos="236,135",
		rects="45,125.5,427,144.5",
		width=5.3056];
	reference_index -> vcf2bed	[_draw_="c 7 -#000000 B 10 282.69 313.72 281.2 303.65 279 286.12 279 271 279 271 279 271 279 179 279 166.48 269.77 156.33 259.86 149.04 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 261.44 147.15 254.25 145.3 258.72 151.22 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 299 223.1 0 40 9 -reference ",
		label=reference,
		lp="299,225",
		pos="e,252.99,144.46 282.69,313.72 281.2,303.65 279,286.12 279,271 279,271 279,271 279,179 279,166.48 269.77,156.33 259.86,149.04"];
	reference_index -> bisulfite_qc	[_draw_="c 7 -#000000 B 13 309.05 313.55 317.58 310.74 327.18 307.66 336 305 385 290.24 446 322.17 446 271 446 271 446 271 446 179 446 158.32 \
464.52 147.5 485.46 141.87 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 485.84 144.29 492.09 140.3 484.72 139.52 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 466 223.1 0 40 9 -reference ",
		label=reference,
		lp="466,225",
		pos="e,493.56,139.95 309.05,313.55 317.58,310.74 327.18,307.66 336,305 385,290.24 446,322.17 446,271 446,271 446,271 446,179 446,158.32 \
464.52,147.5 485.46,141.87"];
	bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 C 7 -#f3cea1 P 4 541.5 260.5 541.5 279.5 784.5 279.5 784.5 260.5 ",
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		fillcolor="#F3CEA1",
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		label="bam to trimmed fastqs and biscuit alignments",
		pos="663,270",
		rects="541.5,260.5,784.5,279.5",
		width=3.375];
	reference_index -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 13 305.7 313.59 314.9 310.36 325.84 306.99 336 305 385.85 295.26 402.08 313.83 450 297 456.63 294.67 456.39 290.38 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 533.27 279.36 540.04 276.35 532.87 274.48 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 496 290.6 0 66 15 -reference_index ",
		label=reference_index,
		lp="496,292.5",
		pos="e,541.55,276.23 305.7,313.59 314.9,310.36 325.84,306.99 336,305 385.85,295.26 402.08,313.83 450,297 456.63,294.67 456.39,290.38 \
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	bam_to_cram	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 299 170.5 299 189.5 439 189.5 439 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 369 177.5 0 124 22 -BAM to CRAM conversion ",
		height=0.27778,
		label="BAM to CRAM conversion",
		pos="369,180",
		rects="299,170.5,439,189.5",
		width=1.9444];
	reference_index -> bam_to_cram	[_draw_="c 7 -#000000 B 4 289.06 313.6 302.97 290.53 341.93 225.9 359.81 196.24 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 361.77 197.73 363.29 190.47 357.58 195.2 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 351 245.6 0 40 9 -reference ",
		label=reference,
		lp="351,247.5",
		pos="e,364.07,189.18 289.06,313.6 302.97,290.53 341.93,225.9 359.81,196.24"];
	trimming_adapter_trim_end -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 1173.48 313.57 1159.88 310.61 1144.28 307.42 1130 305 1016.99 285.86 886.81 277.49 792.65 273.83 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 792.82 271.39 785.73 273.57 792.63 276.28 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1103 290.6 0 72 16 -adapter_trim_end ",
		label=adapter_trim_end,
		lp="1103,292.5",
		pos="e,784.22,273.51 1173.5,313.57 1159.9,310.61 1144.3,307.42 1130,305 1017,285.86 886.81,277.49 792.65,273.83"];
	read_group_id -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 10 1313.72 313.5 1305.55 310.38 1295.95 307.11 1287 305 1222.98 289.94 1205.58 292.95 1140 288 1022.58 279.13 888.53 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 792.77 270.39 785.72 272.69 792.67 275.29 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1276 290.6 0 58 13 -read_group_id ",
		label=read_group_id,
		lp="1276,292.5",
		pos="e,784.21,272.66 1313.7,313.5 1305.6,310.38 1296,307.11 1287,305 1223,289.94 1205.6,292.95 1140,288 1022.6,279.13 888.53,274.87 792.5,\
272.83"];
	trimming_adapter_min_overlap -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 4 858.1 313.52 817.44 304.66 753.63 290.75 710.14 281.27 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 710.84 278.92 703.47 279.82 709.79 283.71 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 823 290.6 0 86 19 -adapter_min_overlap ",
		label=adapter_min_overlap,
		lp="823,292.5",
		pos="e,702,279.5 858.1,313.52 817.44,304.66 753.63,290.75 710.14,281.27"];
	instrument_data_bams -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 13 431.1 313.56 442.9 310.56 456.51 307.35 469 305 495.87 299.94 503.15 302.19 530 297 545.77 293.95 549.3 291.38 \
565 288 576.66 285.49 589.16 283.1 601.2 280.95 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 601.49 283.38 607.96 279.76 600.64 278.56 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 574.5 290.6 0 19 3 -bam ",
		label=bam,
		lp="574.5,292.5",
		pos="e,609.45,279.49 431.1,313.56 442.9,310.56 456.51,307.35 469,305 495.87,299.94 503.15,302.19 530,297 545.77,293.95 549.3,291.38 565,\
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	trimming_max_uncalled -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 551.28 313.52 565.03 306.11 585.96 295.42 605 288 610.58 285.83 616.55 283.78 622.47 281.91 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 623.03 284.3 629.01 279.91 621.6 279.61 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 633.5 290.6 0 57 12 -max_uncalled ",
		label=max_uncalled,
		lp="633.5,292.5",
		pos="e,630.46,279.47 551.28,313.52 565.03,306.11 585.96,295.42 605,288 610.58,285.83 616.55,283.78 622.47,281.91"];
	assay_non_cpg_sites -> vcf2bed	[_draw_="c 7 -#000000 B 10 174.05 313.71 175.24 303.63 177 286.1 177 271 177 271 177 271 177 179 177 164.8 188.3 154.8 201 148.03 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 201.95 150.3 207.21 145.07 199.83 145.88 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 220 223.1 0 86 19 -assay_non_cpg_sites ",
		label=assay_non_cpg_sites,
		lp="220,225",
		pos="e,208.57,144.42 174.05,313.71 175.24,303.63 177,286.1 177,271 177,271 177,271 177,179 177,164.8 188.3,154.8 201,148.03"];
	trimming_adapters -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 4 663 313.58 663 306.52 663 296.24 663 287.55 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 665.45 287.78 663 280.78 660.55 287.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 681.5 290.6 0 37 8 -adapters ",
		label=adapters,
		lp="681.5,292.5",
		pos="e,663,279.26 663,313.58 663,306.52 663,296.24 663,287.55"];
	trimming_min_readlength -> bam_to_trimmed_fastq_and_biscuit_alignments	[_draw_="c 7 -#000000 B 7 1023.39 313.57 1010.73 310.64 996.26 307.47 983 305 920.84 293.42 851.1 285.43 792.63 280.13 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 793.15 277.71 785.96 279.53 792.71 282.59 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 963 290.6 0 64 14 -min_readlength ",
		label=min_readlength,
		lp="963,292.5",
		pos="e,784.45,279.39 1023.4,313.57 1010.7,310.64 996.26,307.47 983,305 920.84,293.42 851.1,285.43 792.63,280.13"];
	pileup -> vcf	[_draw_="c 7 -#000000 B 7 494.62 170.55 493.64 153.14 490.22 112.23 479 80 476.77 73.59 473.37 66.98 470.05 61.31 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 472.27 60.23 466.51 55.56 468.1 62.81 ",
		pos="e,465.71,54.273 494.62,170.55 493.64,153.14 490.22,112.23 479,80 476.77,73.59 473.37,66.979 470.05,61.311"];
	pileup -> vcf2bed	[_draw_="c 7 -#000000 B 7 453.72 172.12 449.43 171.4 445.13 170.69 441 170 391.89 161.84 336.16 152.59 295.22 145.81 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 295.77 143.42 288.46 144.69 294.97 148.25 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 396.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="396.5,157.5",
		pos="e,286.97,144.44 453.72,172.12 449.43,171.4 445.13,170.69 441,170 391.89,161.84 336.16,152.59 295.22,145.81"];
	pileup -> bisulfite_qc	[_draw_="c 7 -#000000 B 4 504.45 170.71 511.23 164.76 520.52 156.61 528.39 149.7 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 529.8 151.72 533.44 145.26 526.57 148.04 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 529.5 155.6 0 13 3 -vcf ",
		label=vcf,
		lp="529.5,157.5",
		pos="e,534.58,144.27 504.45,170.71 511.23,164.76 520.52,156.61 528.39,149.7"];
	vcf2bed -> cpgs	[_draw_="c 7 -#000000 B 7 313.03 125.67 319.02 123.37 324.77 120.52 330 117 340.39 110.01 357.07 80.49 366.94 61.78 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 369.08 62.98 370.13 55.64 364.73 60.72 ",
		pos="e,370.83,54.296 313.03,125.67 319.02,123.37 324.77,120.52 330,117 340.39,110.01 357.07,80.487 366.94,61.782"];
	vcf2bed -> bedgraph_to_bigwig	[_draw_="c 7 -#000000 B 4 236 125.71 236 120.59 236 113.85 236 107.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 238.45 107.78 236 100.78 233.55 107.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 282.5 110.6 0 93 20 -methylation_bedgraph ",
		label=methylation_bedgraph,
		lp="282.5,112.5",
		pos="e,236,99.265 236,125.71 236,120.59 236,113.85 236,107.67"];
	bisulfite_qc -> gathered_directory	[_draw_="c 7 -#000000 B 4 543.14 125.56 541.66 111.14 538.63 81.48 536.71 62.73 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 539.15 62.5 536 55.79 534.28 63 ",
		pos="e,535.85,54.284 543.14,125.56 541.66,111.14 538.63,81.476 536.71,62.727"];
	merge	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 500 215.5 500 234.5 610 234.5 610 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 555 222.5 0 94 15 -Sambamba: merge ",
		height=0.27778,
		label="Sambamba: merge",
		pos="555,225",
		rects="500,215.5,610,234.5",
		width=1.5278];
	bam_to_trimmed_fastq_and_biscuit_alignments -> merge	[_draw_="c 7 -#000000 B 4 641.66 260.5 625.1 253.91 601.96 244.7 583.76 237.45 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 585.11 235.35 577.7 235.04 583.3 239.9 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 629.5 245.6 0 23 4 -bams ",
		label=bams,
		lp="629.5,247.5",
		pos="e,576.29,234.48 641.66,260.5 625.1,253.91 601.96,244.7 583.76,237.45"];
	merge -> pileup	[_draw_="c 7 -#000000 B 7 540.23 215.55 535.89 212.93 531.18 209.95 527 207 521.61 203.2 515.96 198.77 510.92 194.65 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 512.64 192.89 505.7 190.29 509.5 196.66 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 536.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="536.5,202.5",
		pos="e,504.53,189.32 540.23,215.55 535.89,212.93 531.18,209.95 527,207 521.61,203.2 515.96,198.77 510.92,194.65"];
	merge -> bisulfite_qc	[_draw_="c 7 -#000000 B 4 553.95 215.56 552.14 201.14 548.43 171.48 546.09 152.73 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 548.52 152.43 545.22 145.79 543.66 153.04 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 559.5 178.1 0 19 3 -bam ",
		label=bam,
		lp="559.5,180",
		pos="e,545.04,144.28 553.95,215.56 552.14,201.14 548.43,171.48 546.09,152.73"];
	merge -> bam_to_cram	[_draw_="c 7 -#000000 B 4 518.25 215.5 488.19 208.56 445.57 198.7 413.57 191.3 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 414.52 189.01 407.15 189.82 413.41 193.78 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 487.5 200.6 0 19 3 -bam ",
		label=bam,
		lp="487.5,202.5",
		pos="e,405.67,189.48 518.25,215.5 488.19,208.56 445.57,198.7 413.57,191.3"];
	index_cram	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 359.5 80.5 359.5 99.5 478.5 99.5 478.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 419 87.5 0 103 19 -samtools index cram ",
		height=0.27778,
		label="samtools index cram",
		pos="419,90",
		rects="359.5,80.5,478.5,99.5",
		width=1.6528];
	bam_to_cram -> index_cram	[_draw_="c 7 -#000000 B 7 396.29 170.6 408.21 165.34 420.85 157.19 427 145 432.99 133.13 430.01 118.06 426.1 106.86 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 428.46 106.18 423.61 100.57 423.91 107.98 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 440.5 133.1 0 21 4 -cram ",
		label=cram,
		lp="440.5,135",
		pos="e,423.06,99.161 396.29,170.6 408.21,165.34 420.85,157.19 427,145 432.99,133.13 430.01,118.06 426.1,106.86"];
	bedgraph_to_bigwig -> cpg_bigwig	[_draw_="c 7 -#000000 B 4 251.81 80.5 263.53 74.2 279.7 65.51 292.87 58.43 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 293.89 60.67 298.89 55.19 291.57 56.35 ",
		pos="e,300.23,54.478 251.81,80.505 263.53,74.203 279.7,65.514 292.87,58.432"];
	index_cram -> cram	[_draw_="c 7 -#000000 B 4 419 80.71 419 75.59 419 68.85 419 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 421.45 62.78 419 55.78 416.55 62.78 ",
		pos="e,419,54.265 419,80.709 419,75.593 419,68.848 419,62.666"];
}